Phát hiện những thay đổi bất thường trong logP sau khi fluor hóa bằng cách sử dụng mô phỏng động lực học phân tử

O’Hagan D (2010) Fluorine in health care: organofluorine containing blockbuster drugs. J Fluorine Chem 131(11):1071–1081 Wang J, Sanchez-Rosello M, Acena JL, del Pozo C, Sorochinsky AE, Fustero S, Soloshonok VA, Liu H (2014) Fluorine in pharmaceutical industry: fluorine-containing drugs introduced to the market in the last decade (2001–2011). Chem Rev 114(4):2432–2506 Zhou Y, Wang J, Gu Z, Wang S, Zhu W, Acena JL, Soloshonok VA, Izawa K, Liu H (2016) Next generation of fluorine-containing pharmaceuticals, compounds currently in phase II-III clinical trials of major pharmaceutical companies: new structural trends and therapeutic areas. Chem Rev 116(2):422–518 Smart BE (2001) Fluorine substituent effects (on bioactivity). J Fluorine Chem 109(1):3–11 Bohm HJ, Banner D, Bendels S, Kansy M, Kuhn B, Muller K, Obst-Sander U, Stahl M (2004) Fluorine in medicinal chemistry. ChemBioChem 5(5):637–643 Muller K, Faeh C, Diederich F (2007) Fluorine in pharmaceuticals: looking beyond intuition. Science 317(5846):1881–1886 Hagmann WK (2008) The many roles for fluorine in medicinal chemistry. J Med Chem 51(15):4359–4369 Purser S, Moore PR, Swallow S, Gouverneur V (2008) Fluorine in medicinal chemistry. Chem Soc Rev 37(2):320–330 Gillis EP, Eastman KJ, Hill MD, Donnelly DJ, Meanwell NA (2015) Applications of fluorine in medicinal chemistry. J Med Chem 58(21):8315–8359 Swallow S (2015) Fluorine in medicinal chemistry. Prog Med Chem 54:65–133 Yerien DE, Bonesi S, Postigo A (2016) Fluorination methods in drug discovery. Org Biomol Chem 14(36):8398–8427 Huchet QA, Kuhn B, Wagner B, Fischer H, Kansy M, Zimmerli D, Carreira EM, Müller K (2013) On the polarity of partially fluorinated methyl groups. J Fluorine Chem 152:119–128 Huchet QA, Kuhn B, Wagner B, Kratochwil NA, Fischer H, Kansy M, Zimmerli D, Carreira EM, Muller K (2015) Fluorination patterning: a study of structural motifs that impact physicochemical properties of relevance to drug discovery. J Med Chem 58(22):9041–9060 Wuitschik G, Carreira EM, Wagner B, Fischer H, Parrilla I, Schuler F, Rogers-Evans M, Muller K (2010) Oxetanes in drug discovery: structural and synthetic insights. J Med Chem 53(8):3227–3246 Daina A, Michielin O, Zoete V (2014) iLOGP: a simple, robust, and efficient description of n-octanol/water partition coefficient for drug design using the GB/SA approach. J Chem Inform Model 54(12):3284–3301 Wang R, Fu Y, Lai L (1997) A new atom-additive method for calculating partition coefficients. J Chem Inform Comput Sci 37(3):615–621 Cheng T, Zhao Y, Li X, Lin F, Xu Y, Zhang X, Li Y, Wang R, Lai L (2007) Computation of octanol-water partition coefficients by guiding an additive model with knowledge. J Chem Inform Model 47(6):2140–2148 Tetko IV, Tanchuk VY (2002) Application of associative neural networks for prediction of lipophilicity in ALOGPS 2.1 program. J Chem Inform Comput Sci 42(5):1136–1145 Tetko IV, Bruneau P (2004) Application of ALOGPS to predict 1-octanol/water distribution coefficients, logP, and logD, of AstraZeneca in-house database. J Pharm Sci 93(12):3103–3110 Bgu J-P, Bonnet-Delpon D (2008) Bioorganic and medicinal chemistry of fluorine. Wiley, Hoboken Menear KA, Adcock C, Boulter R, Cockcroft XL, Copsey L, Cranston A, Dillon KJ, Drzewiecki J, Garman S, Gomez S, Javaid