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Molecular Recognition of Azelaic Acid and Related Molecules with DNA Polymerase I Investigated by Molecular Modeling Calculations

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Abstract

Molecular recognition has central role on the development of rational drug design. Binding affinity and interactions are two key components which aid to understand the molecular recognition in drug-receptor complex and crucial for structure-based drug design in medicinal chemistry. Herein, we report the binding affinity and the nonbonding interactions of azelaic acid and related compounds with the receptor DNA polymerase I (2KFN). Quantum mechanical calculation was employed to optimize the modified drugs using B3LYP/6-31G(d,p) level of theory. Charge distribution, dipole moment and thermodynamic properties such as electronic energy, enthalpy and free energy of these optimized drugs are also explored to evaluate how modifications impact the drug properties. Molecular docking calculation was performed to evaluate the binding affinity and nonbonding interactions between designed molecules and the receptor protein. We notice that all modified drugs are thermodynamically more stable and some of them are more chemically reactive than the unmodified drug. Promise in enhancing hydrogen bonds is found in case of fluorine-directed modifications as well as in the addition of trifluoroacetyl group. Fluorine participates in forming fluorine bonds and also stimulates alkyl, pi-alkyl interactions in some drugs. Designed drugs revealed increased binding affinity toward 2KFN. A1, A2 and A3 showed binding affinities of −8.7, −8.6 and −7.9 kcal/mol, respectively against 2KFN compared to the binding affinity −6.7 kcal/mol of the parent drug. Significant interactions observed between the drugs and Thr358 and Asp355 residues of 2KFN. Moreover, designed drugs demonstrated improved pharmacokinetic properties. This study disclosed that 9-octadecenoic acid and drugs containing trifluoroacetyl and trifluoromethyl groups are the best 2KFN inhibitors. Overall, these results can be useful for the design of new potential candidates against DNA polymerase I.

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Abbreviations

AzA:

Azelaic acid

DFT:

Density functional theory

ADMET:

Absorption, distribution, metabolism, excretion, toxicity

QM:

Quantum mechanics

CASTp:

Computed Atlas of Surface Topography of proteins

SDF:

Structure Data File

SMILES:

Simplified molecular-input line-entry system

HOMO:

Highest occupied molecular orbital

LUMO:

Lowest unoccupied molecular orbital

hERG:

Human ether-a-go-go-related gene

BBB:

Blood brain barrier

References

  1. Zhang J, Landry MP, Barone PW et al (2013) Molecular recognition using corona phase complexes made of synthetic polymers adsorbed on carbon nanotubes. Nat Nanotechnol 8:959–968. doi:10.1038/nnano.2013.236

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  2. Breiten B, Lockett MR, Sherman W et al (2013) Water networks contribute to enthalpy/entropy compensation in protein-ligand binding. J Am Chem Soc 135:15579–15584. doi:10.1021/ja4075776

    Article  PubMed  CAS  Google Scholar 

  3. Lehn JM (1992) Supramolecular chemistry: from molecular recognition towards molecular information processing and self-organization. Mater Sci Forum 91–93:100. doi:10.4028/www.scientific.net/MSF.91-93.100

    Article  Google Scholar 

  4. Alberts B, Johnson A, Lewis J et al (2002) Protein Function. In: Molecular Biology of the Cell, 4th edn. Garland Science, New York

  5. Persch E, Dumele O, Diederich F (2015) Molecular recognition in chemical and biological systems. Angew Chemie Int Ed. doi:10.1002/anie.201408487

    Article  Google Scholar 

  6. Fersht AR (1987) The hydrogen bond in molecular recognition. Trends Biochem Sci 12:301–304

    Article  CAS  Google Scholar 

  7. Zhao GJ, Han KL (2007) Early time hydrogen-bonding dynamics of photoexcited coumarin 102 in hydrogen-donating solvents: theoretical study. J Phys Chem A 111:2469–2474. doi:10.1021/jp068420j

