Literature DB >> 25921252

An integrated suite of modeling tools that empower scientists in structure- and property-based drug design.

Jianwen A Feng1, Ignacio Aliagas, Philippe Bergeron, Jeff M Blaney, Erin K Bradley, Michael F T Koehler, Man-Ling Lee, Daniel F Ortwine, Vickie Tsui, Johnny Wu, Alberto Gobbi.   

Abstract

Structure- and property-based drug design is an integral part of modern drug discovery, enabling the design of compounds aimed at improving potency and selectivity. However, building molecules using desktop modeling tools can easily lead to poor designs that appear to form many favorable interactions with the protein's active site. Although a proposed molecule looks good on screen and appears to fit into the protein site X-ray crystal structure or pharmacophore model, doing so might require a high-energy small molecule conformation, which would likely be inactive. To help scientists make better design decisions, we have built integrated, easy-to-use, interactive software tools to perform docking experiments, de novo design, shape and pharmacophore based database searches, small molecule conformational analysis and molecular property calculations. Using a combination of these tools helps scientists in assessing the likelihood that a designed molecule will be active and have desirable drug metabolism and pharmacokinetic properties. Small molecule discovery success requires project teams to rapidly design and synthesize potent molecules with good ADME properties. Empowering scientists to evaluate ideas quickly and make better design decisions with easy-to-access and easy-to-understand software on their desktop is now a key part of our discovery process.

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Year:  2015        PMID: 25921252     DOI: 10.1007/s10822-015-9845-4

Source DB:  PubMed          Journal:  J Comput Aided Mol Des        ISSN: 0920-654X            Impact factor:   3.686


  30 in total

1.  Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy.

Authors:  Richard A Friesner; Jay L Banks; Robert B Murphy; Thomas A Halgren; Jasna J Klicic; Daniel T Mainz; Matthew P Repasky; Eric H Knoll; Mee Shelley; Jason K Perry; David E Shaw; Perry Francis; Peter S Shenkin
Journal:  J Med Chem       Date:  2004-03-25       Impact factor: 7.446

2.  Comprehensive analysis of kinase inhibitor selectivity.

Authors:  Mindy I Davis; Jeremy P Hunt; Sanna Herrgard; Pietro Ciceri; Lisa M Wodicka; Gabriel Pallares; Michael Hocker; Daniel K Treiber; Patrick P Zarrinkar
Journal:  Nat Biotechnol       Date:  2011-10-30       Impact factor: 54.908

3.  DEGAS: sharing and tracking target compound ideas with external collaborators.

Authors:  Man-Ling Lee; Ignacio Aliagas; Jennafer Dotson; Jianwen A Feng; Alberto Gobbi; Timothy Heffron
Journal:  J Chem Inf Model       Date:  2011-11-28       Impact factor: 4.956

4.  Moving beyond rules: the development of a central nervous system multiparameter optimization (CNS MPO) approach to enable alignment of druglike properties.

Authors:  Travis T Wager; Xinjun Hou; Patrick R Verhoest; Anabella Villalobos
Journal:  ACS Chem Neurosci       Date:  2010-03-25       Impact factor: 4.418

5.  Significant species difference in amide hydrolysis of GDC-0834, a novel potent and selective Bruton's tyrosine kinase inhibitor.

Authors:  Lichuan Liu; Jason S Halladay; Young Shin; Susan Wong; Melis Coraggio; Hank La; Matthew Baumgardner; Hoa Le; Sashi Gopaul; Jason Boggs; Peter Kuebler; John C Davis; X Charlene Liao; Joseph W Lubach; Alan Deese; C Gregory Sowell; Kevin S Currie; Wendy B Young; S Cyrus Khojasteh; Cornelis E C A Hop; Harvey Wong
Journal:  Drug Metab Dispos       Date:  2011-07-08       Impact factor: 3.922

6.  Molecular shape and medicinal chemistry: a perspective.

Authors:  Anthony Nicholls; Georgia B McGaughey; Robert P Sheridan; Andrew C Good; Gregory Warren; Magali Mathieu; Steven W Muchmore; Scott P Brown; J Andrew Grant; James A Haigh; Neysa Nevins; Ajay N Jain; Brian Kelley
Journal:  J Med Chem       Date:  2010-05-27       Impact factor: 7.446

7.  Discovery of highly potent, selective, and brain-penetrable leucine-rich repeat kinase 2 (LRRK2) small molecule inhibitors.

Authors:  Anthony A Estrada; Xingrong Liu; Charles Baker-Glenn; Alan Beresford; Daniel J Burdick; Mark Chambers; Bryan K Chan; Huifen Chen; Xiao Ding; Antonio G DiPasquale; Sara L Dominguez; Jennafer Dotson; Jason Drummond; Michael Flagella; Sean Flynn; Reina Fuji; Andrew Gill; Janet Gunzner-Toste; Seth F Harris; Timothy P Heffron; Tracy Kleinheinz; Donna W Lee; Claire E Le Pichon; Joseph P Lyssikatos; Andrew D Medhurst; John G Moffat; Susmith Mukund; Kevin Nash; Kimberly Scearce-Levie; Zejuan Sheng; Daniel G Shore; Thuy Tran; Naimisha Trivedi; Shumei Wang; Shuo Zhang; Xiaolin Zhang; Guiling Zhao; Haitao Zhu; Zachary K Sweeney
Journal:  J Med Chem       Date:  2012-10-15       Impact factor: 7.446

8.  Lead optimization of a 4-aminopyridine benzamide scaffold to identify potent, selective, and orally bioavailable TYK2 inhibitors.

