Farnesyl diphosphate synthase inhibitors from in silico screening

Chemical Biology and Drug Design

Volumn 81, Issue 6, 2013, Pages 742-748

  Lindert, Steffen ^a,b   Zhu, Wei ^c   Liu, Yi Liang ^c   Pang, Ran ^d   Oldfield, Eric ^c   Mccammon, J Andrew ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b NSF Center for Theoretical Biological Physics   (United States)

^c UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^d UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

Drug discovery; Molecular modeling; Virtual screening

Indexed keywords

BISPHOSPHONIC ACID DERIVATIVE; GERANYLTRANSFERASE;

ARTICLE; BINDING AFFINITY; BINDING SITE; COMPUTER MODEL; CRYSTAL STRUCTURE; DRUG SCREENING; HUMAN; MOLECULAR DOCKING; MOLECULAR MODEL; OSTEOLYSIS; PRIORITY JOURNAL; PROTEIN CONFORMATION;

ALLOSTERIC SITE; AREA UNDER CURVE; CRYSTALLOGRAPHY, X-RAY; ENZYME INHIBITORS; FURANS; GERANYLTRANSTRANSFERASE; MOLECULAR DOCKING SIMULATION; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; ROC CURVE;

EID: 84878344916     PISSN: 17470277     EISSN: 17470285     Source Type: Journal    
DOI: 10.1111/cbdd.12121     Document Type: Article

References (34)