    Article  PubMed  CAS  Google Scholar 

  8. Zhao J, Chen J, Cui Y et al (2015) A questionable excited-state double-proton transfer mechanism for 3-hydroxyisoquinoline. Phys Chem Chem Phys 17:1142–1150. doi:10.1039/c4cp04135f

    Article  PubMed  CAS  Google Scholar 

  9. Zhao G-J, Han K-L (2012) Hydrogen bonding in the electronic excited state. Acc Chem Res 45:404–413. doi:10.1021/ar200135h

    Article  PubMed  CAS  Google Scholar 

  10. Zhao J, Chen J, Liu J, Hoffmann MR (2015) Competitive excited-state single or double proton transfer mechanisms for bis-2,5-(2-benzoxazolyl)-hydroquinone and its derivatives. Phys Chem Chem Phys 17:11990–11999. doi:10.1039/c4cp05651e

    Article  PubMed  CAS  Google Scholar 

  11. Harada A, Kobayashi R, Takashima Y et al (2010) Recognition. Nat Chem 3:34–37. doi:10.1038/nchem.893

    Article  PubMed  CAS  Google Scholar 

  12. Zhao GJ, Han KL (2008) Effects of hydrogen bonding on tuning photochemistry: concerted hydrogen-bond strengthening and weakening. Chem Phys Chem 9:1842–1846. doi:10.1002/cphc.200800371

    Article  PubMed  CAS  Google Scholar 

  13. Gillis EP, Eastman KJ, Hill MD et al (2015) Applications of fluorine in medicinal chemistry. J Med Chem 58:8315–8359. doi:10.1021/acs.jmedchem.5b00258

    Article  PubMed  CAS  Google Scholar 

  14. Leroux FR, Manteau B, Vors J-P, Pazenok S (2008) Trifluoromethyl ethers–synthesis and properties of an unusual substituent. Beilstein J Org Chem 4:13. doi:10.3762/bjoc.4.13

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  15. Shah P, Westwell AD (2007) The role of fluorine in medicinal chemistry. J Enzyme Inhib Med Chem 22:527–540. doi:10.1080/14756360701425014

    Article  PubMed  CAS  Google Scholar 

  16. Fluorine in medicinal chemistry and chemical biology—Wiley Online Library. http://onlinelibrary.wiley.com/book/10.1002/9781444312096. Accessed 15 Feb 2016

  17. Purser S, Moore PR, Swallow S, Gouverneur V (2008) Fluorine in medicinal chemistry. Chem Soc Rev 37:320–330. doi:10.1039/b610213c

    Article  PubMed  CAS  Google Scholar 

  18. Filler R, Saha R (2009) Fluorine in medicinal chemistry: a century of progress and a 60-year retrospective of selected highlights. Future Med Chem 1:777–791. doi:10.4155/fmc.09.65

    Article  PubMed  CAS  Google Scholar 

  19. Garcia-Diaz M, Bebenek K (2007) Multiple functions of DNA polymerases. CRC Crit Rev Plant Sci 26:105–122. doi:10.1080/07352680701252817

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  20. Lu Y, Liu Y, Xu Z et al (2012) Halogen bonding for rational drug design and new drug discovery. Expert Opin Drug Discov 7:375–383. doi:10.1517/17460441.2012.678829

    Article  PubMed  CAS  Google Scholar 

  21. Lopachin RM, Gavin T, Decaprio A, Barber DS (2012) Application of the hard and soft, acids and bases (HSAB) theory to toxicant–target interactions. Chem Res Toxicol 25:239–251. doi:10.1021/tx2003257

    Article  PubMed  CAS  Google Scholar 

  22. Albà M (2001) Replicative DNA polymerases. Genome Biol 2:REVIEWS3002

    Article  PubMed  PubMed Central  Google Scholar 

  23. Lehman IR, Bessman MJ, Simms ES, Kornberg A (1958) Enzymatic synthesis of deoxyribonucleic acid. I. Preparation of substrates and partial purification of an enzyme from Escherichia coli. J Biol Chem 233:163–170

    PubMed  CAS  Google Scholar 

  24. Ollis DL, Brick P, Hamlin R et al (1985) Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP. Nature 313:762–766. doi:10.1038/313762a0