Authors:  Jun Liang; Anne van Abbema; Mercedesz Balazs; Kathy Barrett; Leo Berezhkovsky; Wade Blair; Christine Chang; Donnie Delarosa; Jason DeVoss; Jim Driscoll; Charles Eigenbrot; Nico Ghilardi; Paul Gibbons; Jason Halladay; Adam Johnson; Pawan Bir Kohli; Yingjie Lai; Yanzhou Liu; Joseph Lyssikatos; Priscilla Mantik; Kapil Menghrajani; Jeremy Murray; Ivan Peng; Amy Sambrone; Steven Shia; Young Shin; Jan Smith; Sue Sohn; Vickie Tsui; Mark Ultsch; Lawren C Wu; Yisong Xiao; Wenqian Yang; Judy Young; Birong Zhang; Bing-yan Zhu; Steven Magnuson
Journal:  J Med Chem       Date:  2013-05-29       Impact factor: 7.446

9.  The design and identification of brain penetrant inhibitors of phosphoinositide 3-kinase α.

Authors:  Timothy P Heffron; Laurent Salphati; Bruno Alicke; Jonathan Cheong; Jennafer Dotson; Kyle Edgar; Richard Goldsmith; Stephen E Gould; Leslie B Lee; John D Lesnick; Cristina Lewis; Chudi Ndubaku; Jim Nonomiya; Alan G Olivero; Jodie Pang; Emile G Plise; Steve Sideris; Sean Trapp; Jeffrey Wallin; Lan Wang; Xiaolin Zhang
Journal:  J Med Chem       Date:  2012-09-11       Impact factor: 7.446

10.  The good, the bad and the twisted: a survey of ligand geometry in protein crystal structures.

Authors:  John Liebeschuetz; Jana Hennemann; Tjelvar Olsson; Colin R Groom
Journal:  J Comput Aided Mol Des       Date:  2012-01-14       Impact factor: 3.686

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  6 in total

1.  Enabling drug discovery project decisions with integrated computational chemistry and informatics.

Authors:  Vickie Tsui; Daniel F Ortwine; Jeffrey M Blaney
Journal:  J Comput Aided Mol Des       Date:  2016-10-31       Impact factor: 3.686

2.  Design and Development of a Series of Potent and Selective Type II Inhibitors of CDK8.

Authors:  Philippe Bergeron; Michael F T Koehler; Elizabeth M Blackwood; Krista Bowman; Kevin Clark; Ron Firestein; James R Kiefer; Klaus Maskos; Mark L McCleland; Linda Orren; Sreemathy Ramaswamy; Laurent Salphati; Steve Schmidt; Elisabeth V Schneider; Jiansheng Wu; Maureen Beresini
Journal:  ACS Med Chem Lett       Date:  2016-04-05       Impact factor: 4.345

3.  GluN2A-Selective Pyridopyrimidinone Series of NMDAR Positive Allosteric Modulators with an Improved in Vivo Profile.

Authors:  Elisia Villemure; Matthew Volgraf; Yu Jiang; Guosheng Wu; Cuong Q Ly; Po-Wai Yuen; Aijun Lu; Xifeng Luo; Mingcui Liu; Shun Zhang; Patrick J Lupardus; Heidi J A Wallweber; Bianca M Liederer; Gauri Deshmukh; Emile Plise; Suzanne Tay; Tzu-Ming Wang; Jesse E Hanson; David H Hackos; Kimberly Scearce-Levie; Jacob B Schwarz; Benjamin D Sellers
Journal:  ACS Med Chem Lett       Date:  2016-10-31       Impact factor: 4.345

4.  chemalot and chemalot_knime: Command line programs as workflow tools for drug discovery.

Authors:  Man-Ling Lee; Ignacio Aliagas; Jianwen A Feng; Thomas Gabriel; T J O'Donnell; Benjamin D Sellers; Bernd Wiswedel; Alberto Gobbi
Journal:  J Cheminform       Date:  2017-06-12       Impact factor: 5.514

5.  Electrostatic-field and surface-shape similarity for virtual screening and pose prediction.

Authors:  Ann E Cleves; Stephen R Johnson; Ajay N Jain
Journal:  J Comput Aided Mol Des       Date:  2019-10-24       Impact factor: 3.686

6.  NF-κB inducing kinase is a therapeutic target for systemic lupus erythematosus.

Authors:  Hans D Brightbill; Eric Suto; Nicole Blaquiere; Nandhini Ramamoorthi; Swathi Sujatha-Bhaskar; Emily B Gogol; Georgette M Castanedo; Benjamin T Jackson; Youngsu C Kwon; Susan Haller; Justin Lesch; Karin Bents; Christine Everett; Pawan Bir Kohli; Sandra Linge; Laura Christian; Kathy Barrett; Allan Jaochico; Leonid M Berezhkovskiy; Peter W Fan; Zora Modrusan; Kelli Veliz; Michael J Townsend; Jason DeVoss; Adam R Johnson; Robert Godemann; Wyne P Lee; Cary D Austin; Brent S McKenzie; Jason A Hackney; James J Crawford; Steven T Staben; Moulay H Alaoui Ismaili; Lawren C Wu; Nico Ghilardi
Journal:  Nat Commun       Date:  2018-01-12       Impact factor: 14.919

  6 in total

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