Efficient estimation of MMGBSA-based BEs for DNA and aromatic furan amidino derivatives

Journal of Biomolecular Structure and Dynamics

Volumn 31, Issue 5, 2013, Pages 522-537

  Srivastava, Hemant Kumar ^a   Sastry, G Narahari ^a  

^a INDIAN INSTITUTE OF CHEMICAL TECHNOLOGY   (India)

Author keywords

DFT based QSAR studies; DNA minor groove binders; MMGBSA based BEs; Molecular dynamics simulations; Pneumocystis carnii agents

Indexed keywords

2,5 BIS(4 AMIDINOPHENYL)FURAN DERIVATIVE; 2,5 BIS[4 (N ALKYLAMIDINO)PHENYL]FURAN DERIVATIVE; ANTIFUNGAL AGENT; AROMATIC FURAN AMIDINO DERIVATIVE; DNA; UNCLASSIFIED DRUG;

ARTICLE; CALCULATION; CORRELATION ANALYSIS; DRUG STRUCTURE; MOLECULAR DOCKING; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; MOLECULAR MECHANICS WITH GENERALIZED BORN SURFACE AREA BASED BINDING ENERGY; PREDICTION; PRIORITY JOURNAL; VALIDATION PROCESS;

PNEUMOCYSTIS CARINII;

EID: 84870020141     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2012.703071     Document Type: Article

References (92)