    Article  PubMed  CAS  Google Scholar 

  25. Allen WJ, Li Y, Waksman G (2010) Bacterial DNA Polymerase I. In: eLS. Wiley, Chichester. doi:10.1002/9780470015902.a0001043.pub2

  26. Klenow H, Henningsen I (1970) Selective elimination of the exonuclease activity of the deoxyribonucleic acid polymerase from Escherichia coli B by limited proteolysis. Proc Natl Acad Sci USA 65:168–175

    Article  PubMed  CAS  Google Scholar 

  27. Derbyshire V, Grindley ND, Joyce CM (1991) The 3′-5′ exonuclease of DNA polymerase I of Escherichia coli: contribution of each amino acid at the active site to the reaction. EMBO J 10:17–24

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  28. Bernad A, Blanco L, Lázaro J et al (1989) A conserved 3′ → 5′ exonuclease active site in prokaryotic and eukaryotic DNA polymerases. Cell 59:219–228. doi:10.1016/0092-8674(89)90883-0

    Article  PubMed  CAS  Google Scholar 

  29. Bhate K, Williams HC (2013) Epidemiology of acne vulgaris. Br J Dermatol 168:474–485. doi:10.1111/bjd.12149

    Article  PubMed  CAS  Google Scholar 

  30. Williams HC, Dellavalle RP, Garner S (2012) Acne vulgaris. Lancet 379:361–372. doi:10.1016/S0140-6736(11)60321-8

    Article  PubMed  Google Scholar 

  31. Goodman G (2006) Acne and acne scarring: the case for active and early intervention. Aust Fam Physician 35:503–504

    PubMed  Google Scholar 

  32. Thappa D, Adityan B, Kumari R (2009) Scoring systems in acne vulgaris. Indian J Dermatol Venereol Leprol 75:323. doi:10.4103/0378-6323.51258

    Article  PubMed  Google Scholar 

  33. James WD (2005) Clinical practice. Acne N Engl J Med 352:1463–1472. doi:10.1056/NEJMcp033487

    Article  PubMed  CAS  Google Scholar 

  34. Lolis MS, Bowe WP, Shalita AR (2009) Acne and systemic disease. Med Clin North Am 93:1161–1181. doi:10.1016/j.mcna.2009.08.008

    Article  PubMed  CAS  Google Scholar 

  35. Titus S, Hodge J (2012) Diagnosis and treatment of acne. Am Fam Physician 86:734–740

    PubMed  Google Scholar 

  36. Fitton A, Goa KL (1991) Azelaic acid. A review of its pharmacological properties and therapeutic efficacy in acne and hyperpigmentary skin disorders. Drugs 41:780–798

    Article  PubMed  CAS  Google Scholar 

  37. Azelaic acid (On the skin)—National Library of Medicine—PubMed Health. http://www.ncbi.nlm.nih.gov/pubmedhealth/PMHT0009168/?report=details. Accessed 16 Feb 2016

  38. Del Rosso JQ, Baum EW, Draelos ZD et al (2006) Azelaic acid gel 15%: clinical versatility in the treatment of rosacea. Cutis 78:6–19

    PubMed  Google Scholar 

  39. Breathnach AS (1999) Azelaic acid: potential as a general antitumoural agent. Med Hypotheses 52:221–226. doi:10.1054/mehy.1997.0647

    Article  PubMed  CAS  Google Scholar 

  40. Graupe K, Cunliffe WJ, Gollnick HP, Zaumseil RP (1996) Efficacy and safety of topical azelaic acid (20 percent cream): an overview of results from European clinical trials and experimental reports. Cutis 57:20–35

    PubMed  CAS  Google Scholar 

  41. Bek-Thomsen M, Lomholt HB, Kilian M (2008) Acne is not associated with yet-uncultured bacteria. J Clin Microbiol 46:3355–3360. doi:10.1128/JCM.00799-08

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  42. Leibl H, Stingl G, Pehamberger H et al (1985) Inhibition of DNA synthesis of melanoma cells by azelaic acid. J Invest Dermatol 85:417–422. doi:10.1111/1523-1747.ep12277084

