Literature DB >> 29322778

Using Genome Sequence to Enable the Design of Medicines and Chemical Probes.

Alicia J Angelbello1, Jonathan L Chen1, Jessica L Childs-Disney1, Peiyuan Zhang1, Zi-Fu Wang1, Matthew D Disney1.   

Abstract

Rapid progress in genome sequencing technology has put us firmly into a postgenomic era. A key challenge in biomedical research is harnessing genome sequence to fulfill the promise of personalized medicine. This Review describes how genome sequencing has enabled the identification of disease-causing biomolecules and how these data have been converted into chemical probes of function, preclinical lead modalities, and ultimately U.S. Food and Drug Administration (FDA)-approved drugs. In particular, we focus on the use of oligonucleotide-based modalities to target disease-causing RNAs; small molecules that target DNA, RNA, or protein; the rational repurposing of known therapeutic modalities; and the advantages of pharmacogenetics. Lastly, we discuss the remaining challenges and opportunities in the direct utilization of genome sequence to enable design of medicines.

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Year:  2018        PMID: 29322778      PMCID: PMC5989578          DOI: 10.1021/acs.chemrev.7b00504

Source DB:  PubMed          Journal:  Chem Rev        ISSN: 0009-2665            Impact factor:   60.622


  642 in total

Review 1.  DNA minor-groove recognition by small molecules.

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Journal:  Nat Prod Rep       Date:  2001-06       Impact factor: 13.423

2.  Inhibition of telomerase by G-quartet DNA structures.

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Journal:  Nature       Date:  1991-04-25       Impact factor: 49.962

Review 3.  Molecular crowding effects on structure and stability of DNA.

Authors:  Daisuke Miyoshi; Naoki Sugimoto
Journal:  Biochimie       Date:  2008-02-21       Impact factor: 4.079

4.  Construction of biologically functional bacterial plasmids in vitro.

Authors:  S N Cohen; A C Chang; H W Boyer; R B Helling
Journal:  Proc Natl Acad Sci U S A       Date:  1973-11       Impact factor: 11.205

Review 5.  Turning mirror-image oligonucleotides into drugs: the evolution of Spiegelmer(®) therapeutics.

Authors:  Axel Vater; Sven Klussmann
Journal:  Drug Discov Today       Date:  2014-09-16       Impact factor: 7.851

6.  Inhibition of bacteriophage T7 RNA polymerase in vitro transcription by DNA-binding pyrrolo[2,1-c][1,4]benzodiazepines.

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Journal:  Biochemistry       Date:  1997-03-04       Impact factor: 3.162

7.  Safety and efficacy of RNAi therapy for transthyretin amyloidosis.

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Journal:  N Engl J Med       Date:  2013-08-29       Impact factor: 91.245

8.  Anti-human immunodeficiency virus hematopoietic progenitor cell-delivered ribozyme in a phase I study: myeloid and lymphoid reconstitution in human immunodeficiency virus type-1-infected patients.

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Journal:  Hum Gene Ther       Date:  2004-03       Impact factor: 5.695

9.  Foci of trinucleotide repeat transcripts in nuclei of myotonic dystrophy cells and tissues.

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Journal:  J Cell Biol       Date:  1995-03       Impact factor: 10.539

10.  Landscape and variation of RNA secondary structure across the human transcriptome.

Authors:  Yue Wan; Kun Qu; Qiangfeng Cliff Zhang; Ryan A Flynn; Ohad Manor; Zhengqing Ouyang; Jiajing Zhang; Robert C Spitale; Michael P Snyder; Eran Segal; Howard Y Chang
Journal:  Nature       Date:  2014-01-30       Impact factor: 49.962

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  34 in total

1.  Targeted Degradation of a Hypoxia-Associated Non-coding RNA Enhances the Selectivity of a Small Molecule Interacting with RNA.

Authors:  Matthew G Costales; Blessy Suresh; Kamalakannan Vishnu; Matthew D Disney
Journal:  Cell Chem Biol       Date:  2019-05-23       Impact factor: 8.116

2.  Identifying and validating small molecules interacting with RNA (SMIRNAs).

Authors:  Matthew D Disney; Sai Pradeep Velagapudi; Yue Li; Matthew G Costales; Jessica L Childs-Disney
Journal:  Methods Enzymol       Date:  2019-05-15       Impact factor: 1.600

3.  Driving factors in amiloride recognition of HIV RNA targets.

Authors:  Neeraj N Patwardhan; Zhengguo Cai; Aline Umuhire Juru; Amanda E Hargrove
Journal:  Org Biomol Chem       Date:  2019-10-30       Impact factor: 3.876

Review 4.  Small molecules with big roles in microRNA chemical biology and microRNA-targeted therapeutics.

Authors:  Rengen Fan; Chaocheng Xiao; Xinqiang Wan; Wenzhang Cha; Yufeng Miao; Yong Zhou; Chenglin Qin; Ting Cui; Fenglian Su; Xiangxiang Shan
Journal:  RNA Biol       Date:  2019-04-03       Impact factor: 4.652

5.  Activity-Based DNA-Encoded Library Screening.

Authors:  Wesley G Cochrane; Marie L Malone; Vuong Q Dang; Valerie Cavett; Alexander L Satz; Brian M Paegel
Journal:  ACS Comb Sci       Date:  2019-03-29       Impact factor: 3.784

6.  Targeting RNA with Small Molecules To Capture Opportunities at the Intersection of Chemistry, Biology, and Medicine.

Authors:  Matthew D Disney
Journal:  J Am Chem Soc       Date:  2019-04-19       Impact factor: 15.419

Review 7.  Drugging the "undruggable" microRNAs.

Authors:  Dejun Liu; Xinqiang Wan; Xiangxiang Shan; Rengen Fan; Wenzhang Zha
Journal:  Cell Mol Life Sci       Date:  2020-10-14       Impact factor: 9.261

Review 8.  Synthetic small-molecule RNA ligands: future prospects as therapeutic agents.

Authors:  A Di Giorgio; M Duca
Journal:  Medchemcomm       Date:  2019-04-30       Impact factor: 3.597

9.  Gini Coefficients as a Single Value Metric to Define Chemical Probe Selectivity.

Authors:  Andrei Ursu; Jessica L Childs-Disney; Alicia J Angelbello; Matthew G Costales; Samantha M Meyer; Matthew D Disney
Journal:  ACS Chem Biol       Date:  2020-07-09       Impact factor: 5.100

Review 10.  Targeting RNA in mammalian systems with small molecules.

Authors:  Anita Donlic; Amanda E Hargrove
Journal:  Wiley Interdiscip Rev RNA       Date:  2018-05-03       Impact factor: 9.957

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