Literature DB >> 32068073

Impact of the Protein Data Bank on antineoplastic approvals.

John D Westbrook1, Rose Soskind2, Brian P Hudson1, Stephen K Burley3.   

Abstract

Open access to 3D structure information from the Protein Data Bank (PDB) facilitated discovery and development of >90% of the 79 new antineoplastic agents (54 small molecules, 25 biologics) with known molecular targets approved by the FDA 2010-2018. Analyses of PDB holdings, the scientific literature and related documents for each drug-target combination revealed that the impact of public-domain 3D structure data was broad and substantial, ranging from understanding target biology (∼95% of all targets) to identifying a given target as probably druggable (∼95% of all targets) to structure-guided lead optimization (>70% of all small-molecule drugs). In addition to aggregate impact assessments, illustrative case studies are presented for three protein kinase inhibitors, an allosteric enzyme inhibitor and seven advanced-stage melanoma therapeutics.
Copyright © 2020 The Authors. Published by Elsevier Ltd.. All rights reserved.

Entities:  

Year:  2020        PMID: 32068073      PMCID: PMC7305983          DOI: 10.1016/j.drudis.2020.02.002

Source DB:  PubMed          Journal:  Drug Discov Today        ISSN: 1359-6446            Impact factor:   7.851


  139 in total

1.  Structural basis for the recognition of nucleophosmin-anaplastic lymphoma kinase oncoprotein by the phosphotyrosine binding domain of Suc1-associated neurotrophic factor-induced tyrosine-phosphorylated target-2.

Authors:  Seizo Koshiba; Hua Li; Yoko Motoda; Tadashi Tomizawa; Takuma Kasai; Naoya Tochio; Takashi Yabuki; Takushi Harada; Satoru Watanabe; Akiko Tanaka; Mikako Shirouzu; Takanori Kigawa; Tadashi Yamamoto; Shigeyuki Yokoyama
Journal:  J Struct Funct Genomics       Date:  2010-05-08

2.  Announcing the worldwide Protein Data Bank.

Authors:  Helen Berman; Kim Henrick; Haruki Nakamura
Journal:  Nat Struct Biol       Date:  2003-12

3.  The T790M mutation in EGFR kinase causes drug resistance by increasing the affinity for ATP.

Authors:  Cai-Hong Yun; Kristen E Mengwasser; Angela V Toms; Michele S Woo; Heidi Greulich; Kwok-Kin Wong; Matthew Meyerson; Michael J Eck
Journal:  Proc Natl Acad Sci U S A       Date:  2008-01-28       Impact factor: 11.205

4.  Structure of a single-chain antibody variable domain (Fv) fragment complexed with a carbohydrate antigen at 1.7-A resolution.

Authors:  A Zdanov; Y Li; D R Bundle; S J Deng; C R MacKenzie; S A Narang; N M Young; M Cygler
Journal:  Proc Natl Acad Sci U S A       Date:  1994-07-05       Impact factor: 11.205

5.  The structure of a dual-specificity tyrosine phosphorylation-regulated kinase 1A-PKC412 complex reveals disulfide-bridge formation with the anomalous catalytic loop HRD(HCD) cysteine.

Authors:  Marina Alexeeva; Espen Åberg; Richard A Engh; Ulli Rothweiler
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2015-04-25

6.  Crystal structure of the complex between programmed death-1 (PD-1) and its ligand PD-L2.

Authors:  Eszter Lázár-Molnár; Qingrong Yan; Erhu Cao; Udupi Ramagopal; Stanley G Nathenson; Steven C Almo
Journal:  Proc Natl Acad Sci U S A       Date:  2008-07-18       Impact factor: 11.205

7.  PDBe: towards reusable data delivery infrastructure at protein data bank in Europe.

Authors:  Saqib Mir; Younes Alhroub; Stephen Anyango; David R Armstrong; John M Berrisford; Alice R Clark; Matthew J Conroy; Jose M Dana; Mandar Deshpande; Deepti Gupta; Aleksandras Gutmanas; Pauline Haslam; Lora Mak; Abhik Mukhopadhyay; Nurul Nadzirin; Typhaine Paysan-Lafosse; David Sehnal; Sanchayita Sen; Oliver S Smart; Mihaly Varadi; Gerard J Kleywegt; Sameer Velankar
Journal:  Nucleic Acids Res       Date:  2018-01-04       Impact factor: 16.971

Review 8.  Protein crystallography and drug discovery: recollections of knowledge exchange between academia and industry.

