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

References

• Aqvist , J. , Medina , C. and Samuelsson , J.E. 1994 . A new method for predicting binding affinity in computer-aided drug design . Protein Engineering , 7 : 385 – 391 .
   PubMedGoogle Scholar
• Badrinarayan , P. and 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 .
   PubMed Web of Science ®Google Scholar
• Becke , A.D. 1993 . Density-functional thermochemistry III. The role of exact exchange . Journal of Chemical Physics , 98 : 5648 – 5652 .
   Web of Science ®Google Scholar
• Bell , C.A. , Dykstra , C.C. , Naiman , N.N. , Cory , M. , Fairley , T.A. and 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 .
   PubMed Web of Science ®Google Scholar
• Bohari , M.H. , Srivastava , H.K. and Sastry , G.N. 2011 . Analogue-based approaches in anti-cancer compound modeling: The relevance of QSAR models . Organic and Medicinal Chemistry Letters , 1 : 3
   PubMedGoogle Scholar
• Boykin , D.W. , Kumar , A. , Spychala , J. , Zhou , M. , Lombardy , R.J. , Wilson , W.D. , … and Neidle , S. 1995 . Dicationic diarylfurans as anti-Pneumocystis carinii agents . Journal of Medicinal Chemistry , 38 : 912 – 916 .
   PubMed Web of Science ®Google Scholar
• Boykin , D.W. , Kumar , A. , Xiao , G. , Wilson , W.D. , Bender , B.C. , McCurdy , D.R. , … and Tidwell , R.R. 1998 . 2,5-bis[4-(N-alkylamidino)phenyl]furans as anti-Pneumocystis carinii agents . Journal of Medicinal Chemistry , 41 : 124 – 129 .
   PubMed Web of Science ®Google Scholar
• Braithwaite , A.W. and Baguley , B.C. 1980 . Existence of an extended series of antitumor compounds which bind to deoxyribonucleic acid by nonintercalative means . Biochemistry , 19 : 1101 – 1106 .
   PubMed Web of Science ®Google Scholar
• Brendle , J.J. , Outlaw , A. , Kumar , A. , Boykin , D.W. , Patrick , D.A. , Tidwell , R.R. and Werbovetz , K.A. 2002 . Antileishmanial activities of several classes of aromatic dications . Antimicrobial Agents and Chemotherapy , 46 : 797 – 807 .
   PubMed Web of Science ®Google Scholar
• Brovarets , O.O. , Yurenko , Y.P. , Dubey , I.Y. and 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 .
   PubMed Web of Science ®Google Scholar
• Burris , H.A. , Dieras , V.C. , Tunca , M. , Earhart , R.H. , Eckardt , J.R. , Rodriguez , G.I. , … and Von-Hoff , D.D. 1997 . Phase I study with the DNA sequence-specific agent adozelesin . Anti-Cancer Drugs , 8 : 588 – 596 .
   PubMed Web of Science ®Google Scholar
• Carter , C.A. , Waud , W.R. , Li , L.H. , DeKoning , T.F. , McGovren , J.P. and Plowman , J. 1996 . Preclinical antitumor activity of bizelesin in mice . Clinical Cancer Research , 2 : 1143 – 1149 .
   PubMed Web of Science ®Google Scholar
• Case , D.A. , Darden , T.A. , Cheatham , T.E. III , Simmerling , C.L. , Wang , J. , Duke , R.E. , … and Kollman , P.A. 2004 . AMBER 8 , San Francisco , CA : University of California, San Francisco .
   Google Scholar
• Chattaraj , P.K. , Sarkar , U. and Roy , D.R. 2006 . Electrophilicity index . Chemical Reviews , 106 : 2065 – 2091 .
   PubMed Web of Science ®Google Scholar
• Chenoweth , D.M. and Dervan , P.B. 2009 . Allosteric modulation of DNA by small molecules . Proceedings of the National Academy of Sciences USA , 106 : 13175 – 13179 .
   PubMed Web of Science ®Google Scholar
• Chourasia , M. , Sastry , G.M. and Sastry , G.N. 2011 . Aromatic – aromatic database, A2ID: An analysis of aromatic networks in proteins . International Journal of Biological Macromolecules , 48 : 540 – 552 .
   PubMed Web of Science ®Google Scholar
• Darden , T. , York , D. and Pederson , L. 1993 . Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems . Journal of Chemical Physics , 98 : 10089 – 10092 .
