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2. Landgraf, A. D., Brenner, R., Ghozayel, M. K., Bum-Erdene, K., Gonzalez-Gutierrez, G., and Meroueh, S. O. (2025) Small-Molecule KRAS Inhibitors by Tyrosine Covalent Bond Formation ChemMedChem 20, e202400624
3. Landgraf, A. D., Yeh, I. J., Ghozayel, M. K., Bum-Erdene, K., Gonzalez-Gutierrez, G., and Meroueh, S. O. (2023) Exploring Covalent Bond Formation at Tyr-82 for Inhibition of Ral GTPase Activation ChemMedChem 18, e202300272
4. Hussain, M. S., Liu, D., Alilain, W. J., and Meroueh, S. O. (2023) Covalent fragment inhibits RhoA activation by guanine exchange factors ACS Chemical Neuroscience 14, 2509-2516
5. Bum-Erdene, K., Ghozayel, M. K., Zhang, M. J., Gonzalez-Gutierrez, G., and Meroueh, S. O. (2023) Chloroacetamide fragment library screening identifies new scaffolds for covalent inhibition of the TEAD· YAP1 interaction RSC Medicinal Chemistry 14, 1803-1816
6. Brenner, R. J., Landgraf, A. D., Bum-Erdene, K., Gonzalez-Gutierrez, G., and Meroueh, S. O. (2023) Crystal packing reveals a potential autoinhibited KRAS dimer interface and a strategy for small-molecule inhibition of RAS signaling Biochemistry 62, 3206-3213
7. Bum‐Erdene, K., Ghozayel, M. K., Xu, D., and Meroueh, S. O. (2022) Covalent fragment screening identifies Rgl2 RalGEF cysteine for targeted covalent inhibition of ral GTPase activation ChemMedChem 17, e202100750
8. Bum-Erdene, K., Yeh, I.-J., Gonzalez-Gutierrez, G., Ghozayel, M. K., Pollok, K., and Meroueh, S. O. (2022) Small-molecule cyanamide pan-tead· yap1 covalent antagonists Journal of Medicinal Chemistry 66, 266-284
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10. Xu, D., Bum-Erdene, K., Leth, J. M., Ghozayel, M. K., Ploug, M., and Meroueh, S. O. (2021) Small-Molecule Inhibition of the uPAR uPA Interaction by Conformational Selection ChemMedChem 16, 377-387
11. Bum-Erdene, K., Liu, D., Xu, D., Ghozayel, M. K., and Meroueh, S. O. (2021) Design and Synthesis of Fragment Derivatives with a Unique Inhibition Mechanism of the uPAR.uPA Interaction ACS Med Chem Lett 12, 60-66
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19. Xu, D., Si, Y., and Meroueh, S. O. (2017) A Computational Investigation of Small-Molecule Engagement of Hot Spots at Protein-Protein Interaction Interfaces J Chem Inf Model 57, 2250-2272
20. Xu, D., Li, L., Zhou, D., Liu, D., Hudmon, A., and Meroueh, S. O. (2017) Structure-Based Target-Specific Screening Leads to Small-Molecule CaMKII Inhibitors ChemMedChem 12, 660-677
21. Xu, D., Bum-Erdene, K., Si, Y., Zhou, D., Ghozayel, M. K., and Meroueh, S. O. (2017) Mimicking Intermolecular Interactions of Tight Protein-Protein Complexes for Small-Molecule Antagonists ChemMedChem 12, 1794-1809
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24. Xu, D., and Meroueh, S. O. (2016) Effect of Binding Pose and Modeled Structures on SVMGen and GlideScore Enrichment of Chemical Libraries J Chem Inf Model 56, 1139-1151
25. Xu, D., Jalal, S. I., Sledge, G. W., and Meroueh, S. O. (2016) Small-molecule binding sites to explore protein-protein interactions in the cancer proteome Mol Biosyst 12, 3067-3087
26. Xu, D., Wang, B., and Meroueh, S. O. (2015) Structure-based computational approaches for small-molecule modulation of protein-protein interactions Methods Mol Biol 1278, 77-92
27. Liu, D., Zhou, D., Wang, B., Knabe, W. E., and Meroueh, S. O. (2015) A New Class of Orthosteric uPAR.uPA Small-Molecule Antagonists Are Allosteric Inhibitors of the uPAR.Vitronectin Interaction ACS Chemical Biology 10, 1521-1534
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29. Wang, B., Buchman, C. D., Li, L., Hurley, T. D., and Meroueh, S. O. (2014) Enrichment of chemical libraries docked to protein conformational ensembles and application to aldehyde dehydrogenase 2 Journal of Chemical Information and Modeling 54, 2105-2116
