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Bioorganic & Medicinal Chemistry, Volume 11, Dec, 2003

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Bioorganic & Medicinal Chemistry, Volume 11, Dec, 2003 MMCC Results Volume 15 No. 2 1 June 2006 Vol. 15, No. 2 1 June 2006 Coverage period: 1 April 2006 through 31 May 2006 Editorial and News About 105 papers from 20 journals are cited. As mentioned last month, the majority of the journal 1. APPLICATIONS ( 78 ) . page 2 reviews are now covered in the main section of the 1.1 Small Molecules – 40 reviews. General & Model systems-1 QSAR — 19 Water and Solvation – 2 Host-guest systems-4 I would call your attention on few highlighted Med Chem & Drug Design – 10 Carbon Nanoparticles – 3 articles, particularly in the Methodology section related to Liquid crystals-1 potentials and parameters. 1.2 Biopolymers – 34 R.Nageswar, Editor Bioinformatics – 3 Protein Dynamics – 5 Protein Folding - 1 Ligand Binding – 7 Protein Structure Prediction – 2 Protein-Protein Inter. – 2 Comp and Homol Modeling – 6 Membrane Proteins — 1 Protein Folding – 1 Free energy- 4 Protein Engg. & Design -2 1.3 Polymers – 1.4 Surfaces, Catalysts, and Materials Subjects — 5 2. METHODOLOGY (32) . page 19 QSAR - 4 Homology modeling – 1 Conformational Search & Anal -2 Mol.Graphics-2 Potentials and Parameters - 4 Ligand Docking — 4 Molecular Dynamics – 3 Surface volme - 1 QM/MM - 9 Protein structure prediction-2 3. JOURNAL REVIEWS (38) . page 26 J. Comp. Chem. 27 (8), 1 June 2006 J. Comp. Chem. 27 (9), 15 July 2006 J. Comp. Chem. 27 (10), 30 July 2006 Current Opinion in Structural Biology 16 (2) April 2006 4. ADDRESSES OF PRINCIPLE AUTHORS page 31 5. COPYRIGHT, DISCLAIMER AND PUBLISHER INFORMATION Page 1 1 June 2006 MMCC Results Volume 15 No. 2 1. APPLICATIONS 1.1. Small Molecules General and Model Systems Crystal structure of the SOCS2-elongin C-elongin B The structural basis for SOCS2 function is elucidated and complex defines a prototypical SOCS box ubiquitin ligase. determined the 1.9-Å crystal structure of the ternary complex of SOCS2 with elongin C and elongin B. The structure defines a prototypical SOCS box ubiquitin A.N. Bullock, J.É. Debreczeni, A.M. Edwards, M. Sundström, and Stefan Knapp* [Univ. of Toronto] ligase with a Src homology 2 (SH2) domain as a substrate recognition motif. The SOCS box and SH2 domain showed a conserved spatial domain arrangement with the BC box and substrate recognition domain of the von Hippel-Lindau tumor suppressor protein. The SOCS box binds elongin BC in a similar fashion to the VHL BC box PNAS. 103, 7637-7642 (2006) and shows extended structural conservation with the F box of the Skp2 ubiquitin ligase. Water and Solvation Water-induced interactions between carbon nano- MD simulations are used to study the hydration of C60 particles. fullerenes, carbon nanotubes, and graphene sheets in aqueous solution and the nature of water-induced interactions between these carbon nanoparticles. The Liwei Li, Dmitry Bedrov, and Grant D. Smith* [Univ. of hydration of these nonpolar carbon nanoparticles does not Utah] exhibit classical hydrophobic character due to the high density of surface atoms resulting in strong water-surface dispersion interactions. Water was found to wet the nanoparticle surfaces independent of nanoparticle surface curvature, with the decrease in the extent of water-water J. Phys. Chem. B. 110, 10509 -10513 (2006) hydrogen bonding with decreasing surface curvature being offset by stronger water-surface interactions. Solvation in supercritical water. MD simulations are used to study the solvation in super critical water under equilibrium and non-equilibrium Jinsong Duan* [Carnegie Mellon Univ.], Y. Shim, and Hyung conditions. The influence of solute charge distributions J. Kim and solvent density on the solvation structures and dynamics is examined with a diatomic probe solute J. Chem.Phys.124, 204504 - 204516 (2006) molecule. It is observed that the solvation structure varies with the solute dipole moment. MMCC Results (ISSN 1061-6381) is published ten times per Assistant Editors: MMCC Results year at the beginning of each month except January and R.Nageswar, Editor August by the independent business, MMCC Results. Mention Anston Feenstra 8013 Los Sabalos Street Vrije Univ., Amsterdam, of software, hardware, or other products is for informational Netherlands San Diego, CA 92126 purposes only and does not constitute an endorsement or Tel. (858) 663-0162 recommendation by MMCC Results nor by the authors of the Naresh Aerra e-mail: [email protected] Rational Labs, Hyderabad., India paper cited. All product names are the trademarks or registered symbols of their respective holders. R.Nageswar,Ph.D. Marginal symbols indicate that the authors acknowledged R.Mutyala RR Labs Inc.,8013 Los Sabalso St. RR Labs Inc., San Diego, CA. the use of a software package from a commercial sourse. A San Diego, CA 92126 refers to Accelrys Inc. and T to Tripos Inc. Other companies Editors Emeritus: Bruce Gelin, Ph.D. are denoted by their name in a box. Papers of special David Busath,M.D. interest are marked by an exclamation point [!]