Quantum kernel applications in medicinal chemistry

Future Medicinal Chemistry

Volumn 4, Issue 11, 2012, Pages 1479-1494

  Huang, Lulu ^a   Massa, Lou ^b  

^a NAVAL RESEARCH LABORATORY   (United States)

^b CITY UNIVERSITY OF NEW YORK   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

1,2 DICHLOROETHANE; INSULIN; PEPTIDE; VIRUS NUCLEOPROTEIN;

APPETITE; CHEMICAL BOND; CRYSTAL STRUCTURE; DRUG DESIGN; DRUG INTERACTION; ENERGY; HYDROGEN BOND; INTERACTIONS WITH RNA; KERNEL ENERGY METHOD; MOLECULAR SIZE; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTEIN DATA BANK; PROTEIN STRUCTURE; QUANTUM CHEMISTRY; QUANTUM MECHANICS; QUANTUM THEORY; REVIEW; VESICULAR STOMATITIS VIRUS; X RAY CRYSTALLOGRAPHY;

EID: 84864645134     PISSN: 17568919     EISSN: 17568927     Source Type: Journal    
DOI: 10.4155/fmc.12.92     Document Type: Review

References (97)

1. Huang L, Massa L, Karle J. Kernel energy method illustrated with peptides. Int. J. Quantum Chem. 103, 808-817 (2005). (Pubitemid 41623453)
2. Huang L, Massa L, Karle J. Kernel energy method: application to insulin. Proc. Natl Acad. Sci. USA 102(36), 12690-12693 (2005). (Pubitemid 41279427)
3. Huang L, Massa L, Karle J. Kernel energy method: application to DNA. Biochemistry 44(50), 16747-16752 (2005). (Pubitemid 41832055)
4. Huang L, Massa L, Karle J. The kernel energy method: basis fuctions and quantum methods. Int. J. Quantum Chem. 106, 447-457 (2006).
5. Huang L, Massa L, Karle J. Kernel energy method: application to a tRNA. Proc. Natl Acad. Sci. USA 103(5), 1233-1237 (2006). (Pubitemid 43191148)
6. Huang L, Massa L, Karle J. Drug-target interaction energies by the kernel energy method: aminoglycoside drugs and ribosomal A-site RNA target. Proc. Natl Acad. Sci. USA 104(11), 4261-4266 (2007). (Pubitemid 47186214)
7. Huang L, Massa L, Karle J. Kernel energy method: the interaction energy of the collagen triple helix. J. Chem. Theor. and Comp. 3(4), 1337-1341 (2007).
8. Huang L, Massa L, Karle J. The Kernel energy method of quantum mechanical approximation carried to fourth order terms. Proc. Natl Acad. Sci. USA 105(6), 1849-1854 (2008). (Pubitemid 351439428)
9. Huang L, Massa L, Karle I, Karle J. Calculation of strong and weak interactions in TDA1 and RangDP52 by kernel energy method. Proc. Natl Acad. Sci. USA 106(10), 3664-3669 (2009).
10. Huang L, Massa L, Karle J. Kernel energy method applied to vesicular stomatitis virus nucleoprotein. Proc. Natl Acad. Sci. USA 106(6), 1731-1736 (2009).
11. Huang L, Massa L, Karle J. Quantum kernels and quantum crystallography: applications in biochemistry. In: Quantum Biochemistry, Electronic Structure and Biological Activity. Matta CF (Ed.). Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany, 3-60 (2010).
12. Weiss SN, Huang L, Massa L. A generalized higher-order kernel energy approximation method. J. Comput. Chem. 31(16), 2889-2899 (2010).
13. Huang L, Massa L. Kernel energy method applied to an energetic nitrate ester. Int. J. Quant. Chem. 111(10), 2180-2186 (2011).
14. Huang L, Massa L. Kernel energy method: drug-target interaction energies for drug design. Proceedings of: the International Symposium on Theory and Computations in Molecular and Materials Sciences, Biology, and Pharmacology. Int. J. Quant. Chem. 110(15), 2886-2893 (2010).
15. Huang L, Massa L. The Kernel energy method: construction of 3 & 4 tuple kernels from a list of double kernel interactions. Theochem. 962(1-3), 72-79 (2010).
16. Huang L, Bohorquez H, Matta CF, Massa L. The kernel energy method: application to graphene and extended aromatics. Int. J. Quant. Chem. 111, 4150-4157 (2011).