30. Peng, X., Wang, F., Li, L., Bum-Erdene, K., Xu, D., Wang, B. et al. (2014) Exploring a structural protein-drug interactome for new therapeutics in lung cancer Molecular Biosystems 10, 581-591
31. Wang, B., Li, L., Hurley, T. D., and Meroueh, S. O. (2013) Molecular recognition in a diverse set of protein-ligand interactions studied with molecular dynamics simulations and end-point free energy calculations Journal of Chemical Information and Modeling 53, 2659-2670
32. Mani, T., Wang, F., Knabe, W. E., Sinn, A. L., Khanna, M., Jo, I. et al. (2013) Small-molecule inhibition of the uPAR.uPA interaction: synthesis, biochemical, cellular, in vivo pharmacokinetics and efficacy studies in breast cancer metastasis Bioorganic & Medicinal Chemistry 21, 2145-2155
33. Mani, T., Liu, D., Zhou, D., Li, L., Knabe, W. E., Wang, F. et al. (2013) Probing binding and cellular activity of pyrrolidinone and piperidinone small molecules targeting the urokinase receptor ChemMedChem 8, 1963-1977
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35. Wang, F., Eric Knabe, W., Li, L., Jo, I., Mani, T., Roehm, H. et al. (2012) Design, synthesis, biochemical studies, cellular characterization, and structure-based computational studies of small molecules targeting the urokinase receptor Bioorganic & Medicinal Chemistry 20, 4760-4773
36. Piekarz, A. D., Due, M. R., Khanna, M., Wang, B., Ripsch, M. S., Wang, R. et al. (2012) CRMP-2 peptide mediated decrease of high and low voltage-activated calcium channels, attenuation of nociceptor excitability, and anti-nociception in a model of AIDS therapy-induced painful peripheral neuropathy Molecular Pain 8, 54
37. Wang, F., Li, J., Sinn, A. L., Knabe, W. E., Khanna, M., Jo, I. et al. (2011) Virtual screening targeting the urokinase receptor, biochemical and cell-based studies, synthesis, pharmacokinetic characterization, and effect on breast tumor metastasis J Med Chem 54, 7193-7205
38. Shi, Q., Meroueh, S. O., Fisher, J. F., and Mobashery, S. (2011) A computational evaluation of the mechanism of penicillin-binding protein-catalyzed cross-linking of the bacterial cell wall Journal of the American Chemical Society 133, 5274-5283
39. Parajuli, B., Kimble-Hill, A. C., Khanna, M., Ivanova, Y., Meroueh, S., and Hurley, T. D. (2011) Discovery of novel regulators of aldehyde dehydrogenase isoenzymes Chemico-Biological Interactions 191, 153-158
40. Li, L., Wang, B., and Meroueh, S. O. (2011) Support vector regression scoring of receptor-ligand complexes for rank-ordering and virtual screening of chemical libraries Journal of Chemical Information and Modeling 51, 2132-2138
41. Li, L., Khanna, M., Jo, I., Wang, F., Ashpole, N. M., Hudmon, A. et al. (2011) Target-specific support vector machine scoring in structure-based virtual screening: computational validation, in vitro testing in kinases, and effects on lung cancer cell proliferation Journal of Chemical Information and Modeling 51, 755-759
42. Khanna, M., Wang, F., Jo, I., Knabe, W. E., Wilson, S. M., Li, L. et al. (2011) Targeting multiple conformations leads to small molecule inhibitors of the uPAR.uPA protein-protein interaction that block cancer cell invasion ACS Chemical Biology 6, 1232-1243
43. Khanna, M., Chelladurai, B., Gavini, A., Li, L., Shao, M., Courtney, D. et al. (2011) Targeting ovarian tumor cell adhesion mediated by tissue transglutaminase Molecular Cancer Therapeutics 10, 626-636
44. Brittain, J. M., Duarte, D. B., Wilson, S. M., Zhu, W., Ballard, C., Johnson, P. L. et al. (2011) Suppression of inflammatory and neuropathic pain by uncoupling CRMP-2 from the presynaptic Ca(2)(+) channel complex Nature Medicine 17, 822-829