H, Kerrigan F, Knights C, Lau A, Loh VM Jr, Matthews IT, Moore S, O’Connor MJ, Smith GC, Martin NM (2008) 4-[3-(4-cyclopropanecarbonylpiperazine-1-carbonyl)-4-fluorobenzyl]-2H-phthalazin- 1-one: a novel bioavailable inhibitor of poly(ADP-ribose) polymerase-1. J Med Chem 51(20):6581–6591 Arikawa Y, Nishida H, Kurasawa O, Hasuoka A, Hirase K, Inatomi N, Hori Y, Matsukawa J, Imanishi A, Kondo M, Tarui N, Hamada T, Takagi T, Takeuchi T, Kajino M (2012) Discovery of a novel pyrrole derivative 1-[5-(2-fluorophenyl)-1-(pyridin-3-ylsulfonyl)-1H-pyrrol-3-yl]-N-methylmethanamin e fumarate (TAK-438) as a potassium-competitive acid blocker (P-CAB). J Med Chem 55(9):4446–4456 Jorgensen WL, Briggs JM, Contreras ML (1990) Relative partition coefficients for organic solutes from fluid simulations. J Phys Chem 94(4):1683–1686 Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004) Development and testing of a general amber force field. J Comput Chem 25(9):1157–1174 Harder E, Damm W, Maple J, Wu C, Reboul M, Xiang JY, Wang L, Lupyan D, Dahlgren MK, Knight JL, Kaus JW, Cerutti DS, Krilov G, Jorgensen WL, Abel R, Friesner RA (2016) OPLS3: a force field providing broad coverage of drug-like small molecules and proteins. J Chem Theory Comput 12(1):281–296 Sugita Y, Okamoto Y (1999) Replica-exchange molecular dynamics method for protein folding. Chem Phys Lett 314(1–2):141–151 Okamoto Y, Kokubo H, Tanaka T (2014) Prediction of ligand binding affinity by the combination of replica-exchange method and double-decoupling method. J Chem Theory Comput 10(8):3563–3569 Steinbrecher T, Mobley DL, Case DA (2007) Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations. J Chem Phys 127(21):214108 Bannan CC, Calabro G, Kyu DY, Mobley DL (2016) Calculating partition coefficients of small molecules in octanol/water and cyclohexane/water. J Chem Theory Comput 12(8):4015–4024 Kirkwood JG (1935) Statistical mechanics of fluid mixtures. J Chem Phys 3(5):300–313 Chipot C, Pohorille A (2007) Free energy calculations: theory and applications in chemistry and biology. Springer, Berlin Case DA, Betz RM, Cerutti DS, Cheatham TE III, Darden TA, Duke RE, Giese TJ, Gohlke H, Goetz AW, Homeyer N, Izadi S, Janowski P, Kaus J, Kovalenko A, Lee TS, LeGrand S, Li P, Lin C, Luchko T, Luo R, Madej B, Mermelstein D, Merz KM, Monard G, Nguyen H, Nguyen HT, Omelyan I, Onufriev A, Roe DR, Roitberg A, Sagui C, Simmerling CL, Botello-Smith WM, Swails J, Walker RC, Wang J, Wolf RM, Wu X, Xiao L, Kollman PA (2016) AMBER 2016, University of California, San Francisco Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, Caricato M, Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Montgomery JA Jr, Peralta JE, Ogliaro F, Bearpark M, Heyd JJ, Brothers E, Kudin KN, Staroverov VN, Kobayashi R, Normand J, Raghavachari K, Rendell A, Burant JC, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam JM, Klene M, Knox JE, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Martin RL, Morokuma K, Zakrzewski VG, Voth GA, Salvador P, Dannenberg JJ, Dapprich S, Daniels AD, Farkas Ö, Foresman JB, Ortiz JV, Cioslowski J, Fox DJ (2009) Gaussian 09 Revision C.01. Gaussian Inc., Wallingford Wang J, Hou T (2011) Application of molecular dynamics simulations in molecular property prediction I: density and heat of vaporization. J Chem Theory Comput 7(7):2151–2165 Mobley DL, Guthrie JP (2014) FreeSolv: a database of experimental and