17. Gopi H, Roy RS, Raghothama SR, Karle I. b-hairpins generated from hybrid peptide sequences containing both α- and β-amino acids. Chim. Acta. 85, 3313-3330 (2002). (Pubitemid 35340161)
18. Karle I, Gopi HN, Balaram P. Peptide hybrids containing α- and β-amino acids:structure of a decapeptide β-hairpin with two facing β-phenylalanine residues. Proc. Natl Acad. Sci. USA 98, 3716-3719 (2001). (Pubitemid 32249837)
19. Karle IL, Perozzo MA, Mishra VK, Balaram P. Crystal structure of the channel-forming polypeptide antiamoebin in a membranemimetic environment. Proc. Natl Acad. Sci. USA 95, 5501-5504 (1998). (Pubitemid 28224123)
20. Karle IL, Flippen-Anderson JL, Agarwalla S, Balaram P. Conformation of the flexible bent helix of Leu'-Zervamicin in Crystal C and a possible gating action for ion passage. Biopolymers 34, 721-735 (1994). (Pubitemid 24155451)
21. Karle IL, Das C, Balaram P. De novo protein design:crystallograohic characterization of a synthetic peptide containing independent helical and hairpin domains. Proc. Natl Acad. Sci. USA 97, 3034-3037 (2000). (Pubitemid 30183250)
22. Karle I, Gopi HN, Balaram P. Crystal structure of a hydrophobic 19-residue peptide helix containing three centrally located D amino acids. Proc. Natl Acad. Sci. USA 100, 13946-13951 (2003). (Pubitemid 37499171)
23. Vijayalakshmi S, Rao RB, Karle IL, Balaram P. Comparison of helix-stabilizing effects of a,a-dislkyl glycines with linear and cycloalkyl side chains. Biopolymers 53, 84-98 (2000). (Pubitemid 30032621)
24. Hehre WJ, Stewart RF, Pople JA. Selfconsistent molecular orbital methods. 1. Use of gaussian expansions of slater-type atomic orbitals. J. Chem. Phys. 51, 2657-2664 (1969).
25. Collins JB, Schleyer PvR, Binkley JS, Pople JA. Self-consistent molecular orbital methods. 17. Geometries and binding energies of second-row molecules. A comparison of three basis sets. J. Chem. Phys. 64, 5142-5151 (1976).
26. Binkley JS, Pople JA, Hehre WJ. Selfconsistent molecular orbital methods. 21. Small split-valence basis sets for first-row elements. J. Am. Chem. Soc. 102, 939-947 (1980).
27. Gordon MS, Binkley JS, Pople JA, Pietro WJ, Hehre WJ. Self-consistent molecular orbital methods. 22. Small split-valence basis sets for second-row elements. J. Am. Chem. Soc. 104, 2797-2803 (1982).
28. Pietro WJ, Francl MM, Hehre WJ, Defrees DJ, Pople JA, Binkley JS. Self-consistent molecular orbital methods. 24. Supplemented small split-valence basis-sets for 2nd-row elements. J. Am. Chem. Soc. 104, 5039-5048 (1982).
29. Dobbs KD, Hehre WJ. Molecular-orbital theory of the properties of inorganic and organometallic compounds. 4. Extended basis-sets for 3rd row and 4th row, maingroup elements. J. Comput. Chem. 7, 359-378 (1986).
30. Dobbs KD, Hehre WJ. Molecular-orbital theory of the properties of inorganic and organometallic compounds. 5. Extended basis-sets for 1st-row transition-metals. J. Comput. Chem. 8, 861-879 (1987).
31. Dobbs KD, Hehre WJ. Molecular-orbital theory of the properties of inorganic and organometallic compounds. 6. Extended basis-sets for 2nd-row transition-metals. J. Comput. Chem. 8, 880-893 (1987).
32. Schaefer A, Horn H, Ahlrichs R. Fully optimized contracted Gaussian-basis sets for atoms Li to Kr. J. Chem. Phys. 97, 2571-2577 (1992).
33. Schaefer A, Huber C, Ahlrichs R. Fully optimized contracted Gaussian-basis sets of triple zeta valence quality for atoms Li to Kr. J. Chem. Phys. 100, 5829-5835 (1994).
34. Ditchfield R, Hehre WJ, Pople JA. Selfconsistent molecular orbital methods. 9. Extended Gaussian-type basis for molecularorbital studies of organic molecules. J. Chem. Phys. 54, 724-728 (1971).