45. Wang, Y., Brittain, J. M., Jarecki, B. W., Park, K. D., Wilson, S. M., Wang, B. et al. (2010) In silico docking and electrophysiological characterization of lacosamide binding sites on collapsin response mediator protein-2 identifies a pocket important in modulating sodium channel slow inactivation Journal of Biological Chemistry 285, 25296-25307
46. Li, L., Li, J., Khanna, M., Jo, I., Baird, J. P., and Meroueh, S. O. (2010) Docking Small Molecules to Predicted Off-Targets of the Cancer Drug Erlotinib Leads to Inhibitors of Lung Cancer Cell Proliferation with Suitable In vitro Pharmacokinetic Properties ACS Medicinal Chemistry Letters 1, 229-233
47. Li, L., Bum-Erdene, K., Baenziger, P. H., Rosen, J. J., Hemmert, J. R., Nellis, J. A. et al. (2010) BioDrugScreen: a computational drug design resource for ranking molecules docked to the human proteome Nucleic Acids Research 38, D765-773
48. Xue, B., Li, L., Meroueh, S. O., Uversky, V. N., and Dunker, A. K. (2009) Analysis of structured and intrinsically disordered regions of transmembrane proteins Molecular Biosystems 5, 1688-1702
49. Matute, J. D., Arias, A. A., Wright, N. A., Wrobel, I., Waterhouse, C. C., Li, X. J. et al. (2009) A new genetic subgroup of chronic granulomatous disease with autosomal recessive mutations in p40 phox and selective defects in neutrophil NADPH oxidase activity Blood 114, 3309-3315
50. Liang, S., Meroueh, S. O., Wang, G., Qiu, C., and Zhou, Y. (2009) Consensus scoring for enriching near-native structures from protein-protein docking decoys Proteins 75, 397-403
51. Liang, S., Li, L., Hsu, W. L., Pilcher, M. N., Uversky, V., Zhou, Y. et al. (2009) Exploring the molecular design of protein interaction sites with molecular dynamics simulations and free energy calculations Biochemistry 48, 399-414
52. Li, L., Liang, S., Pilcher, M. M., and Meroueh, S. O. (2009) Incorporating receptor flexibility in the molecular design of protein interfaces Protein Engineering Design and Selection 22, 575-586
53. Shi, Q., Meroueh, S. O., Fisher, J. F., and Mobashery, S. (2008) Investigation of the mechanism of the cell wall DD-carboxypeptidase reaction of penicillin-binding protein 5 of Escherichia coli by quantum mechanics/molecular mechanics calculations Journal of the American Chemical Society 130, 9293-9303
54. Li, L., and Meroueh, S. O. (2008) Receptor-Ligand Interactions in Biological Systems In Encyclopedia for the Life Sciences, John Wiley and Sons, London p. 19
55. Li, L., Dantzer, J. J., Nowacki, J., O’Callaghan, B. J., and Meroueh, S. O. (2008) PDBcal: a comprehensive dataset for receptor-ligand interactions with three-dimensional structures and binding thermodynamics from isothermal titration calorimetry Chemical Biology and Drug Discovery 71, 529-532
56. Jewell, J. L., Oh, E., Bennett, S. M., Meroueh, S. O., and Thurmond, D. C. (2008) The tyrosine phosphorylation of Munc18c induces a switch in binding specificity from syntaxin 4 to Doc2beta Journal of Biological Chemistry 283, 21734-21746
57. Zhang, W., Shi, Q., Meroueh, S. O., Vakulenko, S. B., and Mobashery, S. (2007) Catalytic mechanism of penicillin-binding protein 5 of Escherichia coli Biochemistry 46, 10113-10121
58. Rosenblum, G., Meroueh, S., Toth, M., Fisher, J. F., Fridman, R., Mobashery, S. et al. (2007) Molecular structures and dynamics of the stepwise activation mechanism of a matrix metalloproteinase zymogen: challenging the cysteine switch dogma Journal of the American Chemical Society 129, 13566-13574
59. Meroueh, S. O., and Mobashery, S. (2007) Conformational transition in the aminoacyl t-RNA site of the bacterial ribosome both in the presence and absence of an aminoglycoside antibiotic Chemical Biology & Drug Design 69, 291-297
60. Meroueh, S. O., Cha, J. Y., and Mobashery, S. (2007) Inhibition of Class A beta-Lactamases In Enzyme-Mediated Resistance to Antibiotics: Mechanisms, Dissemination, and Prospects for Inhibition, Bonomo RA, ed. ASM Press, Washington D. C.