Authors:  Tom L Blundell
Journal:  IUCrJ       Date:  2017-06-29       Impact factor: 4.769

9.  Binding mode of the breakthrough inhibitor AZD9291 to epidermal growth factor receptor revealed.

Authors:  Yuliana Yosaatmadja; Shevan Silva; James M Dickson; Adam V Patterson; Jeff B Smaill; Jack U Flanagan; Mark J McKeage; Christopher J Squire
Journal:  J Struct Biol       Date:  2015-11-02       Impact factor: 2.867

10.  Protein Data Bank: the single global archive for 3D macromolecular structure data.

Authors: 
Journal:  Nucleic Acids Res       Date:  2019-01-08       Impact factor: 16.971

View more
  13 in total

1.  Simplified quality assessment for small-molecule ligands in the Protein Data Bank.

Authors:  Chenghua Shao; John D Westbrook; Changpeng Lu; Charmi Bhikadiya; Ezra Peisach; Jasmine Y Young; Jose M Duarte; Robert Lowe; Sijian Wang; Yana Rose; Zukang Feng; Stephen K Burley
Journal:  Structure       Date:  2022-01-12       Impact factor: 5.006

2.  RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D.

Authors:  Stephen K Burley; Charmi Bhikadiya; Chunxiao Bi; Sebastian Bittrich; Li Chen; Gregg V Crichlow; Jose M Duarte; Shuchismita Dutta; Maryam Fayazi; Zukang Feng; Justin W Flatt; Sai J Ganesan; David S Goodsell; Sutapa Ghosh; Rachel Kramer Green; Vladimir Guranovic; Jeremy Henry; Brian P Hudson; Catherine L Lawson; Yuhe Liang; Robert Lowe; Ezra Peisach; Irina Persikova; Dennis W Piehl; Yana Rose; Andrej Sali; Joan Segura; Monica Sekharan; Chenghua Shao; Brinda Vallat; Maria Voigt; John D Westbrook; Shamara Whetstone; Jasmine Y Young; Christine Zardecki
Journal:  Protein Sci       Date:  2021-11-06       Impact factor: 6.725

3.  Assessing PDB macromolecular crystal structure confidence at the individual amino acid residue level.

Authors:  Chenghua Shao; Sebastian Bittrich; Sijian Wang; Stephen K Burley
Journal:  Structure       Date:  2022-08-31       Impact factor: 5.871

4.  Modernized uniform representation of carbohydrate molecules in the Protein Data Bank.

Authors:  Chenghua Shao; Zukang Feng; John D Westbrook; Ezra Peisach; John Berrisford; Yasuyo Ikegawa; Genji Kurisu; Sameer Velankar; Stephen K Burley; Jasmine Y Young
Journal:  Glycobiology       Date:  2021-09-20       Impact factor: 4.313

5.  PDB-101: Educational resources supporting molecular explorations through biology and medicine.

Authors:  Christine Zardecki; Shuchismita Dutta; David S Goodsell; Robert Lowe; Maria Voigt; Stephen K Burley
Journal:  Protein Sci       Date:  2021-10-18       Impact factor: 6.725

Review 6.  Open-access data: A cornerstone for artificial intelligence approaches to protein structure prediction.

Authors:  Stephen K Burley; Helen M Berman
Journal:  Structure       Date:  2021-05-12       Impact factor: 5.871

Review 7.  Impact of structural biologists and the Protein Data Bank on small-molecule drug discovery and development.

Authors:  Stephen K Burley
Journal:  J Biol Chem       Date:  2021-03-17       Impact factor: 5.157

Review 8.  Targeting protein phosphatase PP2A for cancer therapy: development of allosteric pharmaceutical agents.

Authors:  David L Brautigan; Caroline Farrington; Goutham Narla
Journal:  Clin Sci (Lond)       Date:  2021-07-16       Impact factor: 6.876

Review 9.  RCSB Protein Data Bank tools for 3D structure-guided cancer research: human papillomavirus (HPV) case study.

Authors:  David S Goodsell; Stephen K Burley
Journal:  Oncogene       Date:  2020-09-16       Impact factor: 9.867

10.  RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences.

Authors:  Stephen K Burley; Charmi Bhikadiya; Chunxiao Bi; Sebastian Bittrich; Li Chen; Gregg V Crichlow; Cole H Christie; Kenneth Dalenberg; Luigi Di Costanzo; Jose M Duarte; Shuchismita Dutta; Zukang Feng; Sai Ganesan; David S Goodsell; Sutapa Ghosh; Rachel Kramer Green; Vladimir Guranović; Dmytro Guzenko; Brian P Hudson; Catherine L Lawson; Yuhe Liang; Robert Lowe; Harry Namkoong; Ezra Peisach; Irina Persikova; Chris Randle; Alexander Rose; Yana Rose; Andrej Sali; Joan Segura; Monica Sekharan; Chenghua Shao; Yi-Ping Tao; Maria Voigt; John D Westbrook; Jasmine Y Young; Christine Zardecki; Marina Zhuravleva
Journal:  Nucleic Acids Res       Date:  2021-01-08       Impact factor: 16.971

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.