35. Hehre WJ, Ditchfield R, Pople JA. Selfconsistent molecular orbital methods. 12. Further extensions of Gaussian-type basis sets for use in molecular-orbital studies of organic-molecules. J. Chem. Phys. 56, 2257-2261 (1972).
36. Hariharan PC, Pople JA. Influence of polarization functions on molecular-orbital hydrogenation energies. Mol. Phys. 27, 209-214 (1974).
37. Gordon MS. The isomers of silacyclopropane. Chem. Phys. Lett. 76, 163-168 (1980).
38. Hariharan PC, Pople JA. Influence of polarization functions on molecular-orbital hydrogenation energies. Theo. Chim. Acta 28, 213-222 (1973).
39. Blaudeau JP, McGrath MP, Curtiss LA, Radom L. Extension of Gaussian-2 (G2). Theory to molecules containing third-row atoms K and Ca. J. Chem. Phys. 107, 5016-5021 (1997). (Pubitemid 127560673)
40. Francl MM, Pietro WJ, Hehre WJ et al. Self-Consistent molecular orbital methods. 23. A polarization-type basis set for 2nd-row elements. J. Chem. Phys. 77, 3654-3665 (1982).
41. Binning RC Jr, Curtiss LA. Compact contracted basis-sets for 3rd-row atoms - GAKR. J. Comput. Chem. 11, 1206-1216 (1990).
42. Rassolov VA, Pople JA, Ratner MA, Windus TL. 6-31G* basis set for atoms K through Zn. J. Chem. Phys. 109, 1223-1229 (1998). (Pubitemid 128678537)
43. Rassolov VA, Ratner MA, Pople JA, Redfern PC, Curtiss LA. 6-31G* basis set for third-row atoms. J. Comput. Chem. 22, 976-984 (2001). (Pubitemid 32455735)
44. Dunning TH Jr, Hay PJ. Modern Theoretical Chemistry III. Schaefer HF (Ed.). Plenum, NY, USA 1-28 (1976).
45. Petersson GA, Al-Laham MA. A complete basis set model chemistry. II. Open-shell systems and the total energies of the first-row atoms. J. Chem. Phys. 94, 6081-6090 (1991).
46. Petersson GA, Bennett A, Tensfeldt TG, Al-Laham MA, Shirley WA, Mantzaris J. A complete basis set model chemistry. I. The total energies of closed-shell atoms and hydrides of the first-row atoms. J. Chem. Phys. 89, 2193-2218 (1988).
47. Woon DE, Dunning TH Jr. Gaussian-basis sets for use in correlated molecular calculations. 3. The atoms aluminum through argon. J. Chem. Phys. 98, 1358-1371 (1993).
48. Kendall RA, Dunning TH Jr, Harrison RJ. Electron affinities of the first-row atoms revisited. Systematic basis sets and wave functions. J. Chem. Phys. 96, 6796-6806 (1992).
49. Dunning TH Jr. Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen. J. Chem. Phys. 90, 1007-1023 (1989).
50. Peterson KA, Woon DE, Dunning TH Jr. Benchmark calculations with correlated molecular wave functions. IV. The classical barrier height of the H+H2→H2+H reaction. J. Chem. Phys. 100, 7410-7415 (1994).
51. Wilson A, Mourik TV, Dunning TH Jr. Gaussian basis sets for use in correlated molecular calculations. VI. Sextuple zeta correlation consistent basis sets for boron through neon. J. Mol. Struct. (Theochem) 388, 339-350 (1996).
52. Dewar M, Thiel W. Ground-States of Molecules. 38. The MNDO method: approximations and parameters. J. Am. Chem. Soc. 99, 4899-4907 (1977).
53. James JP. A major enhancement in computational chemistry accuracy: MOPAC 2002, Stewart Computational Chemistry. Fujitsu Computational Chemistry Seminars (2001).
54. Roothan CCJ. New developments in molecular orbital theory. Rev. Mod. Phys. 23, 69-89 (1951).
55. Kohn W, Sham LJ. Self-consistent equations including exchange and correlation effects. Phys. Rev. 140, A1133-A1138 (1965).
56. Pople JA, Seeger R, Krishnan R. Variational configuration interaction methods and comparison with perturbation theory. Int. J. Quant. Chem. Symp. 11, 149-163 (1977).