   Web of Science ®Google Scholar
• de Jonge , M.R. , Koymans , L.M. , Vinkers , H.M. , Daeyaert , F.F. , Heeres , J. , Lewi , P.J. and Janssen , P.A. 2005 . Structure based activity prediction of HIV-1 reverse transcriptase inhibitors . Journal of Medicinal Chemistry , 48 : 2176 – 2183 .
   PubMed Web of Science ®Google Scholar
• De Souza , E.M. , Lansiaux , A. , Bailly , C. , Wilson , W.D. , Hu , Q. , Boykin , D.W. , … and Soeiro , M.N. 2004 . Phenyl substitution of furamidine markedly potentiates its anti-parasitic activity against Trypanosoma cruzi and Leishmania amazonensis . Biochemical Pharmacology , 68 : 593 – 600 .
   PubMed Web of Science ®Google Scholar
• Ditchfield , R. , Hehre , W.J. and 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
   Web of Science ®Google Scholar
• Edinger , S.R. , Cortis , C. , Shenkin , P.S. and 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 .
   Web of Science ®Google Scholar
• Ferrara , P. , Gohlke , H. , Price , D.J. , Klebe , G. and Brooks , C.L. III . 2004 . Assessing scoring functions for protein–ligand interactions . Journal of Medicinal Chemistry , 57 : 3032 – 3047 .
   Google Scholar
• Foster , B.J. , LoRusso , P.M. , Poplin , E. , Zalupski , M. , Valdivieso , M. , Wozniak , A. , … and 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 .
   PubMed Web of Science ®Google Scholar
• Francesconi , I. , Wilson , W.D. , Tanious , F.A. , Hall , J.E. , Bender , B.C. , Tidwell , R.R. , … and Boykin , D.W. 1999 . 2,4-Diphenyl furan diamidines as novel anti-Pneumocystis carinii pneumonia agents . Journal of Medicinal Chemistry , 42 : 2260 – 2265 .
   PubMed Web of Science ®Google Scholar
• Frisch , M.J. , Trucks , G.W. , Schlegel , H.B. , Scuseria , G.E. , Robb , M.A. , Cheeseman , J.R. , … and Pople , J.A. 2003 . Gaussian 03 Revision E.0.1 , Pittsburgh , PA : Gaussian .
   Google Scholar
• García-Nieto , R. , Manzanares , I. , Cuevas , C. and Gago , F. 2000 . Increased DNA binding specificity for antitumor ecteinascidin 743 through protein-DNA interactions? . Journal of Medicinal Chemistry , 16 : 4367 – 4369 .
   Google Scholar
• Gravatt , G.L. , Baguley , B.C. , Wilson , W.R. and 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 .
   PubMed Web of Science ®Google Scholar
• Gresh , N. 1985 . A theoretical study of the interaction of 4′,6 diamidino-2-phenylindole (DAPI) with the double-stranded oligonucleotides (dA-dT)11 and (dA)11·(dT)11 . International Journal of Biological Macromolecules , 7 : 199 – 202 .
   Web of Science ®Google Scholar
• Gresh , N. and 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 .
   PubMed Web of Science ®Google Scholar
• Hochhauser , D. , Meyer , T. , Spanswick , V.J. , Wu , J. , Clingen , P.H. , Loadman , P. , … and 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 .
   PubMed Web of Science ®Google Scholar
• Hopkins , K.T. , Wilson , W.D. , Bender , B.C. , McCurdy , D.R. , Hall , J.E. , Tidwell , R.R. , … and Boykin , D.W. 1998 . Extended aromatic furan amidino derivatives as anti-Pneumocystis carinii agents . Journal of Medicinal Chemistry , 41 : 3872 – 3878 .
   PubMed Web of Science ®Google Scholar
• Houghton , P.J. , Cheshire , P.J. , Hallman , J.D.N. and 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 .
   Web of Science ®Google Scholar
• Hovorun , D.M. , Gorb , L. and 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 .
   Google Scholar
• Jakalian , A. , Bush , B.L. , Jack , D.B. and Bayly , C.I. 2000 . Fast, efficient generation of high-quality atomic charges. AM1-BCC Model . Journal of Computational Chemistry , 21 : 132 – 146 .
   Web of Science ®Google Scholar
• Janardhan , S. , Srivani , P. and 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 .
   Google Scholar
• Jones , G. , Willett , P. , Glen , R.C. , Leach , A.R. and Taylor , R. 1997 . Development and validation of a genetic algorithm for flexible docking . Journal of Molecular Biology , 267 : 727 – 748 .