1. Aqvist, J., Medina, C., & Samuelsson, J.E. (1994). A new method for predicting binding affinity in computer-aided drug design. Protein Engineering, 7, 385-391.
2. Badrinarayan, P., & Sastry, G.N. (2011). Sequence, analysis of p38 MAP kinase: Exploiting DFG-out conformation as a strategy to design new type II leads. Journal of Chemical Information and Modeling, 51, 115-129.
3. Becke, A.D. (1993). Density-functional thermochemistry III. The role of exact exchange. Journal of Chemical Physics, 98, 5648-5652.
4. Bell, C.A., Dykstra, C.C., Naiman, N.N., Cory, M., Fairley, T.A., & Tidwell, R.R. (1993). Structure-activity studies of dicationic substituted bis-benzimidazoles against Giardia lamblia: correlation of antigiardial activity with DNA binding affinity and giardial topoisomerase II inhibition. Antimicrobial Agents and Chemotherapy, 37, 2668-2673.
5. Bohari, M.H., Srivastava, H.K., & Sastry, G.N. (2011). Analogue- based approaches in anti-cancer compound modeling: The relevance of QSAR models. Organic and Medicinal Chemistry Letters, 1, 3.
6. Boykin, D.W., Kumar, A., Spychala, J., Zhou, M., Lombardy, R.J., Wilson, W.D., ...Neidle, S. (1995). Dicationic diarylfurans as anti-Pneumocystis carinii agents. Journal of Medicinal Chemistry, 38, 912-916.
7. Boykin, D.W., Kumar, A., Xiao, G., Wilson, W.D., Bender, B.C., McCurdy, D.R., ...Tidwell, R.R. (1998). 2,5-bis[4- (N-alkylamidino)phenyl]furans as anti-Pneumocystis carinii agents. Journal of Medicinal Chemistry, 41, 124-129.
8. Braithwaite, A.W., & Baguley, B.C. (1980). Existence of an extended series of antitumor compounds which bind to deoxyribonucleic acid by nonintercalative means. Biochemistry, 19, 1101-1106.
9. Brendle, J.J., Outlaw, A., Kumar, A., Boykin, D.W., Patrick, D.A., Tidwell, R.R., & Werbovetz, K.A. (2002). Antileishmanial activities of several classes of aromatic dications. Antimicrobial Agents and Chemotherapy, 46, 797-807.
10. Brovarets, O.O., Yurenko, Y.P., Dubey, I.Y., & Hovorun, D.M. (2012). Can DNA-binding proteins of replisome tautomerize nucleotide bases? Ab initio model study. Journal of Biomolecular Structure and Dynamics, 29, 597-605.
11. Burris, H.A., Dieras, V.C., Tunca, M., Earhart, R.H., Eckardt, J.R., Rodriguez, G.I., ...Von-Hoff, D.D. (1997). Phase I study with the DNA sequence-specific agent adozelesin. Anti-Cancer Drugs, 8, 588-596.
12. Carter, C.A., Waud, W.R., Li, L.H., DeKoning, T.F., McGovren, J.P., & Plowman, J. (1996). Preclinical antitumor activity of bizelesin in mice. Clinical Cancer Research, 2, 1143-1149.
13. Case, D.A., Darden, T.A., Cheatham, T.E.III, Simmerling, C.L., Wang, J., Duke, R.E., ...Kollman, P.A. (2004). AMBER 8. San Francisco, CA: University of California, San Francisco.
14. Chattaraj, P.K., Sarkar, U., & Roy, D.R. (2006). Electrophilicity index. Chemical Reviews, 106, 2065-2091.
15. Chenoweth, D.M., & Dervan, P.B. (2009). Allosteric modulation of DNA by small molecules. Proceedings of the National Academy of Sciences USA, 106, 13175-13179.
16. Chourasia, M., Sastry, G.M., & Sastry, G.N. (2011). Aromatic - aromatic database, A2ID: An analysis of aromatic networks in proteins. International Journal of Biological Macromolecules, 48, 540-552.
17. Darden, T., York, D., & Pederson, L. (1993). Particle mesh Ewald: An N-log(N) method for Ewald sums in large systems. Journal of Chemical Physics, 98, 10089-10092.
18. de Jonge, M.R., Koymans, L.M., Vinkers, H.M., Daeyaert, F.F., Heeres, J., Lewi, P.J., & Janssen, P.A. (2005). Structure based activity prediction of HIV-1 reverse transcriptase inhibitors. Journal of Medicinal Chemistry, 48, 2176-2183.
19. De Souza, E.M., Lansiaux, A., Bailly, C., Wilson, W.D., Hu, Q., Boykin, D.W., ...Soeiro, M.N. (2004). Phenyl substitution of furamidine markedly potentiates its antiparasitic activity against Trypanosoma cruzi and Leishmania amazonensis. Biochemical Pharmacology, 68, 593-600.
