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literature corner

In this section we collect all articles that have been reviewed in our newsletter literature corner.

issue 20

• Reducing Docking Score Variations Arising from Input Differences
  Miklos Feher and Christopher I. Williams
  J. Chem. Inf. Model., 2010, 50 (9), pp 1549-1560
• Three-Dimensional Pharmacophore Modeling of Liver-X Receptor Agonists
  Wenxia Zhao, Qiong Gu, Ling Wang, Hu Ge, Jiabo, Li, and Jun Xu
  J. Chem. Inf. Model., Article ASAP

issue 19

• Ligand-protein docking studies of potential HIV-1 drug compounds using the algorithm FlexX
  George Patargias, Gary Ewart, Carolyn Luscombe and Wolfgang B. Fischer
  Anal Bioanal Chem. 396(7):2559-63, (2010)
• Identification of the First Low-Molecular-Weight Inhibitors of Matriptase-2
  Mihiret Tekeste Sisay, Torsten Steinmetzer, Marit Stirnberg, Eva Maurer, Maya Hammami, Jürgen Bajorath and Michael Gütschow
  J.Med.Chem. Publication Date (Web): July 14, 2010
• In Pursuit of Fully Flexible Protein-Ligand Docking: Modeling the Bilateral Mechanism of Binding
  Angela M. Henzler and Matthias Rarey
  Molecular Informatics, 29:164-173, (2010)

issue 18

• ReCore: A Fast and Versatile Method for Scaffold Hopping Based on Small Molecule Crystal Structure Conformations
  Patrick Maass, Tanja Schulz-Gasch, Martin Stahl, and Matthias Rarey
  J. Chem. Inf. Model., 47 (2), 390 -399, (2007)
• ReCore
  John H. Van Drie
  J. Am. Chem. Soc., 131 (4), 1617, (2009)
• Structure-Based Rational Screening of Novel Hit Compounds with Structural Diversity for Cytochrome P450 Sterol 14α-Demethylase from Penicillium digitatum
  Qingye Zhang, Ding Li, Pei Wei, Jie Zhang, Jian Wan, Yangliang Ren, Zhigang Chen, Deli Liu, Ziniu Yu, and Lingling Feng
  J. Chem. Inf. Model., Publication Date (Web): January 20, 2010

issue 17

• Fragment Shuffling: An Automated Workflow for Three-Dimensional Fragment-Based Ligand Design
  Britta Nisius and Ulrich Rester
  J. Chem. Inf. Model., 2009, 49 (5), pp 1211-1222
• A Structure-Based Approach to Ligand Discovery for 2C-Methyl-d-erythritol-2,4-cyclodiphosphate Synthase: A Target for Antimicrobial Therapy
  Nicola L. Ramsden, Lori Buetow, Alice Dawson, Lauris A. Kemp, Venkatsubramanian Ulaganathan, Ruth Brenk, Gerhard Klebe, and William N. Hunter
  J. Med. Chem., 2009, 52 (8), pp 2531-2542
• Bioisosteric Similarity of Molecules Based on Structural Alignment and Observed Chemical Replacements in Drugs
  Markus Krier and Michael C. Hutter
  J. Chem. Inf. Model., 2009, 49 (5), pp 1280-1297

issue 16

• Discovery of Novel Nitrobenzothiazole Inhibitors for Mycobacterium tuberculosis ATP Phosphoribosyl Transferase (HisG) through Virtual Screening
  Yoonsang Cho, Thomas R. Ioerger, and James C. Sacchettini
  J. Med. Chem. 51(19):5984-92. (2008)
• In Silico Screening for PTPN22 Inhibitors: Active Hits from an Inactive Phosphatase Conformation
  Shuangding Wu, Massimo Bottini, Robert C. Rickert, Tomas Mustelin, and Lutz Tautz
  ChemMedChem. 2009 Jan 28. [Epub ahead of print]
• Identification of Novel HCV RNA-dependent RNA polymerase Inhibitors Using Pharmacophore-Guided Virtual Screening
  Jinyoung Kim, Ki-sun Kim, Dong-Eun Kim and Youhoon Chong
  Chem. Biol. Drug. Des. 2008; 72: 585 – 591