   PubMed Web of Science ®Google Scholar
• Kamal , A. , Bharathi , E.V. , Ramaiah , M.J. , Dastagiri , D. , Reddy , J.S. , Viswanath , A. , … and 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 .
   PubMed Web of Science ®Google Scholar
• Kamal , A. , Rajender Reddy , D.R. , Reddy , M.K. , Balakishan , G. , Shaik , T.B. , Chourasia , M. and 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 .
   PubMed Web of Science ®Google Scholar
• Kamal , A. , Reddy , K.S. , Khan , M.N. , Shetti , R.V. , Ramaiah , M.J. , Pushpavalli , S.N. , … and 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 .
   PubMed Web of Science ®Google Scholar
• Kamal , A. , Shankaraiah , N. , Reddy , C.R. , Prabhakar , S. , Markandeya , N. , Srivastava , H.K. and 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 .
   Web of Science ®Google Scholar
• Kamal , A. , Shetty , R.V.C.R.N.C. , Ramaiah , M.J. , Swapna , P. , Reddy , K.S. , Mallareddy , A. , … and Pal-Bhadra , M. 2011 . Carbazole-pyrrolo[2,1-c][1,4]benzodiazepine conjugates: Design, synthesis, and biological evaluation . MedChemComm , 2 : 780 – 788 .
   Web of Science ®Google Scholar
• 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.
   Google Scholar
• Katritzky , A.R. and Lobanov , V.S. 1995 . QSPR: The correlation and quantitative prediction of chemical and physical properties from structure . Chemical Society Reviews , 24 : 279 – 287 .
   Web of Science ®Google Scholar
• Katritzky , A.R. , Petrukhin , R. , Tatham , D. , Basak , S. and Benfenati , E. 2001 . Interpretation of quantitative structure-property and activity relationships . Journal of Chemical Information and Computer Sciences , 41 : 679 – 685 .
   PubMedGoogle Scholar
• Kiralj , R. and 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 .
   Web of Science ®Google Scholar
• Kirkwood , J.G. 1935 . Statistical mechanics of fluid mixtures . Journal of Chemical Physics , 3 : 300 – 313 .
   Web of Science ®Google Scholar
• Kobayashi , E. , Okamoto , A. , Asada , M. , Okabe , M. , Nagamura , S. , Asai , A. , … and 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 .
   PubMed Web of Science ®Google Scholar
• Kollman , P.A. , Massova , I. , Reyes , C. , Kuhn , B. , Huo , S. , Chong , L. , … and 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 .
   PubMed Web of Science ®Google Scholar
• Laughton , C.A. , Jenkins , T.C. , Fox , K.R. and 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 .
   PubMed Web of Science ®Google Scholar
• Leach, A.R. (2001). Molecular modelling: Principles and applications. Harlow: Addison–Wesley Longman Ltd.
   Google Scholar
• Lee , C. , Yang , W. and 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 .
   PubMed Web of Science ®Google Scholar
• Li , L.H. , DeKoning , T.F. , Kelly , R.C. , Krueger , W.C. , McGovren , J.P. , Padbury , G.E. , … and Gebhard , I. 1992 . Cytotoxicity and antitumor activity of carzelesin, a prodrug cyclopropylpyrroloindole analogue . Cancer Research , 52 : 4904 – 4913 .
   PubMed Web of Science ®Google Scholar
• Lombardy , R.L. , Tanious , F.A. , Ramachandran , K. , Tidwell , R.R. and Wilson , W.D. 1996 . Synthesis and DNA interactions of benzimidazole dications which have activity against opportunistic infections . Journal of Medicinal Chemistry , 39 : 1452
   PubMed Web of Science ®Google Scholar
• Lorusso , D. , Mainenti , S. , Pietragalla , A. , Ferrandina , G. , Foco , G. , Masciullo , V. and Scambia , G. 2009 . Brostallicin (PNU-166196), a new minor groove DNA binder: Preclinical and clinical activity . Expert Opinion on Investigational Drugs , 18 : 1939 – 1946 .
   PubMed Web of Science ®Google Scholar
• Lown , J.W. , Krowicki , K. , Balzarini , J. , Newman , R.A. and 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 .
