62.  Khanna, M., Wang, F., Jo, I., Li, Liwei, Bum-Erdene, K., Li, J., Wang, B., Khanna, R., and Meroueh, S. O., (2011) Targeting Multiple Conformations Leads to a Small-Molecule Inhibitor of the uPAR·uPA Interaction that Blocks Lung and Breast Cancer Cell Invasion, ACS Chem. Biol., , in press. PDF

61.  Li.L., Wang. B., and Meroueh, S. O. (2011) Support Vector Machine Scoring of Receptor-Ligand Complexes for Virtual Screening of Chemical Libraries, J Chem Inf Model, in press. PMID: 21728360. PDF

60.  Wang, F., Li. J., Sinn, A. L., Knabe, W. C., Khanna, May, Jo, I., Silver, J. M., Oh, K., Li, L., Sandusky, G. E., Sledge, G. W., Nakshatri, H., Jones, D. R., Pollok, K. E., Meroueh, S. O. (2011) Virtual Screening Targeting uPAR, Biochemical and Cell-Based Studies, Synthesis of IPR-69, Pharmacokinetic characterization, and effect on Breast Tumor Metastasis, J. Med. Chem., in press. PMID: 21851064. PDF

59.  Brittain, JM., Duarte, DB., Wilson, SM., Zhu, W., Ballard, C., Johnson, PL., Liu, N., Xiong, W., Ripsch, MS., Wang, Y., Fehrenbacher, JC., Fitz, SD., Khanna, M., Park, CK., Schmutzler, BS., Cheon, BM., Due, MR., Brustovetsky, T., Ashpole, NM., Hudmon, A., Meroueh, SO., Hingtgen, CM., Brustovetsky, N., Ji, RR., Hurley, JH., Jin, X., Shekhar, A., Xu, XM., Oxford, GS., Vasko, MR., White, FA., Khanna, R. (2011) Suppression of inflammatory and neuropathic pain by uncoupling CRMP-2 from the presynaptic Ca²⁺ channel complex. Nat. Med. 2011 Jul;17(7):822-9. PMID: 21642979. PDF

58.  Zhang, Q., Zeng, S. X., Zhang, Y., Zhang, Y., Meroueh, S. O. and Lu, Hua (2011) A Small Molecule Inauzhing Inhibits SIRT1 Activity and Suppresses Tumor Growth via Activation of p53, EMBO J, submitted

57.  Li, L., Khanna, M., Jo, I., Wang, F., Ashpole, NM., Hudmon, A., Meroueh, SO. (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. J Chem Inf Model 2011 Apr 25;51(4):755-9 PMID: 21438548 PDF

56.  Khanna, M., Chelladurai, B., Gavini, A., Li, L., Shao, M., Courtney, D., Turchi,J. J., Matei, D., and Meroueh, S. O. (2011) Targeting Ovarian Tumor Cell Adhesion Mediated by Tissue Transglutaminase, Mol. Cancer Ther., 10(4):626-36. PMID: 21330459 PDF

55.  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(14):5274-83. PMID: 21417389 PDF

54.  Li, L.; Bumerdene, K.; Baenziger, P. H.; Hemmert, J. R.; Rosen, J.; Nellis, J.; Pierce, M. ; Meroueh, S. O. (2010) BioDrugScreen: A Computational Drug Design Resource for Ranking Molecules Docked to the Human Proteome, Nucleic Acid Research, 38, D765-73. PDF

53.  Li, L., J. Li, M. Khanna, I. Jo, J.P. Baird, and Meroueh, S. O. (2010) Docking to Erlotinib Off-Targets Leads to Inhibitors of Lung Cancer Cell Proliferation with Suitable in Vitro Pharmacokinetics. ACS Med. Chem. Lett. 1, 229-233. PDF

