Program Chair for the Bioinformatics Program, Rabb School of Continuing Studies, Division of Graduate Professional Studies.


Ph.D., University of California, San Francisco

Field of Specialty

Computer-aided drug design.

Contact Information

Rabb School

Personal Web Page

Alan Cheng

Alan Cheng, PhD, is a Principal Scientist at Amgen's research labs in South San Francisco, CA, where he works on the discovery of new medicines for oncology, cardiac, and neuroscience diseases. His research interests include computer-aided drug design and biological sequence-structure relationships. He received a PhD from the University of California, San Francisco, and undergraduate degrees from the University of California at Berkeley.


Dineen TA, Chen K, Cheng AC, Derakhchan K, Epstein O, Esmay J, Hickman D, Kreiman CE, Marx IE, Wahl RC, Wen PH, Weiss MM, Whittington DA, Wood S, Fremeau RT Jr, White RD, Patel VF. "Inhibitors of β-Site amyloid precursor protein cleaving enzyme (BACE1): Identification of (S)-7-(2-fluoropyridin-3-yl)-3-((3-methyloxetan-3-yl)ethynyl)-5'H-spiro[chromeno[2,3-b]pyridine-5,4'-oxazol]-2'-amine (AMG-8718)." J Med Chem. 57. (2014): 9811-31.

Epstein O, Bryan MC, Cheng AC, Derakhchan K, Dineen TA, Hickman D, Hua Z, Human JB, Kreiman C, Marx IE, Weiss MM, Wahl RC, Wen PH, Whittington DA, Wood S, Zheng XM, Fremeau RT Jr, White RD, Patel VF. "Lead optimization and modulation of hERG activity in a series of aminooxazoline xanthene β-site amyloid precursor protein cleaving enzyme (BACE1) inhibitors." J Med Chem 57. (2014): 9796-810.

Gustin DJ, Li Y, Brown ML, Min X, Schmitt MJ, Wanska M, Wang X, Connors R, Johnstone S, Cardozo M, Cheng AC, Jeffries S, Franks B, Li S, Shen S, Wong M, Wesche H, Xu G, Carlson TJ, Plant M, Morgenstern K, Rex K, Schmitt J, Coxon A, Walker N, Kayser F, Wa. "Structure guided design of a series of sphingosine kinase (SphK) inhibitors." Bioorg Med Chem Lett. 23. (2014): 4608-4616.

Loving KA, Lin A, Cheng AC.. "Structure-based druggability assessment of the mammalian structural proteome with inclusion of light protein flexibility.." PLoS Comput Biol. 10. (2014): e1003741.

Peterson EA, Andrews PS, Be X, Boezio AA, Bush TL, Cheng AC, Coats JR, Colletti AE, Copeland KW, Dupont M, Graceffa R, Grubinska B, Harmange JC, Kim JL, Mullady EL, Olivieri P, Schenkel LB, Stanton MK, Teffera Y, Whittington DA, Cai T, La DS.. "Discovery of triazine-benzimidazoles as selective inhibitors of mTOR.." Bioorg Med Chem Lett. 21. (2013): 2064-2070.

Bryan MC, Whittington DA, Doherty EM, Falsey JR, Cheng AC, Emkey R, Brake RL, Lewis RT.. "Rapid development of piperidine carboxamides as potent and selective Anaplastic Lymphoma Kinase inhibitors." J Med Chem. 55. (2012): 1698-1705.

Huang H, La DS, Cheng AC, Whittington DA, Patel VF, Chen K, Dineen TA, Epstein O, Graceffa R, Hickman D, Kiang YH, Louie S, Luo Y, Wahl RC, Wen PH, Wood S, Fremeau RT Jr.. "Structure- and property-based design of aminooxazoline xanthenes as selective, orally efficacious, and CNS penetrable BACE inhibitors for the treatment of Alzheimer's Disease.." J Med Chem. 55. (2012): 9156-9169.

Jordan JB, Poppe L, Xia X, Cheng AC, Sun Y, Michelsen K, Eastwood H, Schnier PD, Nixey T, Zhong W.. "Fragment based drug discovery: Practical implementation based on 19F NMR spectroscopy." J Med Chem. 55. (2012): 678-687.

Peterson EA, Boezio AA, Andrews PS, Boezio CM, Bush TL, Cheng AC, Choquette D, Coats JR, Colletti AE, Copeland KW, DuPont M, Graceffa R, Grubinska B, Kim JL, Lewis RT, Liu J, Mullady EL, Potashman MH, Romero K, Shaffer PL, Stanton MK, Stellwagen JC, Teff. "Discovery and optimization of potent and selective imidazopyridine and imidazopyridazine mTOR inhibitors.." Bioorg Med Chem Lett. 22. (2012): 4967-4974.