57. Moller C, Plesset MS. Note on an approximation treatment for many-electron systems. Phys. Rev. 46, 618-622 (1934).
58. Bartlett RJ, Purvis GD. Many-body perturbation-theory, coupled-pair manyelectron theory, and importance of quadruple excitations for correlation problem. Int. J. Quant. Chem. 14, 561-581 (1978).
59. Sanger F, Tuppy H. The amino-acid sequence in the phenylalanyl chain of insulin. 2. The investigation of peptides from enzymic hydrolysates. Biochem. J. 49, 481-490 (1951).
60. Hodgkin D. The crystal structure of insulin. Verh. Schweiz. Naturforsch. Ges. 150, 93-101 (1970).
61. Gursky O, Badger J, Li Y, Caspar D. Conformational changes in cubic insulin crystals in the pH range 7-11. Biophys. J. 63, 1210-1220 (1992). (Pubitemid 23004469)
62. Wahl MC, Rao ST, Sundaralingam M. Crystal structure of the B-DNA hexamer d(CTCGAG): model for an A-to-B transition. Biophys. J. 70(6), 2857-2866 (1996). (Pubitemid 26175616)
63. Leonard GA, Hambley TW, McAuley-Hecht K. Anthracycline-DNA interactions at unfavourable base-pair triplet-binding sites: structures of d(CGGCCG)/daunomycin and d(TGGCCA)/adriamycin complexes. Acta Crystallogr. sect. D: Biol. Crystallogr. 49, 458-467 (1993).
64. Soler-Lopez M, Malinina L, Tereshko V, Zarytova V, Subirana JA. Interaction of zinc ions with d(CGCAATTGCG) in a 2.9 A resolution x-ray structure. Biol. Inorg. Chem. 7, 533-538 (2002). (Pubitemid 36061703)
65. Vargason JM, Henderson K, Ho S. A crystallographic map of the transition from B-DNA to A-DNA. Proc. Natl Acad. Sci. USA. 8, 7265-7270 (2001). (Pubitemid 32567937)
66. Tari LW, Secco AS. Base-pair opening and spermine binding-B-DNA features displayed in the crystal structure of a gal operon fragment: implications for protein-DNA recognition. Nucleic Acids Res. 23, 2065-2073 (1995).
67. Valls N, Uson I, Subiriana CJA. A cubic arrangement of DNA double helices based on nickel-guanine interactions. J. Am. Chem. Soc. 126, 7812-7816 (2004). (Pubitemid 38812771)
68. Qiu H, Dewan JC, Seeman NC. A DNA decamer with a sticky end: the crystal structure of d-CGACGATCGT. J. Mol. Biol. 267, 881-898 (1997). (Pubitemid 27192661)
69. Rozenberg H, Rabinovich D, Frolow F, Hegde RS. Structural code for DNA recognition revealed in crystal structures of papillomavirus E2-DNA targets. Proc. Natl Acad. Sci. USA 95, 15194-15199 (1998). (Pubitemid 29018675)
70. Nunn CM, Neidle SJ. Sequence-dependent drug binding to the minor groove of DNA: crystal structure of the DNA dodecamer d(CGCAAATTTGCG)2 complexed with propamidine. Med. Chem. 38, 2317-2325 (1995).
71. Egli M, Williams LD, Gao Q, Rich A. Structure of the pure-spermine form of Z-DNA (magnesium free) at 1-A resolution. Biochemistry 30, 1388-11402 (1991).
72. Shakked Z, Rabinovich D, Kennard O, Cruse WB, Salisbury SA, Viswamitra MA. Sequence-dependent conformation of an A-DNA double helix: the crystal structure of the octamer d(G-G-T-A-T-A-C-C). J. Mol. Biol. 166, 83-201 (1983).
73. Russell R, Murray J, Lentzen G, Haddad J, Mobashery S. The complex of a designer antibiotic with a model aminoacyl site of the 30S ribosomal subunit revealed by x-ray crystallography. J. Am. Chem. Soc. 125, 3410-3411 (2003). (Pubitemid 36512398)
74. Zhang X, Green TJ, Tsao J, Qiu S, Luo M. Role of intermolecular interactions of vesicular stomatitis virus nucleoprotein in RNA encapsidation. J. Virol. 82, 674-682 (2008).
75. Frisch MJ, Trucks GW, Schlegel HB et al. Gaussian 09 Revision A1. Gaussian Inc., Wallingford, CT, USA (2009)
76. Yang W. Direct calculation of electron density in density-functional theory. Phys. Rev. Lett. 66, 1438-1441 (1991).