issue 15

• Fragmental modeling of human glutamate transporter EAAT1 and analysis of its binding modes by docking and pharmacophore mapping.
  Alessandro Pedretti, Laura De Luca, Cristina Sciarrillo, and Giulio Vistoli
  ChemMedChem 3(1):79-90. (2008)
• Selection of a Respiratory Syncytial Virus Fusion Inhibitor Clinical Candidate. 2. Discovery of a Morpholinopropylaminobenzimidazole Derivative (TMC353121)
  Jean-François Bonfanti, Christophe Meyer, Frédéric Doublet, Jérôme Fortin, Philippe Muller, Laurence Queguiner, Tom Gevers, Peggy Janssens, Heidi Szel, Rudy Willebrords, Philip Timmerman, Koen Wuyts, Pieter van Remoortere, Frans Janssens, Piet Wigerinck, and Koen Andries
  J. Med. Chem. 51(4):875-96. (2008)
• Receptor-based modeling and 3D-QSAR for a quantitative production of the butyrylcholinesterase inhibitors based on genetic algorithm.
  Zaheer-ul-Haq, Reaz Uddin, Hongbin Yuan, Pavel A. Petukhov, M. Iqbal Choudhary, and Jeffry D. Madura
  J. Chem. Inf. Model. 48(5):1092-103. (2008)
• A virtual screen for diverse ligands: discovery of selective G protein-coupled receptor antagonists.
  Stanislav Engel, Amanda P. Skoumbourdis, John Childress, Susanne Neumann, Jeffrey R. Deschamps, Craig J. Thomas, Anny-Odile Colson, Stefano Costanzi, and Marvin C. Gershengorn
  J. Am. Chem. Soc. 130(15):5115-23. (2008)

issue 14

• Identification of novel inhibitors of bacterial surface enzyme Staphylococcus aureus Sortase A
  Bala C. Chenna, Bidhan A. Shinkre, Jason R. King, Aaron L. Lucius, Sthanam V. L. Narayana and Sadanandan E. Velu
  Bioorg. Med. Chem. Lett., 18, 380-385, (2008)
• Use of 3D QSAR Models for Database Screening: A Feasibility Study
  Alexander Hillebrecht and Gerhard Klebe
  J. Chem. Inf. Model., 48 (2), 384-96, (2008)
• Human Microsomal Prostaglandin E Synthase-1 (mPGES-1) Binding with Inhibitors and the Quantitative Structure-Activity Correlation
  Mohamed D. M. AbdulHameed, Adel Hamza, Junjun Liu, Xiaoqin Huang and Chang-Guo Zhan
  J. Chem. Inf. Model., 48 (1), 179-85, (2008)
• SwiFT: an index structure for reduced graph descriptors in virtual screening and clustering
  Robert Fischer and Matthias Rarey
  J. Chem. Inf. Model., 48 (4), 1341-53, (2007)

issue 13

• Discovery and optimization of novel, non-steroidal glucocorticoid receptor modulators
  Nicholas C. Ray, Robin D. Clark, David E. Clark, Karen Williams, H.G. Hickin, Peter H. Crackett, Hazel J. Dyke, Peter M. Lockey, Melanie Wong, René Devos, Anne White, and Joseph K. Belanoff.
  Bioorg. Med. Chem. Lett., 17, (17), 4901-4905, (2007)
• GPCR Structure-Based Virtual Screening Approach for CB2 Antagonist Search
  Jian-Zhong Chen, Junmei Wang, and Xiang-Qun Xie
  J. Chem. Inf. Model., 47 (4), 1626 -1637, (2007)
• ReCore: A Fast and Versatile Method for Scaffold Hopping Based on Small Molecule Crystal Structure Conformations
  Patrick Maass, Tanja Schulz-Gasch, Martin Stahl, and Matthias Rarey
  J. Chem. Inf. Model., 47 (2), 390 -399, (2007)
• Supervised Scoring Models with Docked Ligand Conformations for Structure-Based Virtual Screening
  Reiji Teramoto and Hiroaki Fukunishi
  J. Chem. Inf. Model., 47 (5), 1858 -1867, (2007)