52.  Wang, Y., Brittain, J. M., Jarecki, B. W., Park, K. D., Wilson, S. M., Wang, B., Hale, R., Meroueh, S. O., Cummins, T. R., and Khanna, R., (2010) In silico docking and electrophysiological characterization of lacosamide binding sites on collapsin response mediator protein 2 (CRMP-2) identifies a pocket important in modulating sodium channel slow inactivation. Journal of Biological Chemistry, 285, 25296-307. PMID: 20538611. PDF

51.  Liang, S. D., Li, L. W., Hsu, W. L., Pilcher, M. N., Uversky, V., Zhou, Y. Q., Dunker, A. K., and Meroueh, S. O. (2009) Exploring the Molecular Design of Protein Interaction Sites with Molecular Dynamics Simulations and Free Energy Calculations, Biochemistry 48, 399-414. PDF

50.  Liang, S. D., Meroueh, S. O., Wang, G. C., Qiu, C., and Zhou, Y. Q. (2009) Consensus scoring for enriching near-native structures from protein-protein docking decoys, Proteins-Structure Function and Bioinformatics 75, 397-403. PDF

49.  Xue, B., Oldfield, C., Li, L., Meroueh, S. O., Dunker, A. K., and Uversky, V. Analysis of structured and intrinsically disordered regions of integral transmembrane proteins, Molecular Biosystems, 5,1688-1702. PDF

48.  Matute, J. D., Arias, A. A., Wright, N., Wrobel, I., Waterhouse, C. C. M., Li, X. J., Marchal, M. S., Stull, N. D., Lewis, D. B., Steele, M., Kellner, J. D., Yu, M., Meroueh, S. O., Nauseef, W. M., and Dinauer, M. C. (2009) A new genetic subgroup of chronic granulomatous disease with defects in p40phox in a box who presented with colitis, Blood, 114, 3309. PDF

47.  Li, L., Liang, S., Pilcher, M. M., and Meroueh, S. O. Incorporating receptor flexibility in the molecular design of protein interfaces, Protein Engineering Design and Selection, 22, 575-86. PDF

46.  Li, Liwei; O’Callaghan, B. J.; Dantzer, J. J. and Meroueh S. O. PDBcal: A Comprehensive Dataset for Receptor-Ligand Interactions with Three-Dimensional structures and Binding Thermodynamics from Isothermal Titration Calorimetry. Chem. Biol. & Drug Design. 71:529-32. (2008) PDF

45.  Li, L., and Meroueh, S. O. Receptor-Ligand Interactions in Biological Systems. In: Encyclopedia for the Life Sciences, p 19, John Wiley and Sons, London. (2008)

44.  Jewell, J. L., Oh, E., Bennett, S. M., Meroueh, S. O., and Thurmond, D. C. The Tyrosine Phosphorylation of Munc18c Induces a Switch in Binding Specificity from Syntaxin 4 to Doc2{beta}, The Journal of biological chemistry 283, 21734-21746. (2008) PDF

43.  Shi, Q., Meroueh, S. O., Fisher, J. F., and Mobashery, S. 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. (2008) PDF

42.  Meroueh, S. O.; Cha, J.; Mobashery, S. Inhibition of Class A ß-Lactamases, In Enzyme-Mediated Resistance to Antibiotics: Mechanisms, Dissemination, and Prospects for Inhibition, Bonomo, R. A.; Tolmasky, M. E., Eds.; ASM Press, 2007, pp101-114, Washington D.C.

41.  Meroueh, S. O. and Mobashery, S., Conformational Transition in the Aminoacyl t-RNA Site of the Bacterial Ribosome both in the Presence and Absence of an Aminoglycoside Antibiotic. Chemical Biology and Drug Design 2007, 69, (5), 291-297. PDF

40.  Rosenblum, G.*; Meroueh, S.*; Toth, M.; Fisher, J. F.; Fridman, R.; Mobashery, S.; Sagi, I. Molecular Structures and Dynamics of the Stepwise Activation Mechanism of a Matrix Metalloproteinase Zymogen: Challenging the Cysteine Switch Dogma, J. Am. Chem. Soc. 2007 129(44),13566-74. (Authors contributed equally) PDF