   PubMed Web of Science ®Google Scholar
• Mallena , S. , Lee , M.P. , Bailly , C. , Neidle , S. , Kumar , A. , Boykin , D.W. and Wilson , W.D. 2004 . Thiophene-based diamidine forms a ‘super’ at binding minor groove agent . Journal of the American Chemical Society , 126 : 13659 – 13669 .
   PubMed Web of Science ®Google Scholar
• McDonnell , G. and Russell , A.D. 1999 . Antiseptics and disinfectants: Activity, action, and resistance . Clinical Microbiology Reviews , 12 : 147 – 179 .
   PubMed Web of Science ®Google Scholar
• McKinney , J.D. , Richard , A. , Waller , C. , Newman , M.C. and Gerberick , F. 2000 . The practice of structure activity relationships (SAR) in toxicology . Toxicological Sciences , 56 : 8 – 17 .
   PubMed Web of Science ®Google Scholar
• Nikolaienko , T.Y. , Bulavin , L.A. and Hovorun , D.M. 2011 . How flexible are dna constituents? The quantum mechanical study . Journal of Biomolecular Structure and Dynamics , 29 : 563 – 575 .
   PubMed Web of Science ®Google Scholar
• Othman , O.E. and Ahmed , S. 2004 . Cytogenetic effect of the trypanocidal drug berenil in blood cultures of river buffalo . Journal of Biological Sciences , 4 : 180 – 184 .
   Google Scholar
• Parr , R.G. , Donnelly , R.A. , Levy , M. and Palke , W.E. 1978 . Electronegativity: The density functional viewpoint . Journal of Chemical Physics , 68 : 3801
   Web of Science ®Google Scholar
• Parr , R.G. and Pearson , R.G. 1983 . Absolute hardness: Companion parameter to absolute electronegativity . Journal of the American Chemical Society , 105 : 7512 – 7516 .
   Web of Science ®Google Scholar
• Parr , R.G. , Szentpaly , L. and Liu , S. 1999 . Electrophilicity index . Journal of the American Chemical Society , 121 : 1922 – 1924 .
   Web of Science ®Google Scholar
• Parthasarathi , R. , Subramanian , V. , Roy , D.R. and Chattaraj , P.K. 2004 . Electrophilicity index as a possible descriptor of biological activity . Bioorganic & Medicinal Chemistry , 12 : 5533 – 5543 .
   PubMed Web of Science ®Google Scholar
• Pasha , F.A. , Muddassar , M. and Cho , S.J. 2009 . Molecular docking and 3D QSAR studies of Chk2 inhibitors . Chemical Biology and Drug Design , 73 : 292 – 300 .
   PubMed Web of Science ®Google Scholar
• Pasha , F.A. , Srivastava , H.K. and Singh , P.P. 2005 . Comparative QSAR study of phenol derivatives with the help of density functional theory . Bioorganic & Medicinal Chemistry , 13 : 6823 – 6829 .
   PubMed Web of Science ®Google Scholar
• Pearson , R.G. 1997 . Chemical hardness: Applications from molecules to solids , Weinheim : Wiley-VCH .
   Google Scholar
• Pezzoni , G. , Grandi , M. , Biasoli , G. , Capolongo , L. , Ballinari , D. , Giuliani , F.C. , … and Spreafico , F. 1991 . Biological profile of FCE 24517, a novel benzoyl mustard analogue of distamycin A . British Journal of Cancer , 64 : 1047 – 1050 .
   PubMed Web of Science ®Google Scholar
• Purschke , M. , Rubio , N. , Held , K.D. and Redmond , R.W. 2010 . Phototoxicity of Hoechst 33342 in time-lapse fluorescence microscopy . Photochemical & Photobiological Sciences , 9 : 1634 – 1639 .
   PubMed Web of Science ®Google Scholar
• Puzanov , I. , Lee , W. , Chen , A.P. , Calcutt , M.W. , Hachey , D.L. , Vermeulen , W.L. , … and 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 .
   PubMed Web of Science ®Google Scholar
• Ravindra , G.K. , Achaiah , G. and 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 .
   PubMed Web of Science ®Google Scholar
• Renneberg , D. and Dervan , P.B. 2003 . Imidazopyridine/pyrrole and hydroxybenzimidazole/pyrrole pairs for DNA minor groove recognition . Journal of the American Chemical Society , 125 : 5707 – 5716 .
   PubMed Web of Science ®Google Scholar
• Schultz , T.W. , Cronin , M.T.D. , Walker , J.D. and Aptula , A.O. 2003 . Quantitative structure-activity relationships (QSARs) in toxicology: A historical perspective . Journal of Molecular Structure: THEOCHEM , 622 : 1 – 22 .