issue 12

• From Modeling to Medicinal Chemistry: Automatic Generation of Two-Dimensional Complex Diagrams
  Katrin Stierand and Matthias Rarey
  Chem. Med. Chem., 2 (6), 853 – 860 (2007)
• Chemical Fragment Spaces for de novo Design
  Harald Mauser and Martin Stahl
  J. Chem. Inf. Model., 47 (2), 318-324 (2007)
• Homology Modeling of Human Fyn Kinase Structure: Discovery of Rosmarinic Acid as a New Fyn Kinase Inhibitor and in Silico Study of Its Possible Binding Modes
  Dubravko Jelic, Boris Mildner, Sanja Kostrun, Krunoslav Nujic, Donatella Verbanac, Ognjen Culic, Roberto Antolovic, and Wolfgang Brandt
  J. Med. Chem., 50 (6), 1090-1100 (2007)

issue 11

• Interpretation of Scoring Functions Using 3D Molecular Fields. Mapping the Diacyl-Hydrazine-Binding Pocket of an Insect Ecdysone Receptor
  B. Bordas, I. Belai, A. Lopata, and Z. Szanto
  J. Chem. Inf. Model., 47 (1), 176-185 (2007)
• A Structure-Based 3D-QSAR(CoMSIA) Study on a Series of Aryl Diketoacids (ADK) as Inhibitors of HCV RNA-dependent RNA Polymerase
  J. Kim, J. H. Han, and Y. Chong
  Bull. Korean Chem. Soc. 27, 11, 1919-1922 (2006)
• Docking studies of agonists and antagonists suggest an activation pathway of the A₃ adenosine receptor
  S. Kim, Z. Gao , L. S. Jeong , and K.A. Jacobson
  J. Mol. Graph. Model. 25 (4), 562-577 (2006)

issue 10

• FlexNovo: structure-based searching in large fragment spaces.
  J. Degen, M. Rarey
  Chem. Med. Chem., 1(8), 854-68 (2006)
• Prediction of Multiple Binding Modes of the CDK2 Inhibitors, Anilinopyrazoles, Using the Automated Docking Programs GOLD, FlexX, and LigandFit: An Evaluation of Performance.
  H. Sato, L. M. Shewchuk, and J. Tang
  J. Chem. Inf. Model., ASAP article
• Virtual Screening for beta-Secretase (BACE1) Inhibitors Reveals the Importance of Protonation States at Asp32 and Asp228.
  T. Polgár and G. M. Keserü
  J. Med. Chem., 48, 3749-3755 (2005)

issue 09

• New leads for selective GSK-3 inhibition: pharmacophore mapping and virtual screening studies.
  Dhilon S. Patel and Prasad V. Bharatam
  J. Comput.-Aided Mol. Des. 20, 55-66 (2006)
• Current Status of Virtual Screening as Analysed by Target Class.
  Martin J. Stoermer
  Med. Chem. 2, 89-112 (2006)
• Successful computer guided planned synthesis of (4R)-thiazolidine carboxylic acid and its 2-substituted analogues as urease inhibitors.
  KM Khan et. al.
  Mol. Divers. 10, 223-231 (2006)

issue 08

• Ligand Selectivity for the Acetylcholine Binding Site of the Rat α5β2 and α3β4 Nicotinic Subtypes Investigated by Molecular Docking
  Bisson, W. H.; Scapozza, L.; Westera, G.; Mu, L.; Schubiger, P. A
  J.Med.Chem, 48, 5123-5130 (2005)
• In silico fragment-based discovery of DPP-IV S1 pocket binders
  Rummey, C.; Nordhoff, S.; Thiemann, M.; Metz, G.
  Bioorg Med Chem Lett, 16(5), 1405-1409 (2006)
• Virtual Screening of Biogenic Amine-Binding G-Protein Coupled Receptors: Comparative Evaluation of Protein- and Ligand-Based Virtual Screening Protocols
  Guichou, J.-F.; Viaud, J.; Mettling, C.; Subra, G; Lin, Y.-L.; Chavanieu, A.
  J. Med. Chem. 48 (17), 5448-5465 (2005)