61. Li, L., Uversky, V. N., Dunker, A. K., and Meroueh, S. O. (2007) A computational investigation of allostery in the catabolite activator protein Journal of the American Chemical Society 129, 15668-15676
62. Rekharsky, M., Hesek, D., Lee, M., Meroueh, S. O., Inoue, Y., and Mobashery, S. (2006) Thermodynamics of interactions of vancomycin and synthetic surrogates of bacterial cell wall Journal of the American Chemical Society 128, 7736-7737
63. Rahaman, A., Song, H., Wang, A. X., Meroueh, S. O., and Hase, W. L. (2006) Chemical Dynamics Simulations of Energy Transfer and Unimolecular Decomposition in Collision-Induced Dissociation (CID) and Surface-Induced Dissociation (SID) In Principles of Mass Spectrometry Applied to Biomolecules, Litschitz C, and Laskin J, eds. Wiley, New York 379-432
64. Murray, J. B., Meroueh, S. O., Russell, R. J., Lentzen, G., Haddad, J., and Mobashery, S. (2006) Interactions of designer antibiotics and the bacterial ribosomal aminoacyl-tRNA site Chemistry and Biology 13, 129-138
65. Meroueh, S. O., Bencze, K. Z., Hesek, D., Lee, M., Fisher, J. F., Stemmler, T. L. et al. (2006) Three-dimensional structure of the bacterial cell wall peptidoglycan Proceedings of the National Academy of Sciences of the United States of America 103, 4404-4409
66. Hesek, D., Toth, M., Meroueh, S. O., Brown, S., Zhao, H., Sakr, W. et al. (2006) Design and characterization of a metalloproteinase inhibitor-tethered resin for the detection of active MMPs in biological samples Chemistry and Biology 13, 379-386
67. Toth, M., Osenkowski, P., Hesek, D., Brown, S., Meroueh, S., Sakr, W. et al. (2005) Cleavage at the stem region releases an active ectodomain of the membrane type 1 matrix metalloproteinase Biochemical Journal 387, 497-506
68. Osenkowski, P., Meroueh, S. O., Pavel, D., Mobashery, S., and Fridman, R. (2005) Mutational and structural analyses of the hinge region of membrane type 1-matrix metalloproteinase and enzyme processing Journal of Biological Chemistry 280, 26160-26168
69. Meroueh, S. O., Fisher, J. F., Schlegel, H. B., and Mobashery, S. (2005) Ab initio QM/MM study of class A beta-lactamase acylation: dual participation of Glu166 and Lys73 in a concerted base promotion of Ser70 Journal of the American Chemical Society 127, 15397-15407
70. Li, J., Cross, J. B., Vreven, T., Meroueh, S. O., Mobashery, S., and Schlegel, H. B. (2005) Lysine carboxylation in proteins: OXA-10 beta-lactamase Proteins 61, 246-257
71. Lee, M., Bernardo, M. M., Meroueh, S. O., Brown, S., Fridman, R., and Mobashery, S. (2005) Synthesis of chiral 2-(4-phenoxyphenylsulfonylmethyl)thiiranes as selective gelatinase inhibitors Organic Letters 7, 4463-4465
72. Ikejiri, M., Bernardo, M. M., Meroueh, S. O., Brown, S., Chang, M., Fridman, R. et al. (2005) Design, synthesis, and evaluation of a mechanism-based inhibitor for gelatinase A Journal of Organic Chemistry 70, 5709-5712
73. Fisher, J. F., Meroueh, S. O., and Mobashery, S. (2005) Bacterial resistance to beta-lactam antibiotics: compelling opportunism, compelling opportunity Chemical Reviews 105, 395-424
74. Cross, J. B., Vreven, T., Meroueh, S. O., Mobashery, S., and Schlegel, H. B. (2005) Computational investigation of irreversible inactivation of the zinc-dependent protease carboxypeptidase A Journal of Physical Chemistry B 109, 4761-4769
75. Lim, I. T., Meroueh, S. O., Lee, M., Heeg, M. J., and Mobashery, S. (2004) Strategy in inhibition of cathepsin B, a target in tumor invasion and metastasis Journal of the American Chemical Society 126, 10271-10277
76. Kim, C., Haddad, J., Vakulenko, S. B., Meroueh, S. O., Wu, Y., Yan, H. et al. (2004) Fluorinated aminoglycosides and their mechanistic implication for aminoglycoside 3′-phosphotransferases from Gram-negative bacteria Biochemistry 43, 2373-2383
77. Golemi-Kotra, D., Meroueh, S. O., Kim, C., Vakulenko, S. B., Bulychev, A., Stemmler, A. J. et al. (2004) The importance of a critical protonation state and the fate of the catalytic steps in class A beta-lactamases and penicillin-binding proteins Journal of Biological Chemistry 279, 34665-34673