39.  Zhang, W.; Shi, Q.; Meroueh, S. O.; Vakulenko, S. B.; Mobashery, S., Catalytic Mechanism of Penicillin-Binding Protein 5 of Escherichia coli. J. Biol. Chem. 2007, 46, 10113-10121. PDF

38.  Li, Liwei; Uversky N. V.; Dunker, K. A.; Meroueh, S. O. A Computational Investigation of Allostery in the Catabolite Activator Protein. J. Am. Chem. Soc. (2007) 129(50), 15668-76 PDF

37.  Samy Meroueh: Normal Mode Analysis Theoretical and Applications to Biological and Chemical Systems. Briefings in Bioinformatics 8(5): 378-379 (2007) PDF

36.  Rekharsky, M.; Hesek, D.; Lee, M.; Meroueh, S. O.; Inoue, Y.; Mobashery, S., Thermodynamics of interactions of vancomycin and synthetic surrogates of bacterial cell wall. J. Am. Chem. Soc. 2006, 128, (24), 7736-7737.

35.  Fisher, J. F.; Meroueh, S. O.; Mobashery, S., Nanomolecular and Supramolecular Paths toward the Bacterial Peptidoglycan Structure. Microbe 2006, 1, 420-427. PDF

34.  Meroueh, S. O.; Bencze, K. Z.; Hesek, D.; Lee, M.; Fisher, J. F.; Stemmler, T. L.; Mobashery, S., Three-Dimensional Structure of the Bacterial Cell Wall Peptidoglycan. Proc. Natl. Acad. Sci. USA 2006, 103, (12), 4404-4409. PDF

33.  Hesek, D.; Toth, M.; Meroueh, O.; Brown, S.; Zhao, H.; Sakr, W.; Fridman, R.; Mobashery, S., Design and Characterization of a Metalloproteinase Inhibitor-Tethered Resin for the Detection of Active MMPs in Biological Samples. Chem. Biol. 2006, 13, 379-388. PDF

32.  Murray, J. B.; Meroueh, S. O.; Russell, R. J.; Lentzen, G.; Haddad, J.; Mobashery, S., Interactions of Designer Antibiotics and the Bacterial Ribosomal Aminoacyl-tRNA Site. Chem. Biol. 2006, 13, (2), 129-38. PDF

31.  Rahaman, A., Song, H., Wang, A. X., Meroueh, S. O., and Hase, W. L. Chemical Dynamics Simulations of Energy Transfer and Unimolecular Decomposition in Collision-Induced Dissociation (CID) and Surface-Induced Dissociation (SID). Principles of Mass Spectrometry Applied to Biomolecules (Litschitz, C., and Laskin, J., Eds.), pp 379-432, Wiley, New York.

30.   Toth, M.; Osenkowski, P.; Hesek, D.; Brown, S.; Meroueh, S. O. ; Sakr, W.; Mobashery, S.; Fridman, R., Cleavage at the Stem Region Releases an Active Ectodomain of the Membrane Type 1 Matrix Metalloproteinase. Biochem. J. 2005, 387, 497-506.

29.   Osenkowski, P.; Meroueh, S. O. ; Pavel, D.; Mobashery, S.; Fridman, R., Mutational and Structural Analyses of the Hinge Region of Membrane Type 1-Matrix Metalloproteinase and Enzyme Processing. J. Biol. Chem. 2005, 280, (28), 26160-26168. PDF

28.  Meroueh, S. O. ; Fisher, J. F.; Schlegel, H. B.; Mobashery, S., Ab initio QM/MM Study of Class A Beta-Lactamase Acylation: Dual Participation of Glu166 and Lys73 in a Concerted Base Promotion of Ser70. J. Am. Chem. Soc. 2005, 127, (44), 15397-15407.