issue 07

• A Critical Assessment of Docking Programs and Scoring Functions
  G. L. Warren, C. W. Andrews, A.-M. Capelli, B. Clarke, J. LaLonde, M. H. Lambert, M. Lindvall, N. Nevins, S. F. Semus, S. Senger, G. Tedesco, I. D. Wall, J. M. Woolven, C. E. Peishoff, and M. S. Head
  J. Med. Chem. 49 (20) 5912-5931 (2006)
• Improved FlexX Docking Using FlexS Determined Base Fragment Placement
  S. S. Cross
  J. Chem. Inf. Model. 45, 993-1001 (2005)
• Virtual Screening of Biogenic Amine-Binding G-Protein Coupled Receptors: Comparative Evaluation of Protein- and Ligand-Based Virtual Screening Protocols
  A. Evers, G. Hessler, H. Matter, and T. Klabunde
  J. Med. Chem. 48 (17), 5448-5465 (2005)

issue 06

• Virtual Screening in Drug Discovery
  J. Alvarez and B. Shoichet (Eds)
• Design of Small-Sized Libraries by Combinatorial Assembly of Linkers and Functional Groups to a given Scaffold: Application to the Structure-Based Optimization of a Phosphodiesterase 4 Inhibitor
  M. Krier, J.X. de Araújo-Júnior, M. Schmitt, J. Duranton, H. Justiano-Basaran, C. Lugnier, J.-J. Bourguignon, and D. Rognan
  J. Med. Chem. 48 (11), 3816-3822 (2005)
• Virtual docking approaches to Protein kinase B inhibition
  M. Forino, D. Jung, J.B. Easton, P.J. Houghton, and M. Pellechia
  J. Med. Chem. 48 (7), 2278-2281 (2005)

issue 05

• FlexX-Scan: Fast Structure-Based Virtual Screening
  I. Schellhammer and M. Rarey
  PROTEINS: Structure, Function, and Genetics 57, 504-517 (2004)
• Combination of a Naive Bayes Classifier with Consensus Scoring Improves Enrichment of High-Throughput Docking Results
  A.E. Klon, M. Glick, and J.W. Davies
  J. Med. Chem.; (Letter), 47 (18), 4356-4359 (2004)
• Virtual Screening: finding needles in a haystack on a shoestring
  D.E. Clark, N.V. Harris, A.G. Roach, and A.D. Baxter
  Drug Discovery World 2, 37-41, (2004)

issue 04

• Identification of Compounds with Nanomolar Binding Affinity for Checkpoint Kinase-1 Using Knowledge-Based Virtual Screening
  P.D. Lyne, P.W. Kenny, D.A. Cosgrove, C. Deng, S. Zabludoff, J.J. Wendoloski, and S. Ashwell
  J. Med. Chem. 47, 1962-1968 (2004)
• Identifying the binding mode of a molecular scaffold
  D. Chema, D. Eren, A. Yayon, A. Goldblum, and A. Zaliani
  J. Comput. Aided. Mol. Des. 18, 23-40 (2004)
• Automated Drawing of Structural Molecular Formulas under Constraints
  P. Fricker, M. Gastreich, and M. Rarey
  J. Chem. Inf. Comput. Sci. 44, 1065-1078 (2004)

issue 03

• Novel technologies for virtual screening
  T. Lengauer, C. Lemmen, M. Rarey and M. Zimmermann
  Drug Discovery Today 9 (1), 27-34 (2004)
• The FlexX Database Docking Environment – Rational Extraction of Receptor Based Pharmacophores
  H. Claussen, M. Gastreich, V. Apelt, J. Greene, S.A. Hindle, and C. Lemmen
  Current Drug Discovery Technologies 1, 49-60 (2004)
• Molecular Similarity Searching Using Atom Environments, Information-Based Feature Selection, and a Naïve Bayesian Classifier
  A. Bender, H.Y. Mussa, R.C. Glen and S. Reiling
  J. Chem. Inf. Comput. Sci. 44, 170-178 (2004)