Amegadzie A, Bryan MC, Chen JJ, Cheng AC, Dineen T, Epstein O, Gore VK, Hua Z, Human JB, Huang H, Kreiman C, La D, Liu Q, Ma VV, Marx I, Patel VF, Qian W, Weiss M, White R, Yuan CC.. Spiro-tetracyclic ring compounds as beta-secretase modulators and methods of use. Patent WO 2010/030954.

Boezio A,. Cheng A,. Coats J, Copeland K, Graceffa R, Harmange JC, Huang H, La D, Olivieri P, Peterson E. Indole/benzimidazole compounds as mTOR kinase inhibitors. Patent WO/2010/096314.

Cee VJ, Schenkel LB, Hodous BL, Deak HL, Nguyen HN, Olivieri PR, Romero K, Bak A, Be X, Bellon S, Bush TL, Cheng AC, Chung G, Coats S, Eden PM, Hanestad K, Gallant PL, Gu Y, Huang X, Kendall RL, Lin MH, Morrison MJ, Patel VF, Radinsky R, Rose PE, Ross S,. "Discovery of a potent, selective, and orally bioavailable pyridinyl-pyrimidine phthalazine aurora kinase inhibitor." J Med Chem 53. (2010): 6368-6377.

Cheng AC, Eksterowicz J, Geuns-Meyer S, Sun Y.. "Analysis of kinase inhibitor selectivity using a thermodynamics-based partition index." J Med Chem 43. (2010): 4502-4510.

Cheng, Alan. "Preparation, solid state characterization, and single crystal structure analysis of N-(4-(6-(4-(trifluoromethyl)phenyl)pyrimidin-4-yloxy)benzo[d]thiazol-2-yl)acetamide crystal forms.." CrystEngComm. 13. (2010): 1170-1180.

Liu H, Kuhn C, Feru F, Jacques SL, Deshmukh GD, Ye P, Rennie GR, Johnson T, Kazmirski S, Low S, Coli R, Ding YH, Cheng AC, Tecle H, English JM, Stanton R, Wu JC.. "Enhanced selectivity profile of pyrazole-urea based DFG-out p38-alpha inhibitors." Bioorg Med Chem Lett 20. (2010): 4885-4891.

Cee V.J., Cheng A.C., Romero K., Bellon S., Mohr C., Whittington D.A., Bak A, Bready J, Caenepeel S, Coxon A, Deak HL, Fretland J, Gu Y, Hodous BL, Huang X, Kim JL, Lin J, Long AM, Nguyen H, Olivieri PR, Patel VF, Wang L, Zhou Y, Hughes P, Geuns-Meyer S.. "Pyridyl-pyrimidine benzimidazole derivatives as potent, selective, and orally bioavailable inhibitors of Tie-2 kinase.." Bioorg Med Chem Lett. 19. (2009): 424-427.

Czyznikowska Z, Lipkowski P, Gora RW, Zalesny R, Cheng AC.. "On the nature of intermolecular interactions in nucleic acid base-amino acid side-chain complexes." J Phys Chem B 113. (2009): 11511-11520.

Marx IE, DiMauro EF, Cheng A, Emkey R, Hitchcock SA, Huang L, Huang MY, Human J, Lee JH, Li X, Martin MW, White RD, Fremeau RT Jr, Patel VF.. "Discovery of alpha-amidosulfones as potent and selective agonists of CB2: synthesis, SAR, and pharmacokinetic properties.." Bioorg Med Chem Lett. 19. (2009): 31-35.

Patel S.D., Habeski W.M., Cheng A.C., de la Cruz E., Loh C., Kablaoui N.M.. "Quinazolin-4-piperidin-4-methyl sulfamide PC-1 inhibitors: Alleviating hERG interactions through structure based design.." Bioorg Med Chem Lett. (2009).

Stockman B.J., Kothe M., Kohls D., Weibley L., Connolly B.J., Sheils A.L., Cao Q., Cheng A.C., Yang L., Kamath A.V., Ding Y-H., Charlton M.E.. "Identification of allosteric PIF-pocket ligands for PDK1 using NMR-based fragment screening and 1H-15N TROSY experiments.." Chemical Biol & Drug Design 73. (2009): 179-188.

Tecle H, Feru F, Liu H, Kuhn C, Rennie G, Morris M, Shao J, Cheng AC, Gikunju D, Miret J, Coli R, Xi SH, Clugston SL, Low S, Kazmirski S, Ding YH, Cao Q, Johnson TL, Deshmukh GD, Dinitto JP, Wu JC, English JM. "The design, synthesis and potential utility of fluorescence probes that target DFG-out conformation of p38 for high throughput screening binding assa." Chem Biol Drug Des 74. (2009): 547-55.

Albrecht BK, Bellon S, Booker S, Cheng AC, D'Amico D, D'Angelo N, Harmange J-C, Kim T-S, Liu L, Norman MH, Siegmund AC, Stec M, Xi N, Yang K. Nitrogen-containing heterocyclyl ketones as HGF inhibitors and their preparation, pharmaceutical compositions and use in the treatment of diseases. Patent WO 2008/103277.