   Web of Science ®Google Scholar
• Scigress Explorer version 7.7; (2008). Fujitsu: Tokyo, Japan.
   Google Scholar
• Srinivasan , J. , Miller , J. , Kollman , P.A. and 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 .
   PubMed Web of Science ®Google Scholar
• Srivani , P. , Srinivas , E. , Raghu , R. and Sastry , G.N. 2007 . Molecular modeling studies of pyridopurinone derivatives – Potential phosphodiesterase 5 inhibitors . Journal of Molecular Graphics and Modeling , 26 : 378 – 390 .
   PubMed Web of Science ®Google Scholar
• 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 .
   Web of Science ®Google Scholar
• Srivastava , H.K. , Chourasia , M. , Kumar , D. and Sastry , G.N. 2011 . Comparison of computational methods to model DNA minor groove binders . Journal of Chemical Information and Modeling , 51 : 558 – 571 .
   PubMed Web of Science ®Google Scholar
• Srivastava , H.K. , Pasha , F.A. , Mishra , S.K. and Singh , P.P. 2009 . Novel applications of atomic softness and QSAR study of testosterone derivatives . Medicinal Chemistry Research , 18 : 455 – 466 .
   Web of Science ®Google Scholar
• Stuedli , A.N. , Boykin , D. , Tidwell , R.R. and Brun , R. 2011 . Novel diamidines with activity against Babesia Divergens in vitro and Babesia Microti in vivo . Antimicrobial Agents and Chemotherapy , 55 : 3439 – 3445 .
   PubMed Web of Science ®Google Scholar
• SYBYL 6.9.2; Tripos Inc. (2004). 1699 South Hanley Road, St. Louis, MO 63144–2917.
   Google Scholar
• Thompsan , J.J. and 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 .
   PubMed Web of Science ®Google Scholar
• Tidwell , R.R. , Jones , S.K. , Naiman , N.A. , Berger , L.C. , Brake , W.B. , Dykstra , C.C. and Hall , J.E. 1993 . Activity of cationically substituted bis-benzimidazoles against experimental Pneumocystis carinii pneumonia . Antimicrobial Agents and Chemotherapy , 37 : 1713 – 1716 .
   PubMed Web of Science ®Google Scholar
• Vijay , D. and Sastry , G.N. 2008 . Exploring the size dependence of cyclic and acyclic -systems on cation-pi binding . Physical Chemistry Chemical Physics , 10 : 582 – 590 .
   PubMed Web of Science ®Google Scholar
• Walker , D.L. , Reid , J.M. and 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 .
   PubMed Web of Science ®Google Scholar
• Wang , J. , Wolf , R.M. , Caldwell , J.W. , Kollman , P.A. and Case , D.A. 2004 . Development and testing of a general Amber force field . Journal of Computational Chemistry , 25 : 1157 – 1174 .
   PubMed Web of Science ®Google Scholar
• Warren , G.L. , Andrews , C.W. , Capelli , A.M. , Clarke , B. , LaLonde , J. , Lambert , M.H. , … and Head , M.S. 2006 . A critical assessment of docking programs and scoring functions . Journal of Medicinal Chemistry , 49 : 5912 – 5931 .
   PubMed Web of Science ®Google Scholar
• Warren , C.L. , Kratochvil , N.C. , Hauschild , K.E. , Foister , S. , Brezinski , M.L. , Dervan , P.B. , … and Ansari , A.Z. 2005 . Defining the sequence-recognition profile of DNA-binding molecules . Proceedings of the National Academy of Sciences USA , 103 : 867 – 872 .
   Web of Science ®Google Scholar
• Yurenko , Y.P. , Zhurakivsky , R.O. , Samijlenko , S.P. and 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 .
   PubMed Web of Science ®Google Scholar
• Zakrzewska , K. , Lavery , R. and Pullman , B. 1984 . The solvation contribution to the binding energy of DNA with non-intercalating antibiotics . Nucleic Acids Research , 12 : 6559 – 6574 .
   PubMed Web of Science ®Google Scholar
• 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 .
   PubMedGoogle Scholar
• Zwanzig , R.W. 1954 . High-temperature equation of state by a perturbation method. 1. Nonpolar gases . Journal of Chemical Physics , 22 : 1420 – 1426 .
   Web of Science ®Google Scholar