27.  Li, J.; Cross, J. B.; Vreven, T.; Meroueh, S. O. ; Mobashery, S.; Schlegel, H. B., Lysine Carboxylation in Proteins: OXA-10 Beta-Lactamase. Proteins 2005, 61, (2), 246-257. PDF

26.  Lee, M.; Bernardo, M. M.; Meroueh, S. O. ; Brown, S.; Fridman, R.; Mobashery, S., Synthesis of Chiral 2-(4-Phenoxyphenylsulfonylmethyl)-Thiiranes as Selective Gelatinase Inhibitors. Org. Lett. 2005, 7, (20), 4463-4465.

25.   Ikejiri, M.; Bernardo, M. M.; Meroueh, S. O. ; Brown, S.; Chang, M.; Fridman, R.; Mobashery, S., Design, Synthesis, and Evaluation of a Mechanism-Based Inhibitor for Gelatinase A. J. Org. Chem. 2005, 70, (14), 5709-5712.

24.  Fisher, J. F.; Meroueh, S. O.; Mobashery, S., Bacterial Resistance to Beta-Lactam Antibiotics: Compelling Opportunism, Compelling Opportunity. Chem. Rev. 2005, 105, (2), 395-424.

23.  Cross, J. B.; Vreven, T.; Meroueh, S. O.; Mobashery, S.; Schlegel, H. B., Computational Investigation of Irreversible Inactivation of the Zinc-Dependent Protease Carboxypeptidase A. J. Phys. Chem. B 2005, 109, (10), 4761-4769.

22.  Kim, C.; Haddad, J.; Vakulenko, S. B.; Meroueh, S. O.; Wu, Y.; Yan, H.; Mobashery, S., Fluorinated Aminoglycosides and their Mechanistic Implication for Aminoglycoside 3 '-Phosphotransferases from Gram-Negative Bacteria. Biochemistry 2004, 43, (9), 2373-2383.

21.  Golemi-Kotra, D.; Meroueh, S. O.; Kim, C.; Vakulenko, S. B.; Bulychev, A.; Stemmler, A. J.; Stemmler, T. L.; Mobashery, S., The Importance of a Critical Protonation State and the Fate of the Catalytic Steps in Class A Beta-Lactamases and Penicillin-Binding Proteins. J. Biol. Chem. 2004, 279, (33), 34665-34673.

20.  Brown, S.; Meroueh, S. O.; Fridman, R.; Mobashery, S., Quest for Selectivity in Inhibition of Matrix Metalloproteinases. Curr. Top. Med. Chem. 2004, 4, (12), 1227-1238.

19.  Birck, C.; Cha, J. Y.; Cross, J.; Schulze-Briese, C.; Meroueh, S. O.; Schlegel, H. B.; Mobashery, S.; Samama, J. P., 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. J. Am. Chem. Soc. 2004, 126, (43), 13945-13947.

18.  T. Lim, S. O. Meroueh, M. Lee, M. J. Heeg, S. Mobashery "Strategy in Inhibition of Cathepsin B, A Target in Tumor Invasion and Metastasis" J. Am. Chem. Soc. 2004, 126, 10271-10277.

17.  Wilkinson, A. S.; Bryant, P. K.; Meroueh, S. O.; Page, M. G. P.; Mobashery, S.; Wharton, C. W., 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 2003, 42, (7), 1950-1957.

16.  Wang, J. P.; Meroueh, S. O.; Wang, Y. F.; Hase, W. L., Efficiency of Energy Transfer in Protonated Diglycine and Dialanine SID - Effects of Collision Angle, Peptide Ion Size, and Intramolecular Potential. Int. J. Mass. Spectrom. 2003, 230, (1), 57-64.

15.  Song, K. Y.; Meroueh, O.; Hase, W. L., Dynamics of Cr(CO)(6)(+) Collisions with Hydrogenated Surfaces. J. Chem. Phys. 2003, 118, (6), 2893-2902.

14.  Rosenblum, G.; Meroueh, S. O.; Kleifeld, O.; Brown, S.; Singson, S. P.; Fridman, R.; Mobashery, S.; Sagi, I., Structural Basis for Potent Slow Binding Inhibition of Human Matrix Metalloproteinase-2 (MMP-2). J. Biol. Chem. 2003, 278, (29), 27009-27015.

