IBBR Publications

Mackerell AD, Jo S, Lakkaraju SKaushik, Lind C, Yu W. Identification and characterization of fragment binding sites for allosteric ligand design using the site identification by ligand competitive saturation hotspots approach (SILCS-Hotspots). Biochim Biophys Acta Gen Subj. 2020 ;1864(4):129519.

Goel H, Yu W, Ustach VD, Aytenfisu AH, Sun D, Mackerell AD. Impact of electronic polarizability on protein-functional group interactions. Phys Chem Chem Phys. 2020 ;22(13):6848-6860.

Chauhan J, Yu W, Cardinale S, Opperman TJ, Mackerell AD, Fletcher S, de Leeuw EPh. Optimization of a Benzothiazole Indolene Scaffold Targeting Bacterial Cell Wall Assembly. Drug Des Devel Ther. 2020 ;14:567-574.

Xu X, Godoy-Ruiz R, Adipietro KA, Peralta C, Ben-Hail D, Varney KM, Cook ME, Roth BM, Wilder PT, Cleveland T, et al. Structure of the cell-binding component of the binary toxin reveals a di-heptamer macromolecular assembly. Proc Natl Acad Sci U S A. 2020 .

Ustach VD, Lakkaraju SKaushik, Jo S, Yu W, Jiang W, Mackerell AD. Optimization and Evaluation of Site-Identification by Ligand Competitive Saturation (SILCS) as a Tool for Target-Based Ligand Optimization. J Chem Inf Model. 2019 .

Donohue E, Khorsand S, Mercado G, Varney KM, Wilder PT, Yu W, Mackerell AD, Alexander P, Van QN, Moree B, et al. Second harmonic generation detection of Ras conformational changes and discovery of a small molecule binder. Proc Natl Acad Sci U S A. 2019 .

Swaroop A, Oyer JA, Will CM, Huang X, Yu W, Troche C, Bulic M, Durham BH, Wen QJeremy, Crispino JD, et al. An activating mutation of the NSD2 histone methyltransferase drives oncogenic reprogramming in acute lymphocytic leukemia. Oncogene. 2018 .

Yu W, Jo S, Lakkaraju SKaushik, Weber DJ, Mackerell AD. Exploring protein-protein interactions using the Site-Identification by Ligand Competitive Saturation (SILCS) methodology. Proteins. 2018 .

Yu W, Mackerell AD. Computer-Aided Drug Design Methods. Methods Mol Biol. 2017 ;1520:85-106.

Cardenas MG, Oswald E, Yu W, Xue F, Mackerell AD, Melnick AM. The Expanding Role of the BCL6 Oncoprotein as a Cancer Therapeutic Target. Clin Cancer Res. 2017 ;23(4):885-893.

Liang D, Yu W, Nguyen N, Deschamps JR, Imler GH, Li Y, Mackerell AD, Jiang C, Xue F. Iodobenzene-Catalyzed Synthesis of Phenanthridinones via Oxidative C-H Amidation. J Org Chem. 2017 ;82(7):3589-3596.

Sarkar A, Yu W, Desai UR, Mackerell AD, Mosier PD. Estimating glycosaminoglycan-protein interaction affinity: water dominates the specific antithrombin-heparin interaction. Glycobiology. 2016 ;26(10):1041-1047.

Heinzl GA, Huang W, Yu W, Giardina BJ, Zhou Y, Mackerell AD, Wilks A, Xue F. Iminoguanidines as Allosteric Inhibitors of the Iron-Regulated Heme Oxygenase (HemO) of Pseudomonas aeruginosa. J Med Chem. 2016 ;59(14):6929-42.

Cavalier MC, Melville Z, Aligholizadeh E, E Raman P, Yu W, Fang L, Alasady M, Pierce AD, Wilder PT, Mackerell AD, et al. Novel protein-inhibitor interactions in site 3 of Ca(2+)-bound S100B as discovered by X-ray crystallography. Acta Crystallogr D Struct Biol. 2016 ;72(Pt 6):753-60.

Cardenas MG, Yu W, Beguelin W, Teater MR, Geng H, Goldstein RL, Oswald E, Hatzi K, Yang S-N, Cohen J, et al. Rationally designed BCL6 inhibitors target activated B cell diffuse large B cell lymphoma. J Clin Invest. 2016 ;126(9):3351-62.

Lanning ME, Yu W, Yap JL, Chauhan J, Chen L, Whiting E, Pidugu LS, Atkinson T, Bailey H, Li W, et al. Structure-based design of N-substituted 1-hydroxy-4-sulfamoyl-2-naphthoates as selective inhibitors of the Mcl-1 oncoprotein. Eur J Med Chem. 2016 ;113:273-92.

Yang W, Sun X, Yu W, Rai R, Deschamps JR, Mitchell LA, Jiang C, Mackerell AD, Xue F. Facile Synthesis of Spirocyclic Lactams from β-Keto Carboxylic Acids. Org Lett. 2015 ;17(12):3070-3.

Lakkaraju SKaushik, Yu W, E Raman P, Hershfeld AV, Fang L, Deshpande DA, Mackerell AD. Mapping functional group free energy patterns at protein occluded sites: nuclear receptors and G-protein coupled receptors. J Chem Inf Model. 2015 ;55(3):700-8.

Yu W, Lakkaraju SKaushik, E Raman P, Fang L, Mackerell AD. Pharmacophore modeling using site-identification by ligand competitive saturation (SILCS) with multiple probe molecules. J Chem Inf Model. 2015 ;55(2):407-20.

Fletcher S, Yu W, Huang J, Kwasny SM, Chauhan J, Opperman TJ, Mackerell AD, de Leeuw EPH. Structure-activity exploration of a small-molecule Lipid II inhibitor. Drug Des Devel Ther. 2015 ;9:2383-94.

Lakkaraju SKaushik, E Raman P, Yu W, Mackerell AD. Sampling of Organic Solutes in Aqueous and Heterogeneous Environments Using Oscillating Excess Chemical Potentials in Grand Canonical-like Monte Carlo-Molecular Dynamics Simulations. J Chem Theory Comput. 2014 ;10(6):2281-2290.

Yu W, Lakkaraju SKaushik, E Raman P, Mackerell AD. Site-Identification by Ligand Competitive Saturation (SILCS) assisted pharmacophore modeling. J Comput Aided Mol Des. 2014 ;28(5):491-507.

E Raman P, Yu W, Lakkaraju SK, Mackerell AD. Inclusion of multiple fragment types in the site identification by ligand competitive saturation (SILCS) approach. J Chem Inf Model. 2013 ;53(12):3384-98.

Cao X, Yap JL, M Newell-Rogers K, Peddaboina C, Jiang W, Papaconstantinou HT, Jupitor D, Rai A, Jung K-Y, Tubin RP, et al. The novel BH3 α-helix mimetic JY-1-106 induces apoptosis in a subset of cancer cells (lung cancer, colon cancer and mesothelioma) by disrupting Bcl-xL and Mcl-1 protein-protein interactions with Bak. Mol Cancer. 2013 ;12(1):42.

Yu W, Lopes PEM, Roux B, Mackerell AD. Six-site polarizable model of water based on the classical Drude oscillator. J Chem Phys. 2013 ;138(3):034508.