    Article  PubMed  CAS  Google Scholar 

  43. Bojar RA, Holland KT, Cunliffe WJ (1991) The in vitro antimicrobial effects of zelaic acid upon Propionibacterium acnes strain P37. J Antimicrob Chemother 28:843–853

    Article  PubMed  CAS  Google Scholar 

  44. Gleeson MP, Gleeson D (2009) QM/MM calculations in drug discovery: a useful method for studying binding phenomena? J Chem Inf Model 49:670–677. doi:10.1021/ci800419j

    Article  PubMed  CAS  Google Scholar 

  45. Becke AD (1988) Density-functional exchange-energy approximation with correct asymptotic behavior. Phys Rev A 38:3098–3100. doi:10.1103/PhysRevA.38.3098

    Article  CAS  Google Scholar 

  46. Lee C, Yang W, Parr RG (1988) Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys Rev B 37:785–789. doi:10.1103/PhysRevB.37.785

    Article  CAS  Google Scholar 

  47. Frisch MJ, Trucks GW, Schlegel HB et al (2009) Gaussian 09, Revision A.02. Gaussian Inc Wallingford CT 34, Wallingford CT. doi:10.1159/000348293

  48. Ray SS, Bonanno JB, Rajashankar KR et al (2002) Cocrystal structures of diaminopimelate decarboxylase: mechanism, evolution, and inhibition of an antibiotic resistance accessory factor. Structure 10:1499–1508. doi:10.1016/S0969-2126(02)00880-8

    Article  PubMed  CAS  Google Scholar 

  49. Parr RG, Yang W (1989) Density-functional theory of atoms and molecules. Int J Quantum Chem. doi:10.1002/qua.560470107

    Article  Google Scholar 

  50. Pearson RG (1995) The HSAB principle—more quantitative aspects. Inorg Chim Acta 240:93–98. doi:10.1016/0020-1693(95)04648-8

    Article  CAS  Google Scholar 

  51. Pearson RG (1986) Absolute electronegativity and hardness correlated with molecular orbital theory. Proc Natl Acad Sci USA 83:8440–8441. doi:10.1073/pnas.83.22.8440

    Article  PubMed  CAS  Google Scholar 

  52. Brautigam CA, Sun S, Piccirilli JA, Steitz TA (1999) Structures of normal single-stranded DNA and deoxyribo-3′-S-phosphorothiolates bound to the 3′-5′ exonucleolytic active site of DNA polymerase I from Escherichia coli. Biochemistry 38:696–704. doi:10.1021/bi981537g

    Article  PubMed  CAS  Google Scholar 

  53. Guex N, Peitsch MC (1997) SWISS-MODEL and the Swiss-PDBVIEWER: an environment for comparative protein modeling. Electrophoresis 18:2714–2723. doi:10.1002/elps.1150181505

    Article  PubMed  CAS  Google Scholar 

  54. Dundas J, Ouyang Z, Tseng J et al (2006) CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids Res 34:116–118. doi:10.1093/nar/gkl282

    Article  CAS  Google Scholar 

  55. DeLano WL (2002) The PyMOL molecular graphics system. Schrödinger LLC wwwpymolorg Version 1.:http://www.pymol.org. doi: citeulike-article-id:240061

  56. Trott O, Olson AJ (2010) Software news and update AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 31:455–461. doi:10.1002/jcc.21334

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  57. Morris GM, Lim-Wilby M (2008) Molecular docking. Methods Mol Biol 443:365–382. doi:10.1007/978-1-59745-177-2_19

    Article  PubMed  CAS  Google Scholar 

  58. Trott O, Olson AJ (2010) AutoDock Vina. J Comput Chem 31:445–461. doi:10.1002/jcc.21334

    Article  CAS  Google Scholar 

  59. Updated L (2013) Accelrys discovery studio 4.0 product release document

  60. Laskowski RA, Swindells MB (2011) LigPlot+: multiple ligand-protein interaction diagrams for drug discovery. J Chem Inf Model 51:2778–2786. doi:10.1021/ci200227u