20. Ditchfield, R., Hehre, W.J., & Pople, J.A. (1971). Self-consistent molecular-orbital methods. IX. An extended gaussian-type basis for molecular-orbital studies of organic molecules. Journal of Chemical Physics, 54, 724.
21. Edinger, S.R., Cortis, C., Shenkin, P.S., & Friesner, R.A. (1997). Solvation free energies of peptides: Comparison of approximate continuum solvation models with accurate solution of the poisson-boltzmann equation. Journal of Physical Chemistry B, 101, 1190-1197.
22. Ferrara, P., Gohlke, H., Price, D.J., Klebe, G., & Brooks, C.L. III (2004). Assessing scoring functions for protein-ligand interactions. Journal of Medicinal Chemistry, 57, 3032-3047.
23. Foster, B.J., LoRusso, P.M., Poplin, E., Zalupski, M., Valdivieso, M., Wozniak, A., ...Baker, L.H. (1996). Phase I trial of adozelesin using the treatment schedule of daily 35 every 3 weeks. Investigational New Drugs, 13, 321-326.
24. Francesconi, I., Wilson, W.D., Tanious, F.A., Hall, J.E., Bender, B.C., Tidwell, R.R., ...Boykin, D.W. (1999). 2,4-Diphenyl furan diamidines as novel anti-Pneumocystis carinii pneumonia agents. Journal of Medicinal Chemistry, 42, 2260-2265.
25. Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., ...Pople, J.A. (2003). Gaussian 03 Revision E.0.1. Pittsburgh, PA: Gaussian.
26. García-Nieto, R., Manzanares, I., Cuevas, C., & Gago, F. (2000). Increased DNA binding specificity for antitumor ecteinascidin 743 through protein-DNA interactions? Journal of Medicinal Chemistry, 16, 4367-4369.
27. Gravatt, G.L., Baguley, B.C., Wilson, W.R., & Denny, W.A. (1994). DNA-directed alkylating agents. 6. Synthesis and antitumor activity of dna minor groove-targeted aniline mustard analogs of pibenzimol (Hoechst 33258). Journal of Medicinal Chemistry, 37, 4338-4345.
28. Gresh, N. (1985). A theoretical study of the interaction of 4′,6 diamidino-2-phenylindole (DAPI) with the doublestranded oligonucleotides (dA-dT)11 and (dA)11·(dT)11. International Journal of Biological Macromolecules, 7, 199-202.
29. Gresh, N., & Pullman, B. (1984). A theoretical study of the non-intercalative binding of berenil and stilbamidine to double-stranded (dA-dT)n oligomers. Molecular ZPharmacology, 25, 452-458.
30. Hochhauser, D., Meyer, T., Spanswick, V.J., Wu, J., Clingen, P.H., Loadman, P., ...Jodrell, D. (2009). Phase I study of sequence-selective minor groove DNA binding agent SJG-136 in patients with advanced solid tumors. Clinical Cancer Research, 15, 2140-2147.
31. Hopkins, K.T., Wilson, W.D., Bender, B.C., McCurdy, D.R., Hall, J.E., Tidwell, R.R., ...Boykin, D.W. (1998). Extended aromatic furan amidino derivatives as anti-Pneumocystis carinii agents. Journal of Medicinal Chemistry, 41, 3872-3878.
32. Houghton, P.J., Cheshire, P.J., Hallman, J.D.N., & Houghton, J.A. (1996). Therapeutic efficacy of the cyclopropylpyrroloindole, carzelesin, against xenografts derived from adult and childhood solid tumors. Cancer Chemotherapy and Pharmacololy, 36, 45-52.
33. Hovorun, D.M., Gorb, L., & Leszczynski, J. (1999). From the nonplanarity of the amino group to the structural nonrigidity of the molecule: A post-Hartree-Fock ab initio study of 2-aminoimidazole. International Journal of Quantum Chemistry, 74, 245-253.
34. Jakalian, A., Bush, B.L., Jack, D.B., & Bayly, C.I. (2000). Fast, efficient generation of high-quality atomic charges. AM1-BCC Model. Journal of Computational Chemistry, 21, 132-146.
35. Janardhan, S., Srivani, P., & Sastry, G.N. (2006). 2D and 3D quantitative structure-activity relationship studies on a series of bispyridinium compounds as choline kinase inhibitors. QSAR & Combinatorial Science, 25, 860-872.
36. Jones, G., Willett, P., Glen, R.C., Leach, A.R., & Taylor, R. (1997). Development and validation of a genetic algorithm for flexible docking. Journal of Molecular Biology, 267, 727-748.