13.  Meroueh, S. O.; Minasov, G.; Lee, W.; Shoichet, B. K.; Mobashery, S., Structural Aspects for Evolution of Beta-Lactamases from Penicillin-Binding Proteins. J. Am. Chem. Soc. 2003, 125, (32), 9612-9618.

12.  Golemi-Kotra, D.; Cha, J. Y.; Meroueh, S. O.; Vakulenko, S. B.; Mobashery, S., Resistance to Beta-Lactam Antibiotics and its Mediation by the Sensor Domain of the Transmembrane BlaR Signaling Pathway in Staphylococcus aureus. J. Biol. Chem. 2003, 278, (20), 18419-18425.

11.  Fridman, R.; Toth, M.; Chvyrkova, I.; Meroueh, S. O.; Mobashery, S., Cell Surface Association of Matrix Metalloproteinase-9 (Gelatinase B). Cancer and Metastasis Rev 2003, 22, (2-3), 153-166.

10.  Toth, M.; Hernandez-Barrantes, S.; Osenkowski, P.; Bernardo, M. M.; Gervasi, D. C.; Shimura, Y.; Meroueh, O.; Kotra, L. P.; Galvez, B. G.; Arroyo, A. G.; Mobashery, S.; Fridman, R., Complex Pattern of Membrane type 1 Matrix Metalloproteinase Shedding - Regulation by Autocatalytic Cell Surface Inactivation of Active Enzyme. J. Biol. Chem. 2002, 277, (29), 26340-26350.

9.  Meroueh, S. O.; Wang, Y. F.; Hase, W. L., Direct Dynamics Simulations of Collision- and Surface-Induced Dissociation of N-Protonated Glycine. Shattering Fragmentation. J. Phys. Chem. A 2002, 106, (42), 9983-9992.

8.  Meroueh, S. O.; Roblin, P.; Golemi, D.; Maveyraud, L.; Vakulenko, S. B.; Zhang, Y.; Samama, J. P.; Mobashery, S., Molecular Dynamics at the Root of Expansion of Function in the M69L Inhibitor-Resistant TEM Beta-Lactamase from Escherichia coli. J. Am. Chem. Soc. 2002, 124, (32), 9422-9430.

7.  Meroueh, O.; Hase, W. L., Dynamics of Energy Transfer in Peptide-Surface Collisions. J. Am. Chem. Soc. 2002, 124, (7), 1524-1531.

6.  Maveyraud, L.; Golemi-Kotra, D.; Ishiwata, A.; Meroueh, O.; Mobashery, S.; Samama, J. P., High-Resolution X-ray Structure of an Acyl-Enzyme Species for the Class D OXA-10 Beta-Lactamase. J. Am. Chem. Soc. 2002, 124, (11), 2461-2465.

5.  Sun, L. P.; Claire, P. D.; Meroueh, O.; Hase, W. L., Dynamics of Ar+CH4/Ni{111} Collision-Induced Desorption. J. Chem. Phys. 2001, 114, (1), 535-544.

4.  Meroueh, O.; Hase, W. L., Effect of Surface Stiffness on the Efficiency of Surface-Induced Dissociation. Phys. Chem. Chem. Phys. 2001, 3, (12), 2306-2314.

3.  Sawilowsky, E. F.; Meroueh, O.; Schlegel, H. B.; Hase, W. L., Structures, Energies, and Electrostatics for Methane Complexed with Alumina clusters. J. Phys. Chem. A 2000, 104, (21), 4920-4927.

2.  Meroueh, O.; Hase, W. L., Energy Transfer Pathways in the Collisional Activation of Peptides. Int. J. Mass. Spectrom. 2000, 201, (1-3), 233-244.

1.  Meroueh, O.; Hase, W. L., Collisional Activation of Small Peptides. J. Phys. Chem. A 1999, 103, (20), 3981-3990.