78. Brown, S., Meroueh, S. O., Fridman, R., and Mobashery, S. (2004) Quest for selectivity in inhibition of matrix metalloproteinases Current Topics in Medicinal Chemistry 4, 1227-1238
79. Birck, C., Cha, J. Y., Cross, J., Schulze-Briese, C., Meroueh, S. O., Schlegel, H. B. et al. (2004) X-ray crystal structure of the acylated beta-lactam sensor domain of BlaR1 from Staphylococcus aureus and the mechanism of receptor activation for signal transduction Journal of the American Chemical Society 126, 13945-13947
80. Wilkinson, A. S., Bryant, P. K., Meroueh, S. O., Page, M. G., Mobashery, S., and Wharton, C. W. (2003) A dynamic structure for the acyl-enzyme species of the antibiotic aztreonam with the Citrobacter freundii beta-lactamase revealed by infrared spectroscopy and molecular dynamics simulations Biochemistry 42, 1950-1957
81. Wang, J., Meroueh, S. O., Wang, Y., and Hase, W. L. (2003) Efficiency of energy transfer in protonated diglycine and dialanine SID International Journal of Mass Spectrometry 230, 57-63
82. Song, K., Meroueh, O., and Hase, W. L. (2003) Dynamics of Cr(CO)[sub 6][sup +] collisions with hydrogenated surfaces The Journal of Chemical Physics 118, 2893
83. Rosenblum, G., Meroueh, S. O., Kleifeld, O., Brown, S., Singson, S. P., Fridman, R. et al. (2003) Structural basis for potent slow binding inhibition of human matrix metalloproteinase-2 (MMP-2) Journal of Biological Chemistry 278, 27009-27015
84. Meroueh, S. O., Minasov, G., Lee, W., Shoichet, B. K., and Mobashery, S. (2003) Structural aspects for evolution of beta-lactamases from penicillin-binding proteins Journal of the American Chemical Society 125, 9612-9618
85. Golemi-Kotra, D., Cha, J. Y., Meroueh, S. O., Vakulenko, S. B., and Mobashery, S. (2003) Resistance to beta-lactam antibiotics and its mediation by the sensor domain of the transmembrane BlaR signaling pathway in Staphylococcus aureus Journal of Biological Chemistry 278, 18419-18425
86. Fridman, R., Toth, M., Chvyrkova, I., Meroueh, S. O., and Mobashery, S. (2003) Cell surface association of matrix metalloproteinase-9 (gelatinase B) Cancer Metastasis Reviews 22, 153-166
87. Toth, M., Hernandez-Barrantes, S., Osenkowski, P., Bernardo, M. M., Gervasi, D. C., Shimura, Y. et al. (2002) Complex pattern of membrane type 1 matrix metalloproteinase shedding. Regulation by autocatalytic cells surface inactivation of active enzyme Journal of Biological Chemistry 277, 26340-26350
88. Meroueh, S. O., Wang, Y., and Hase, W. L. (2002) Direct Dynamics Simulations of Collision- and Surface-Induced Dissociation of N-Protonated Glycine. Shattering Fragmentation† The Journal of Physical Chemistry A 106, 9983-9992
89. Meroueh, S. O., Roblin, P., Golemi, D., Maveyraud, L., Vakulenko, S. B., Zhang, Y. et al. (2002) Molecular dynamics at the root of expansion of function in the M69L inhibitor-resistant TEM beta-lactamase from Escherichia coli Journal of the American Chemical Society 124, 9422-9430
90. Meroueh, O., and Hase, W. L. (2002) Dynamics of energy transfer in peptide-surface collisions Journal of the American Chemical Society 124, 1524-1531
91. Maveyraud, L., Golemi-Kotra, D., Ishiwata, A., Meroueh, O., Mobashery, S., and Samama, J. P. (2002) High-resolution X-ray structure of an acyl-enzyme species for the class D OXA-10 beta-lactamase Journal of the American Chemical Society 124, 2461-2465
92. Sun, L., de Sainte Claire, P., Meroueh, O., and Hase, W. L. (2001) Dynamics of Ar+CH[sub 4]/Ni{111} collision-induced desorption The Journal of Chemical Physics 114, 535
93. Meroueh, O., and Hase, W. L. (2001) Effect of surface stiffness on the efficiency of surface-induced dissociation Physical Chemistry Chemical Physics 3, 2306-2314
94. Sawilowsky, E. F., Meroueh, O., Schlegel, H. B., and Hase, W. L. (2000) Structures, Energies, and Electrostatics for Methane Complexed with Alumina Clusters The Journal of Physical Chemistry A 104, 4920-4927
95. Meroueh, O., and Hase, W. L. (2000) Energy transfer pathways in the collisional activation of peptides International Journal of Mass Spectrometry 201, 233-244