37. Kamal, A., Bharathi, E.V., Ramaiah, M.J., Dastagiri, D., Reddy, J.S., Viswanath, A., ...Zingde, S. (2010a). Quinazolinone linked pyrrolo[2,1-c][1,4] benzodiazepine (PBD) conjugates: Design, synthesis and biological evaluation as potential anticancer agents. Bioorganic & Medicinal Chemistry, 18, 526-542.
38. Kamal, A., Rajender Reddy, D.R., Reddy, M.K., Balakishan, G., Shaik, T.B., Chourasia, M., & Sastry, G.N. (2009). Remarkable enhancement in the DNA-binding ability of C2-fluoro substituted pyrrolo[2,1-c][1,4]benzodiazepines and their anticancer potential. Bioorganic & Medicinal Chemistry, 17, 1557-1572.
39. Kamal, A., Reddy, K.S., Khan, M.N., Shetti, R.V., Ramaiah, M.J., Pushpavalli, S.N., ...Barkume, M. (2010c). Synthesis, DNA-binding ability and anticancer activity of benzothiazole/ benzoxazole-pyrrolo [2,1-c][1,4] benzodiazepine conjugates. Bioorganic & Medicinal Chemistry, 18, 4747-4761.
40. Kamal, A., Shankaraiah, N., Reddy, C.R., Prabhakar, S., Markandeya, N., Srivastava, H.K., & Sastry, G.N. (2010b). Synthesis of bis-1,2,3-triazolo- bridged unsymmetrical pyrrolobenzodiazepine trimers via 'click' chemistry and their DNA-binding studies. Tetrahedron, 66, 5489-5506.
41. Kamal, A., Shetty, R.V.C.R.N.C., Ramaiah, M.J., Swapna, P., Reddy, K.S., Mallareddy, A., ...Pal-Bhadra, M. (2011). Carbazole-pyrrolo[2,1-c][1,4] benzodiazepine conjugates: Design, synthesis, and biological evaluation. MedChem- Comm, 2, 780-788.
42. Katritzky, A.R., Lobanov, V.S., & Karelson, M. (1994). Copyright 1994-1996, CODESSA 2.0, Comprehensive descriptors for structural and statistical analysis, University of Florida, USA.
43. Katritzky, A.R., & Lobanov, V.S. (1995). QSPR: The correlation and quantitative prediction of chemical and physical properties from structure. Chemical Society Reviews, 24, 279-287.
44. Katritzky, A.R., Petrukhin, R., Tatham, D., Basak, S., & Benfenati, E. (2001). Interpretation of quantitative structureproperty and activity relationships. Journal of Chemical Information and Computer Sciences, 41, 679-685.
45. Kiralj, R., & Ferreira, M.M.C. (2009). Basic validation procedures for regression models in QSAR and QSPR studies: Theory and application. Journal of the Brazilian Chemical Society, 20, 770-787.
46. Kirkwood, J.G. (1935). Statistical mechanics of fluid mixtures. Journal of Chemical Physics, 3, 300-313.
47. Kobayashi, E., Okamoto, A., Asada, M., Okabe, M., Nagamura, S., Asai, A., ...Hirata, T. (1994). Characteristics of antitumor activity of KW-2189, a novel water-soluble derivative of duocarmycin, against murine and human tumors. Cancer Research, 54, 2404-2410.
48. Kollman, P.A., Massova, I., Reyes, C., Kuhn, B., Huo, S., Chong, L., ...Cheatham, T.E.III (2000). Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Accounts of Chemical Research, 33, 889-897.
49. Laughton, C.A., Jenkins, T.C., Fox, K.R., & Neidle, S. (1990). Interaction of berenil with the tyrT DNA sequence studied by footprinting and molecular modelling. Implications for the design of sequence-specific DNA recognition agents. Nucleic Acids Research, 18, 4479-4488.
50. Leach, A.R. (2001). Molecular modelling: Principles and applications. Harlow: Addison-Wesley Longman Ltd.
51. Lee, C., Yang, W., & Parr, R.G. (1988). Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Physical Review B, 37, 785-789.
52. Li, L.H., DeKoning, T.F., Kelly, R.C., Krueger, W.C., McGovren, J.P., Padbury, G.E., ...Gebhard, I. (1992). Cytotoxicity and antitumor activity of carzelesin, a prodrug cyclopropylpyrroloindole analogue. Cancer Research, 52, 4904-4913.
53. Lombardy, R.L., Tanious, F.A., Ramachandran, K., Tidwell, R. R., & Wilson, W.D. (1996). Synthesis and DNA interactions of benzimidazole dications which have activity against opportunistic infections. Journal of Medicinal Chemistry, 39, 1452.