1. Mao J., Mukherjee S., Zhang Y., Cao R., Sanders J.M., Song Y., Meints G.A., Gao Y.G., Mukkamala D., Hudock M.P., Oldfield E. (2006) Solid-state NMR, crystallographic, and computational investigation of bisphosphonates and farnesyl diphosphate synthase-bisphosphonate complexes. J Am Chem Soc;128:14485-14497.
2. Stresing V., Daubine F., Benzaid I., Monkkonen H., Clezardin P. (2007) Bisphosphonates in cancer therapy. Cancer Lett;257:16-35.
3. Jahnke W., Rondeau J.M., Cotesta S., Marzinzik A., Pelle X., Geiser M., Strauss A. et al. (2010) Allosteric non-bisphosphonate FPPS inhibitors identified by fragment-based discovery. Nat Chem Biol;6:660-666.
4. Buhaescu I., Izzedine H. (2007) Mevalonate pathway: a review of clinical and therapeutical implications. Clin Biochem;40:575-584.
5. Gnant M., Mlineritsch B., Schippinger W., Luschin-Ebengreuth G., Postlberger S., Menzel C., Jakesz R. et al. (2009) Endocrine therapy plus zoledronic acid in premenopausal breast cancer. N Engl J Med;360:679-691.
6. US Patent No. 5, 756, 423 May 26, 1998. US Patent No. 5, 756, 423 May 26, 1998.
7. Cromartie T.H., Fisher K.J., Grossman J.N. (1999) The discovery of a novel site of action for herbicidal bisphosphonates. Pestic Biochem Physiol;63:114-126.
8. Oldfield E. (2010) Targeting isoprenoid biosynthesis for drug discovery: bench to bedside. Acc Chem Res;43:1216-1226.
9. van Beek E., Pieterman E., Cohen L., Lowik C., Papapoulos S. (1999) Farnesyl pyrophosphate synthase is the molecular target of nitrogen-containing bisphosphonates. Biochem Biophys Res Commun;264:108-111.
10. Rondeau J.M., Bitsch F., Bourgier E., Geiser M., Hemmig R., Kroemer M., Lehmann S., Ramage P., Rieffel S., Strauss A., Green J.R., Jahnke W. (2006) Structural basis for the exceptional in vivo efficacy of bisphosphonate drugs. ChemMedChem;1:267-273.
11. Oldfield E., Lin F.Y. (2012) Terpene biosynthesis: modularity rules. Angew Chem Int Ed Engl;51:1124-1137.
12. Durrant J.D., Cao R., Gorfe A.A., Zhu W., Li J., Sankovsky A., Oldfield E., McCammon J.A. (2011) Non-bisphosphonate inhibitors of isoprenoid biosynthesis identified via computer-aided drug design. Chem Biol Drug Des;78:323-332.
13. Sanders J.M., Song Y., Chan J.M., Zhang Y., Jennings S., Kosztowski T., Odeh S. et al. (2005) Pyridinium-1-yl bisphosphonates are potent inhibitors of farnesyl diphosphate synthase and bone resorption. J Med Chem;48:2957-2963.
14. Zhang Y., Cao R., Yin F., Hudock M.P., Guo R.T., Krysiak K., Mukherjee S. et al. (2009) Lipophilic bisphosphonates as dual farnesyl/geranylgeranyl diphosphate synthase inhibitors: an X-ray and NMR investigation. J Am Chem Soc;131:5153-5162.
15. Amaro R., Baron R., McCammon J. (2008) An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. J Comput Aided Mol Des;22:693-705.
16. Lin J.H., Perryman A.L., Schames J.R., McCammon J.A. (2002) Computational drug design accommodating receptor flexibility: the relaxed complex scheme. J Am Chem Soc;124:5632-5633.
17. Lin J.H., Perryman A.L., Schames J.R., McCammon J.A. (2003) The relaxed complex method: accommodating receptor flexibility for drug design with an improved scoring scheme. Biopolymers;68:47-62.
18. Trott O., Olson A.J. (2009) AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem;31:455-461.
19. Friesner R.A., Banks J.L., Murphy R.B., Halgren T.A., Klicic J.J., Mainz D.T., Repasky M.P., Knoll E.H., Shelley M., Perry J.K., Shaw D.E., Francis P., Shenkin P.S. (2004) Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem;47:1739-1749.
20. Halgren T.A., Murphy R.B., Friesner R.A., Beard H.S., Frye L.L., Pollard W.T., Banks J.L. (2004) Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J Med Chem;47:1750-1759.
21. Christen M., Hunenberger P.H., Bakowies D., Baron R., Burgi R., Geerke D.P., Heinz T.N., Kastenholz M.A., Krautler V., Oostenbrink C., Peter C., Trzesniak D., Van Gunsteren W.F. (2005) The GROMOS software for biomolecular simulation: GROMOS05. J Comput Chem;26:1719-1751.
22. O'Boyle N.M., Banck M., James C.A., Morley C., Vandermeersch T., Hutchison G.R. (2011) Open Babel: an open chemical toolbox. J Cheminform;3:33.
23. Dolinsky T.J., Czodrowski P., Li H., Nielsen J.E., Jensen J.H., Klebe G., Baker N.A. (2007) PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res;35:W522-W525.
24. Dolinsky T.J., Nielsen J.E., McCammon J.A., Baker N.A. (2004) PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res;32:W665-W667.
25. Morris G.M., Huey R., Lindstrom W., Sanner M.F., Belew R.K., Goodsell D.S., Olson A.J. (2009) AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem;30:2785-2791.
26. Lee H.S., Choi J., Kufareva I., Abagyan R., Filikov A., Yang Y., Yoon S. (2008) Optimization of high throughput virtual screening by combining shape-matching and docking methods. J Chem Inf Model;48:489-497.
27. Friesner R.A., Murphy R.B., Repasky M.P., Frye L.L., Greenwood J.R., Halgren T.A., Sanschagrin P.C., Mainz D.T. (2006) Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J Med Chem;49:6177-6196.
28. Webb M.R. (1992) A continuous spectrophotometric assay for inorganic phosphate and for measuring phosphate release kinetics in biological systems. Proc Natl Acad Sci USA;89:4884-4887.
29. Durrant J.D., McCammon J.A. (2010) NNScore: a neural-network-based scoring function for the characterization of protein-ligand complexes. J Chem Inf Model;50:1865-1871.
30. Lipinski C.A., Lombardo F., Dominy B.W., Feeney P.J. (2001) Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev;46:3-26.
31. Zhu W., Zhang Y., Sinko W., Hensler M.E., Olson J., Molohon K.J., Lindert S. et al. (2013) Antibacterial drug leads targeting isoprenoid biosynthesis. Proc Natl Acad Sci USA;110:123-128.
32. Butler M.M., Williams J.D., Peet N.P., Moir D.T., Panchal R.G., Bavari S., Shinabarger D.L., Bowlin T.L. (2010) Comparative in vitro activity profiles of novel bis-indole antibacterials against gram-positive and gram-negative clinical isolates. Antimicrob Agents Chemother;54:3974-3977.
33. Panchal R.G., Ulrich R.L., Lane D., Butler M.M., Houseweart C., Opperman T., Williams J.D., Peet N.P., Moir D.T., Nguyen T., Gussio R., Bowlin T., Bavari S. (2009) Novel broad-spectrum bis-(imidazolinylindole) derivatives with potent antibacterial activities against antibiotic-resistant strains. Antimicrob Agents Chemother;53:4283-4291.
34. Opperman T.J. (2010) Poster Session, 50th Interscience Conference on Antimicrobial Agents and Chemotherapy, September 12-15, Boston.