Cheng AC.. "Predicting selectivity and druggability in drug discovery.." Annual Reports Comp Chem. 4. (2008): 23-37.

Deak, H.L., Newcomb, J.R., Nunes, J.J., Boucher, C., Cheng, A.C., DiMauro, E.F., Epstein, L.F., Gallant, P., Hodous, B.L., Huang, X., Lee, J.H., Patel, V.F., Schneider, S., Turci, S.M., Zhu, X.. "N-(3-(phenylcarbamoyl)arylpyrimidine)-5-carboxamides as potent and selective inhibitors of Lck: structure, synthesis and SAR." Bioorg Med Chem Lett 18. 3 (2008): 1172-1176.

DiMauro EF, Buchanan JL, Cheng A, Emkey R, Hitchcock SA, Huang L, Huang MY, Janosky B, Lee JH, Li X, Martin MW, Tomlinson SA, White RD, Zheng XM, Patel VF, Fremeau RT Jr.. "Structural modifications of N-arylamide oxadiazoles: Identification of N-arylpiperidine oxadiazoles as potent and selective agonists of CB2.." Bioorg Med Chem Lett. 18. (2008): 4267-4274.

Cheng, A.C., Coleman, R.G., Smyth, K.T., Cao, Q., Soulard, P., Caffrey, D.R., Salzberg, A.C., Huang, E.S.. "Structure-based maximal affinity model predicts small-molecule druggability." Nature Biotech. 25. (2007): 71-75.

Dimauro, E.F., Newcomb, J,, Nunes, J.J., Bemis, J.E., Boucher, C., Buchanan, J.L., Buckner, W.H., Cheng, A., Faust, T., Hsieh, F., Huang, X., Lee, J.H., Marshall, T.L., Martin, M.W., McGowan, D.C., Schneider, S., Turci, S.M., White, R.D., Zhu, X.. "Discovery of 4-amino-5,6-biaryl-furo[2,3-d]pyrimidines as inhibitors of Lck: Development of an expedient and divergent synthetic route and preliminary SAR." Bioorg Med Chem Lett 17. (2007): 2305-2309.

Kothe, M., Kohls, D., Low, S., Coli, R., Cheng, A.C., Jacques, S.L., Johnson, T.L., Lewis, C., Loh, C., Nonomiya, J., Sheils, A.L., Verdries, K.A., Wynn, T.A., Kuhn, C., Ding, Y.H.. "Structure of the catalytic domain of human polo-like kinase 1." Biochemistry 46. (2007): 5960 -5971.

Armstrong, K.A., Tidor, B., and Cheng, A.C.. "Optimal charges in lead optimization: A structure-based neuraminidase case study." J Med Chem 49. (2006): 2470-2477.

Coleman, R.G., Salzberg, A.C., and Cheng, A.C.. "Structure-based identification of small molecule binding sites using a free energy model." J Chem Inf Model 46. (2006): 2631-2637.

Coleman, R.G., Burr, M.A., Souvaine, D.L., and Cheng, A.C.. "An intuitive approach to measuring protein surface curvature." Proteins 61. (2005): 1068-1074.

Cheng, A.C., and Frankel, A.D.. "Ab-initio interaction energies of amino acid side-chain hydrogen bond interactions with nucleic acid bases." J Am Chem Soc 126. (2004): 434-435.

Ryan G. Coleman, Michael Burr, Diane L. Souvaine, and Alan C. Cheng. Transformations and algorithms for least sum of squares hypersphere fitting.. Candadian Conference on Computational Geometry Proceedings, 2004.

Cheng, A.C., Chen, W.W., Fuhrmann, C.N., and Frankel, A.D.. "Recognition of nucleic acid bases and base-pairs by hydrogen bonding to amino acid side-chains." J Mol Biol 327. (2003): 781-796.

Walberer, B.J., Cheng, A.C., and Frankel, A.D.. "Structural diversity and isomorphism of hydrogen-bonded base interactions in nucleic acids." J Mol Biol 327. (2003): 767-780.

Cheng, A.. "Ab-initio Evidence for a Three-Hydrogen Bond Arginine-Wobble Interaction." 15th Gibbs Conference on Biothermodynamics, Carbondale, IL. 2001.

Cheng, A.C., Calabro, V., and Frankel, A.D.. "Design of RNA-binding proteins and ligands." Curr Opin Struct Biol 11. (2001): 478-484.

Cheng,Alan. "Hydrogen Bonds as a Specificity Determinant in Protein-RNA Interactions." 6th Annual RNA Society Meeting, Banff, Canada. 2001.

Cheng,Alan. "Strategies for Specific Recognition of RNA Using Hydrogen-Bonding." Biophysics, Tiburon, CA. University of California-San Francisco, Oct. 2001.

Courses Taught

RBIF 102 Genomics and Genetics
RBIF 110 Cheminformatics
RBIF 120 Research Topics in Computational Biology