54. Lorusso, D., Mainenti, S., Pietragalla, A., Ferrandina, G., Foco, G., Masciullo, V., & Scambia, G. (2009). Brostallicin (PNU-166196), a new minor groove DNA binder: Preclinical and clinical activity. Expert Opinion on Investigational Drugs, 18, 1939-1946.
55. Lown, J.W., Krowicki, K., Balzarini, J., Newman, R.A., & De- Clercq, E. (1989). Novel linked antiviral and antitumor agents related to netropsin and distamycin: Synthesis and biological evaluation. Journal of Medicinal Chemistry, 32, 2368-2375.
56. Mallena, S., Lee, M.P., Bailly, C., Neidle, S., Kumar, A., Boykin, D.W., & Wilson, W.D. (2004). Thiophene-based diamidine forms a 'super' at binding minor groove agent. Journal of the American Chemical Society, 126, 13659-13669.
57. McDonnell, G., & Russell, A.D. (1999). Antiseptics and disinfectants: Activity, action, and resistance. Clinical Microbiology Reviews, 12, 147-179.
58. McKinney, J.D., Richard, A., Waller, C., Newman, M.C., & Gerberick, F. (2000). The practice of structure activity relationships (SAR) in toxicology. Toxicological Sciences, 56, 8-17.
59. Nikolaienko, T.Y., Bulavin, L.A., & Hovorun, D.M. (2011). How flexible are dna constituents? The quantum mechanical study. Journal of Biomolecular Structure and Dynamics, 29, 563-575.
60. Othman, O.E., & Ahmed, S. (2004). Cytogenetic effect of the trypanocidal drug berenil in blood cultures of river buffalo. Journal of Biological Sciences, 4, 180-184.
61. Parr, R.G., Donnelly, R.A., Levy, M., & Palke, W.E. (1978). Electronegativity: The density functional viewpoint. Journal of Chemical Physics, 68, 3801.
62. Parr, R.G., & Pearson, R.G. (1983). Absolute hardness: Companion parameter to absolute electronegativity. Journal of the American Chemical Society, 105, 7512-7516.
63. Parr, R.G., Szentpaly, L., & Liu, S. (1999). Electrophilicity index. Journal of the American Chemical Society, 121, 1922-1924.
64. Parthasarathi, R., Subramanian, V., Roy, D.R., & Chattaraj, P.K. (2004). Electrophilicity index as a possible descriptor of biological activity. Bioorganic & Medicinal Chemistry, 12, 5533-5543.
65. Pasha, F.A., Muddassar, M., & Cho, S.J. (2009). Molecular docking and 3D QSAR studies of Chk2 inhibitors. Chemical Biology and Drug Design, 73, 292-300.
66. Pasha, F.A., Srivastava, H.K., & Singh, P.P. (2005). Comparative QSAR study of phenol derivatives with the help of density functional theory. Bioorganic & Medicinal Chemistry, 13, 6823-6829.
67. Pearson, R.G. (1997). Chemical hardness: Applications from molecules to solids. Weinheim: Wiley-VCH.
68. Pezzoni, G., Grandi, M., Biasoli, G., Capolongo, L., Ballinari, D., Giuliani, F.C., ...Spreafico, F. (1991). Biological profile of FCE 24517, a novel benzoyl mustard analogue of distamycin A. British Journal of Cancer, 64, 1047-1050.
69. Purschke, M., Rubio, N., Held, K.D., & Redmond, R.W. (2010). Phototoxicity of Hoechst 33342 in time-lapse fluorescence microscopy. Photochemical & Photobiological Sciences, 9, 1634-1639.
70. Puzanov, I., Lee, W., Chen, A.P., Calcutt, M.W., Hachey, D.L., Vermeulen, W.L., ...Rothenberg, M.L. (2011). Phase I pharmacokinetic and pharmacodynamic study of SJG-136, a novel DNA sequence selective minor groove cross-linking agent, in advanced solid tumors. Clinical Cancer Research, 17, 3794-3802.
71. Ravindra, G.K., Achaiah, G., & Sastry, G.N. (2008). Molecular modeling studies of phenoxypyrimidinyl imidazoles as p38 kinase inhibitors using QSAR and docking. European Journal of Medicinal Chemistry, 43, 830-838.
72. Renneberg, D., & Dervan, P.B. (2003). Imidazopyridine/pyrrole and hydroxybenzimidazole/pyrrole pairs for DNA minor groove recognition. Journal of the American Chemical Society, 125, 5707-5716.
73. Schultz, T.W., Cronin, M.T.D., Walker, J.D., & Aptula, A.O. (2003). Quantitative structure-activity relationships (QSARs) in toxicology: A historical perspective. Journal of Molecular Structure: THEOCHEM, 622, 1-22.