77. Lee C, Yang W. The divide-and-conquer density-functional approach: molecular internal rotation and density of states. J. Chem. Phys. 96, 2408-2411 (1992).
78. Yang W, Lee T-S. A density-matrix divideand- conquer approach for electronic structure calculations of large molecules. J. Chem. Phys. 103, 5674-5678 (1995).
79. Lee T-S, York DM, Yang W. Linear-scaling semiempirical quantum calculations for macromolecules. J. Chem. Phys. 105, 2744 (1996).
80. York DM, Lee T-S, Yang W. Parameterization and efficient implementation of a solvent model for linear-scaling semiempirical quantum mechanical calculations of biological macromolecules. Chem. Phys. Lett. 263, 297-304 (1996). (Pubitemid 126168983)
81. York DM, Lee T-S, Yang W. Quantum mechanical study of aqueous polarization effects on biological macromolecules. J. Am. Chem. Soc. 118, 10940-10941 (1996). (Pubitemid 26390044)
82. Mezey PG. Macromolecular density matrices and electron densities with adjustable nuclear geometries. J. Math. Chem. 18, 141-168 (1995). (Pubitemid 126012642)
83. Exner TE, Mezey PG. The field-adapted ADMA approach: introducing point charges. J. Phys. Chem. A 108, 4301-4309 (2004).
84. Zhang DW, Zhang JZH. Molecular fractionation with conjugate caps for full quantum mechanical calculation of protein-molecule interaction energy. J. Chem. Phys. 119, 3599-3605 (2003).
85. Zhang DW, Xiang Y, Zhang JZH. New advance in computational chemistry: full quantum mechanical ab initio computation of streptavidin-biotin interaction energy. J. Phys. Chem. B 107,12039-12041 (2003).
86. Zhang JZH, He X. A new method for direct calculation of total energy of protein. J. Chem. Phys. 122(3), 031103 (2005).
87. Chen X, Zhang Y, Zhang JZH. An efficient approach for ab initio energy calculation of biopolymers. J. Chem. Phys. 122, 184105 (2005).
88. Kitaura K, Ikeo E, Asada T. Fragment molecular orbital method: an approximate computational method for large molecules. Chem. Phys. Lett. 313, 701-706 (1999). (Pubitemid 129556715)
89. Deev V, Collins MA. Approximate ab initio energies by systematic molecular fragmentation. J. Chem. Phys. 122, 154102 (2005).
90. Collins MA, Deev VA. Accuracy and efficiency of electronic energies from systematic molecular fragmentation. J. Chem. Phys. 125, 104104 (2006).
91. Li W, Li S, Jiang YS. Generalized energybased fragmentation approach for computing the ground-state energies and properties of large molecules. J. Phys. Chem. A 111, 2193-2199 (2007). (Pubitemid 46543220)
92. Řezáč J, Dennis R, Salahub DR. Multilevel fragment-based approach (MFBA): a novel hybrid computational method for the study of large molecules. J. Chem. Theory Comput. 6, 91-99 (2010).
93. Babu K, Gadre SR. Ab initio quality one-electron properties of large molecules: development and testing of molecular tailoring approach. J. Comput. Chem. 24, 484-495 (2002).
94. Gadre SR, Ganesh V. Molecular tailoring approach: towards PC-based ab initio treatment of large molecules. J. Theor. Comput. Chem. 5, 835-855 (2006).
95. Gadre SR, Rahalkar AP, Ganesh V. Ab initio treatment of large molecules: cut-and-stitch the Tailor's way. IANCAS News Bulletin V, 267-276 (2006).
96. Elango M, Subramanian V, Rahalkar AP, Gadre SR, Sathyamurthy N. Structure, energetics, and reactivity of boric acid nanotubes: a molecular tailoring approach. J. Phys. Chem. A 112, 7699-7704 (2008).
97. Gadre SR, Jovan Jose KV, Rahalkar AP. Molecular tailoring approach for exploring structures, energetics and properties of clusters. J. Chem. Sci. 122, 47-56 (2010).