    Article  PubMed  CAS  Google Scholar 

  61. Cheng F, Li W, Zhou Y et al (2012) AdmetSAR: a comprehensive source and free tool for assessment of chemical ADMET properties. J Chem Inf Model 52:3099–3105. doi:10.1021/ci300367a

    Article  PubMed  CAS  Google Scholar 

  62. Garbett NC, Chaires JB (2012) Thermodynamic studies for drug design and screening. Expert Opin Drug Discov 7:299–314. doi:10.1517/17460441.2012.666235

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  63. Lien EJ, Guo Z-R, Li R-L, Su C-T (1982) Use of dipole moment as a parameter in drug-receptor interaction and quantitative structure-activity relationship studies. J Pharm Sci 71:641–655. doi:10.1002/jps.2600710611

    Article  PubMed  CAS  Google Scholar 

  64. Lien EJ, Guo ZR, Li RL, Su CT (1982) Use of dipole moment as a parameter in drug-receptor interaction and quantitative structure–activity relationship studies. J Pharm Sci 71:641–655

    Article  PubMed  CAS  Google Scholar 

  65. Rahman A, Hoque MM, Khan MAK et al (2016) Non-covalent interactions involving halogenated derivatives of capecitabine and thymidylate synthase: a computational approach. Springerplus 5:1–18. doi:10.1186/s40064-016-1844-y

    Article  CAS  Google Scholar 

  66. Saleh MA, Solayman M, Hoque MM et al (2016) Inhibition of DNA topoisomerase type IIα (TOP2A) by Mitoxantrone and its halogenated derivatives: a combined density functional and molecular docking study. Biomed Res Int 2016:12

    Article  CAS  Google Scholar 

  67. Heinz H, Suter UW (2004) Atomic charges for classical simulations of polar systems. J Phys Chem B 108:18341–18352. doi:10.1021/jp048142t

    Article  CAS  Google Scholar 

  68. Gross KC, Seybold PG, Hadad CM (2002) Comparison of different atomic charge schemes for predicting pKa variations in substituted anilines and phenols. Int J Quantum Chem 90:445–458. doi:10.1002/qua.10108

    Article  CAS  Google Scholar 

  69. Fukui K, Yonezawa T, Shingu H (1952) A molecular orbital theory of reactivity in aromatic hydrocarbons. J Chem Phys 20:722. doi:10.1063/1.1700523

    Article  CAS  Google Scholar 

  70. Ayers PW, Parr RG, Pearson RG (2006) Elucidating the hard/soft acid/base principle: a perspective based on half-reactions. J Chem Phys 124:194107. doi:10.1063/1.2196882

    Article  PubMed  CAS  Google Scholar 

  71. Parr RG, Zhou Z (1993) Absolute hardness : unifying concept for identifying shells and subshells in nuclei, atoms, molecules, and metallic clusters. Acc Chem Res 26:256–258. doi:10.1021/ar00029a005

    Article  CAS  Google Scholar 

  72. Aihara J (1999) Reduced HOMO-LUMO gap as an index of kinetic stability for polycyclic aromatic hydrocarbons. J Phys Chem A 103:7487–7495. doi:10.1021/jp990092i

    Article  CAS  Google Scholar 

  73. Manolopoulos DE, May JC, Down SE (1991) Theoretical studies of the fullerenes: c34 to C70. Chem Phys Lett 181:105–111. doi:10.1016/0009-2614(91)90340-F

    Article  CAS  Google Scholar 

  74. Aihara J (2000) Correlation found between the HOMO–LUMO energy separation and the chemical reactivity at the most reactive site for isolated-pentagon isomers of fullerenes. Phys Chem Chem Phys 2:3121–3125. doi:10.1039/b002601h

    Article  CAS  Google Scholar 

  75. Gelb MH, Svaren JP, Abeles RH (1985) Fluoro ketone inhibitors of hydrolytic enzymes. Biochemistry 24:1813–1817. doi:10.1021/bi00329a001