74. Scigress Explorer version 7.7; (2008). Fujitsu: Tokyo, Japan.
75. Srinivasan, J., Miller, J., Kollman, P.A., & Case, D.A. (1998). Continuum solvent studies of the stability of RNA hairpin loops and helices. Journal of Biomolecular Structure and Dynamics, 16, 671-682.
76. Srivani, P., Srinivas, E., Raghu, R., & Sastry, G.N. (2007). Molecular modeling studies of pyridopurinone derivatives - Potential phosphodiesterase 5 inhibitors. Journal of Molecular Graphics and Modeling, 26, 378-390.
77. Srivastava, H.K. (2009). A comparative QSPR study of alkanes with the help of computational chemistry. Bulletin of the Korean Chemical Society, 30, 67-76.
78. Srivastava, H.K., Chourasia, M., Kumar, D., & Sastry, G.N. (2011). Comparison of computational methods to model DNA minor groove binders. Journal of Chemical Information and Modeling, 51, 558-571.
79. Srivastava, H.K., Pasha, F.A., Mishra, S.K., & Singh, P.P. (2009). Novel applications of atomic softness and QSAR study of testosterone derivatives. Medicinal Chemistry Research, 18, 455-466.
80. Stuedli, A.N., Boykin, D., Tidwell, R.R., & Brun, R. (2011). Novel diamidines with activity against Babesia Divergens in vitro and Babesia Microti in vivo. Antimicrobial Agents and Chemotherapy, 55, 3439-3445.
81. SYBYL 6.9.2; Tripos Inc. (2004). 1699 South Hanley Road, St. Louis, MO 63144-2917.
82. Thompsan, J.J., & Lill, M.A. (2011). Solvent interaction energy calculations on molecular dynamics trajectories: Increasing the efficiency using systematic frame selection. Journal of Chemical Information and Modeling, 51, 2680-2689.
83. Tidwell, R.R., Jones, S.K., Naiman, N.A., Berger, L.C., Brake, W.B., Dykstra, C.C., & Hall, J.E. (1993). Activity of cationically substituted bis-benzimidazoles against experimental Pneumocystis carinii pneumonia. Antimicrobial Agents and Chemotherapy, 37, 1713-1716.
84. Vijay, D., & Sastry, G.N. (2008). Exploring the size dependence of cyclic and acyclic -systems on cation-pi binding. Physical Chemistry Chemical Physics, 10, 582-590.
85. Walker, D.L., Reid, J.M., & Ames, M.M. (1994). Preclinical pharmacology of bizelesin, a potent bifunctional analog of the DNA-binding antibiotic CC-1065. Cancer Chemotherapy and Pharmacology, 34, 317-322.
86. Wang, J., Wolf, R.M., Caldwell, J.W., Kollman, P.A., & Case, D.A. (2004). Development and testing of a general Amber force field. Journal of Computational Chemistry, 25, 1157-1174.
87. Warren, G.L., Andrews, C.W., Capelli, A.M., Clarke, B., LaLonde, J., Lambert, M.H., ...Head, M.S. (2006). A critical assessment of docking programs and scoring functions. Journal of Medicinal Chemistry, 49, 5912-5931.
88. Warren, C.L., Kratochvil, N.C., Hauschild, K.E., Foister, S., Brezinski, M.L., Dervan, P.B., ...Ansari, A.Z. (2005). Defining the sequence-recognition profile of DNA-binding molecules. Proceedings of the National Academy of Sciences USA, 103, 867-872.
89. Yurenko, Y.P., Zhurakivsky, R.O., Samijlenko, S.P., & Hovorun, D.M. (2011). Intramolecular CH- - -O hydrogen bonds in the AI and BI DNA-like conformers of canonical nucleosides and their Watson-Crick pairs. Quantum chemical and AIM analysis. Journal of Biomolecular Structure and Dynamics, 29, 51-65.
90. Zakrzewska, K., Lavery, R., & Pullman, B. (1984). The solvation contribution to the binding energy of DNA with nonintercalating antibiotics. Nucleic Acids Research, 12, 6559-6574.
91. Zimmer, C. (1975). Effects of the antibiotics netropsin and distamycin-A on the structure and function of nucleic acids. Progress in Nucleic Acid Research and Molecular Biology, 15, 285-318.
92. Zwanzig, R.W. (1954). High-temperature equation of state by a perturbation method. 1. Nonpolar gases. Journal of Chemical Physics, 22, 1420-1426.