. Dr. Gelin was founder of MMCC Results and edited volumes 1-6. Dr. David Busath edited volumes 7-14 Copyright © 2006 MMCC Results Page 2 MMCC Results Volume 15 No. 2 1 June 2006 Medicinal Chemistry and Drug Design Evaluation of glycolamide esters of indomethacin as A number of novel indomethacin glycolamide esters are potential cyclooxygenase-2 (COX-2) inhibitors. tested for their cyclooxygenase inhibition in vitro properties. Many compounds proved to be selective S. Khanna, M. Madan, A. Vangoori, R. Banerjee, COX-2 inhibitors, and subtle structural changes in the R.Thaimattam, S.K. Jafar Sadik Basha, M. Ramesh, Seshagiri substituents on the glycolamide ester moiety altered the Rao and Manojit Pal* [Dr. Reddy’s Labs Ltd] inhibitory properties. Molecular modeling studies are used to rationalize their in vitro data and [1-(4- chlorobenzoyl)-5-methoxy-2-methyl-1H-indol-3-yl]acetic Bioorg. Med. Chem. 14, 4820-4833 (2006) acid 2-morpholin-4-yl-2-oxo ethyl ester, is identified as a promising compound. Synthesis, docking, and in vitro activity of A novel series of thiosemicarbazone, aminoacyl- thiosemicarbazones, aminoacyl-thiosemicarbazides and thiazolidone and their derivatives structures have anti- acyl-thiazolidones against Trypanosoma cruzi. Trypanosoma cruzi activity. Biological evaluation showed that some of these compounds are able to inhibit A.C. Lima Leite* [Univ. Federal de Pernambuco], R.S. de the growth of T. cruzi in concentrations non-cytotoxic to Lima, D.R. de M. Moreira, M.V. de O. Cardoso, A.C.G. de mammalian cells. Docking studies are performed to Brito, L.M. Farias dos Santos, M.Z. Hernandes, A.C. investigate the binding pattern of these compounds for Kiperstok, R.S. de Lima and M.B.P. Soares the T. cruzi cruzain (TCC) protein, have a significant correlation with experimental data. Bioorg. Med. Chem. 14, 3749-3757 (2006) Synthesis, antiviral activity, and pharmacokinetic Potent analogues of oximinoarylsulfonamides of HIV-1 evaluation of P3 pyridylmethyl analogs of aspartyl protease, provided low nanomolar EC50 values oximinoarylsulfonyl HIV-1 protease inhibitors. against both wild-type HIV and resistant mutant virus (A17). Pharmacokinetic results of these compounds J.T. Randolph* [Abbott Labs], P.P. Huang, W.J. Flosi, David showed good exposure when co-administered orally with DeGoey, L.L. Klein, C.M. Yeung, C. Flentge, Mingua Sun, an equal amount of ritonavir in the rat, with average AUC Chen Zhao, Tatyana Dekhtyar, Hongmei Mo, Lynn Colletti, >8 μg h/mL. The 3-pyridylmethyl analog gave the best Warren Kati, K.C. Marsh, A. Molla and D.J. Kempf overall exposure, is the potent inhibitor of cytochrome P450 3A (Ki = 2.4 nM). Bioorg. Med. Chem. 14, 4035-4046 (2006) A density functional study of flavonoid compounds with DFT/B3LYP with the 6-31G* basis set is employed to anti-HIV activity. calculate a set of molecular properties of 26 flavonoid compounds with anti-HIV activity. The multiple linear J. Lameira, C.N. Alves* [Univ. of Federal do Para], V. regression method is used to correlate the biological Moliner and E. Silla activity and structural properties. The anti-HIV activity of compounds are related with the molecular hydrophobicity, the electronegativity and the charges on Euro.J. Med. Chem. 41, 616-623 (2006) some key atoms, while that the toxicity is related with the electronic affinities (EA), ClogP and charge on atom 8. The influence of target family and functional activity on The ligands for peptide GPCRs are found to be less the physicochemical properties of pre-clinical compounds. efficient than the ligands for monoamine GPCRs. The changes in the property values during the optimization process are found to vary only across the target families, Richard Morphy* [Organon Labs] with the main determinant of the drug-likeness of the optimized compounds. Agonists for monoamine GPCRs, opioid receptors and ion channels are typically smaller and less lipophilic than the antagonists, but there is no J. Med. Chem., 49 (10), 2898 -2908 (2006) difference between the agonists and the antagonists for peptide GPCRs and nuclear receptors. Page 3 1 June 2006 MMCC Results Volume 15 No. 2 Medicinal Chemistry and Drug Design (cont’d) An integrated in silico-3D model-driven discovery of a Discovery of a novel, potent, and selective novel, potent, and selective amidosulfonamide 5-HT1A amidosulfonamide nonazapirone 5-HT1A agonist for the agonist (PRX-00023) for the treatment of anxiety and treatment of anxiety and depression, for generalized depression. anxiety disorder (GAD) is reported. PREDICT methodology is used to model the 3D structure of 5- Oren M. Becker* [Predix Pharm.], D.S. Dhanoa, Y. Marantz, HT1A, and then performing in silico screening on that Dongli Chen, Sharon Shacham, Srinivasa Cheruku, Alexander structure leading to the discovery of a 1 nM lead Heifetz, Pradyumna Mohanty, Merav Fichman, Anurag compound. The lead compound is optimized following a Sharadendu, Raphael Nudelman, Michael Kauffman, and strategy devised based on in silico 3D models and Silvia Noiman realized through an in silico-driven optimization process, rapidly overcoming selectivity issues (affinity to 5-HT1A J.
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