    Article  PubMed  CAS  Google Scholar 

  76. Nair HK, Quinn DM (1993) M-alkyl alpha, alpha, alpha-trifluoroacetophenones—a new class of potent transition-state analog inhibitors of acetylcholinesterase. Bioorg Med Chem Lett 3:2619–2622. doi:10.1016/S0960-894x(01)80727-7

    Article  CAS  Google Scholar 

  77. Veale CA, Bernstein PR, Bohnert CM et al (1997) Orally active trifluoromethyl ketone inhibitors of human leukocyte elastase. J Med Chem 40:3173–3181. doi:10.1021/jm970250z

    Article  PubMed  CAS  Google Scholar 

  78. Furuya T, Kamlet AS, Ritter T (2011) Catalysis for fluorination and trifluoromethylation. Nature 473:470–477. doi:10.1038/nature10108

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  79. McClinton MA, McClinton DA (1992) Trifluoromethylations and related reactions in organic chemistry. Tetrahedron 48:6555–6666. doi:10.1016/S0040-4020(01)80011-9

    Article  CAS  Google Scholar 

  80. Ji Y, Brueckl T, Baxter RD et al (2011) Innate C–H trifluoromethylation of heterocycles. Proc Natl Acad Sci USA 108:14411–14415. doi:10.1073/pnas.1109059108

    Article  PubMed  Google Scholar 

  81. Lishchynskyi A, Novikov MA, Martin E et al (2013) Trifluoromethylation of aryl and heteroaryl halides with fluoroform-derived CuCF3: scope, limitations, and mechanistic features. J Org Chem 78:11126–11146. doi:10.1021/jo401423h

    Article  PubMed  CAS  Google Scholar 

  82. Sarwar MG, Ajami D, Theodorakopoulos G et al (2013) Amplified halogen bonding in a small space. J Am Chem Soc 135:13672–13675. doi:10.1021/ja407815t

    Article  PubMed  CAS  Google Scholar 

  83. Sarwar MG, Dragisic B, Salsberg LJ et al (2010) Thermodynamics of halogen bonding in solution: substituent, structural, and solvent effects. J Am Chem Soc 132:1646–1653. doi:10.1021/ja9086352

    Article  PubMed  CAS  Google Scholar 

  84. Beale TM, Chudzinski MG, Sarwar MG, Taylor MS (2013) Halogen bonding in solution: thermodynamics and applications. Chem Soc Rev. doi:10.1039/c2cs35213c

    Article  PubMed  Google Scholar 

  85. Hoque MM, Halim MA, Rahman MM et al (2013) Synthesis and structural insights of substituted 2-iodoacetanilides and 2-iodoanilines. J Mol Struct 1054–1055:367–374. doi:10.1016/j.molstruc.2013.10.011

    Article  CAS  Google Scholar 

  86. Sarwar MG, Dragisić B, Dimitrijević E, Taylor MS (2013) Halogen bonding between anions and iodoperfluoroorganics: solution-phase thermodynamics and multidentate-receptor design. Chem A Eur J 19:2050–2058. doi:10.1002/chem.201202689

    Article  CAS  Google Scholar 

  87. Sarwar MG, Dragisic B, Sagoo S, Taylor MS (2010) A tridentate halogen-bonding receptor for tight binding of halide anions. Angew Chem Int Ed Engl 49:1674–1677. doi:10.1002/anie.200906488

    Article  PubMed  CAS  Google Scholar 

  88. Bissantz C, Kuhn B, Stahl M (2010) A medicinal chemist’s guide to molecular interactions. J Med Chem 53:5061–5084. doi:10.1021/jm100112j

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  89. Hunter CA (2004) Quantifying intermolecular interactions: guidelines for the molecular recognition toolbox. Angew Chemie Int Ed 43:5310–5324. doi:10.1002/anie.200301739

    Article  CAS  Google Scholar 

  90. Zhurkin VB, Tolstorukov MY, Xu F et al (2005) Sequence-dependent variability of B-DNA. DNA conform transcription. Springer, Boston, pp 18–34