calculated hydration free energies, with input files. J Comput Aided Mol Des 28(7):711–720 Martinez L, Andrade R, Birgin EG, Martinez JM (2009) PACKMOL: a package for building initial configurations for molecular dynamics simulations. J Comput Chem 30(13):2157–2164 PubChem Identifier: CID 15981397 URL: https://pubchem.ncbi.nlm.nih.gov/compound/15981397 Mobley DL, Dumont E, Chodera JD, Dill KA (2007) Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent. J Phys Chem B 111(9):2242–2254 Roe DR, Cheatham TE (2013) PTRAJ and CPPTRAJ: software for processing and analysis of molecular dynamics trajectory data. J Chem Theory Comput 9(7):3084–3095 Haynes WM, Lide DR (2011) CRC handbook of chemistry and physics: a ready-reference book of chemical and physical data, 92nd edn. CRC Press, Boca Raton Garrido NM, Queimada AJ, Jorge M, Macedo EA, Economou IG (2009) 1-octanol/water partition coefficients of n-alkanes from molecular simulations of absolute solvation free energies. J Chem Theory Comput 5(9):2436–2446 Bhatnagar N, Kamath G, Chelst I, Potoff JJ (2012) Direct calculation of 1-octanol-water partition coefficients from adaptive biasing force molecular dynamics simulations. J Chem Phys 137(1):014502 Fischer NM, van Maaren PJ, Ditz JC, Yildirim A, van der Spoel D (2015) Properties of organic liquids when simulated with long-range lennard-jones interactions. J Chem Theory Comput 11(7):2938–2944 PhysProp Database (2017) http://esc.syrres.com/fatepointer/search.asp. Accessed 21 Sept 2017 Mobley DL, Wymer KL, Lim NM, Guthrie JP (2014) Blind prediction of solvation free energies from the SAMPL4 challenge. J Comput Aided Mol Des 28(3):135–150 Bannan CC, Burley KH, Chiu M, Shirts MR, Gilson MK, Mobley DL (2016) Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge. J Comput Aided Mol Des 30(11):927–944 Rustenburg AS, Dancer J, Lin B. Feng J, Ortwine DF, Mobley DL, Chodera JD (2016) Measuring experimental cyclohexane–water distribution coefficients for the SAMPL5 challenge. J Comput Aided Mol Des 30(11):945–958 Scott DR, Munson KB, Marcus EA, Lambrecht NWG, Sachs G (2015) The binding selectivity of vonoprazan (TAK-438) to the gastric H+,K+-ATPase. Aliment Pharmacol Ther 42(11–12):1315–1326 JChem for Office 5.12.3.966 (2013) (http://www.chemaxon.com) JChem for Office (Excel) was used for chemical database access, structure based property calculation, search and reporting Weiser J, Shenkin PS, Still WC (1999) Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO). J Comput Chem 20(2):217–230 Jorgensen WL, McDonald NA, Selmi M, Rablen PR (1995) Importance of polarization for dipolar solutes in low-dielectric media: 1,2-dichloroethane and water in cyclohexane. J Am Chem Soc 117(47):11809–11810 Leontyev I, Stuchebrukhov A (2011) Accounting for electronic polarization in non-polarizable force fields. Phys Chem Chem Phys 13(7):2613–2626 DeBolt SE, Kollman PA (1995) Investigation of structure, dynamics, and solvation in 1-octanol and its water-saturated solution: molecular dynamics and free-energy perturbation studies. J Am Chem Soc 117(19):5316–5340 MacCallum JL, Tieleman DP (2002) Structures of neat and hydrated 1-octanol from computer simulations. J Am Chem Soc 124(50):15085–15093 Hyohdoh I, Furuichi N, Aoki T (2013) Fluorine scanning by nonselective fluorination: enhancing Raf/MEK inhibition while keeping physicochemical properties. ACS Med Chem Lett 4(11):1059–1063