    Chapter  Google Scholar 

  91. Wade RC, Goodford PJ (1989) The role of hydrogen-bonds in drug binding. Prog Clin Biol Res 289:433–444

    PubMed  CAS  Google Scholar 

  92. Zhao GJ, Liu JY, Zhou LC, Han KL (2007) Site-selective photoinduced electron transfer from alcoholic solvents to the chromophore facilitated by hydrogen bonding: a new fluorescence quenching mechanism. J Phys Chem B 111:8940–8945. doi:10.1021/jp0734530

    Article  PubMed  CAS  Google Scholar 

  93. Zhao G-J, Han K-L (2008) Site-specific solvation of the photoexcited protochlorophyllide a in methanol: formation of the hydrogen-bonded intermediate state induced by hydrogen-bond strengthening. Biophys J 94:38–46. doi:10.1529/biophysj.107.113738

    Article  PubMed  CAS  Google Scholar 

  94. Lee HR, Helquist SA, Kool ET, Johnson KA (2008) Importance of hydrogen bonding for efficiency and specificity of the human mitochondrial DNA polymerase. J Biol Chem 283:14402–14410. doi:10.1074/jbc.M705007200

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  95. Derbyshire V, Freemont PS, Sanderson MR et al (1988) Genetic and crystallographic studies of the 3′,5′-exonucleolytic site of DNA polymerase I. Science 240:199–201

    Article  PubMed  CAS  Google Scholar 

  96. Kuduva SS, Craig DC, Nangia A, Desiraju GR (1999) Cubanecarboxylic acids. Crystal engineering considerations and the role of C-H···O hydrogen bonds in determining O-H···O networks. J Am Chem Soc 121:1936–1944. doi:10.1021/ja981967u

    Article  CAS  Google Scholar 

  97. Meadows ES, De Wall SL, Barbour LJ et al (2000) Structural and dynamic evidence for C − H···O hydrogen bonding in lariat ethers: implications for protein structure. J Am Chem Soc 122:3325–3335. doi:10.1021/ja9940672

    Article  CAS  Google Scholar 

  98. Amin ML (2013) P-glycoprotein inhibition for optimal drug delivery. Drug Target Insights 2013:27–34. doi:10.4137/DTI.S12519

    Article  CAS  Google Scholar 

  99. Sanguinetti MC, Tristani-Firouzi M (2006) hERG potassium channels and cardiac arrhythmia. Nature 440:463–469. doi:10.1038/nature04710

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

We are grateful to our donors who supported to build a computational platform in Bangladesh http://grc-bd.org/donate/.

Author’s Contribution

MAH, MGS and MAKK conceived the idea. MAH, MGS, MAKK and MMH designed the drugs. JS performed the quantum calculations. JS, AMK and AR performed the molecular docking, ADME calculations, data collection and draft writing. All authors read and approved the manuscript.

Funding

This research does not receive any external funding.

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Author notes

  1. Mohammad A. Halim

    Present address: Institut Lumière Matière, Université Lyon 1 – CNRS, Université de Lyon, 69622, Villeurbanne Cedex, France

Authors and Affiliations

  1. Division of Computer-Aided Drug Design, BICCB, Green Research Centre, 38 Green Road West, Dhaka, 1205, Bangladesh

    Jakaria Shawon, Akib Mahmud Khan, Adhip Rahman, Mohammad Mazharol Hoque & Mohammad A. Halim

  2. Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, 1000, Bangladesh

    Jakaria Shawon & Akib Mahmud Khan

  3. Department of General Studies, Jubail University College, Jubail Industrial City, 31961, Saudi Arabia

    Mohammad Abdul Kader Khan

  4. Fakultät für Chemie und Biochemie, Organische Chemie I, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801, Bochum, Germany

    Mohammed G. Sarwar

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Shawon, J., Khan, A.M., Rahman, A. et al. Molecular Recognition of Azelaic Acid and Related Molecules with DNA Polymerase I Investigated by Molecular Modeling Calculations. Interdiscip Sci Comput Life Sci 10, 525–537 (2018). https://doi.org/10.1007/s12539-016-0186-3

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  • DOI: https://doi.org/10.1007/s12539-016-0186-3

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