期刊论文详细信息
Chemistry Central Journal
Lost in chemical space? Maps to support organometallic catalysis
Natalie Fey1 
[1] School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
关键词: Principal component analysis;    Organometallic catalysis;    Drug discovery;    Chemoinformatics;    Structure–property relationships;    Design of experiments;    Computational chemistry;    Chemical space;   
Others  :  1219944
DOI  :  10.1186/s13065-015-0104-5
 received in 2015-01-19, accepted in 2015-05-08,  发布年份 2015
PDF
【 摘 要 】

Descriptors calculated from molecular structures have been used to map different areas of chemical space. A number of applications for such maps can be identified, ranging from the fine-tuning and optimisation of catalytic activity and compound properties to virtual screening of novel compounds, as well as the exhaustive exploration of large areas of chemical space by automated combinatorial building and evaluation. This review focuses on organometallic catalysis, but also touches on other areas where similar approaches have been used, with a view to assessing the extent to which chemical space has been explored.

【 授权许可】

   
2015 Fey.

【 预 览 】
附件列表
Files Size Format View
20150720013118757.pdf 1617KB PDF download
Fig. 5. 48KB Image download
Fig. 4. 94KB Image download
Fig. 3. 30KB Image download
Fig. 2. 55KB Image download
Fig. 1. 24KB Image download
【 图 表 】

Fig. 1.

Fig. 2.

Fig. 3.

Fig. 4.

Fig. 5.

【 参考文献 】
  • [1]Drew KLM, Baiman H, Khwaounjoo P, Yu B, Reynisson J. Size estimation of chemical space: how big is it? J Pharm Pharmacol. 2012; 64:490-5.
  • [2]Van Deursen R, Reymond J-L. Chemical space travel. ChemMedChem. 2007; 2:636-40.
  • [3]Kirkpatrick P, Ellis C. Chemical space. Nature. 2004; 432:823.
  • [4]Reymond J-L, Ruddigkeit L, Blum L, van Deursen R. The enumeration of chemical space. WIREs Comput Mol Sci. 2012; 2:717-33.
  • [5]Jover J, Fey N. The computational road to better catalysts. Chem Asian J. 2014; 9:1714-23.
  • [6]Virshup AM, Contreras-García J, Wipf P, Yang W, Beratan DN. Stochastic voyages into uncharted chemical space produce a representative library of all possible drug-like compounds. J Am Chem Soc. 2013; 135:7296-303.
  • [7]Fey N, Tsipis A, Harris SE, Harvey JN, Orpen AG, Mansson RA. Development of a ligand knowledge base, part 1: computational descriptors for phosphorus donor ligands. Chem Eur J. 2006; 12:291-302.
  • [8]Cooney KD, Cundari TR, Hoffman NW, Pittard KA, Temple MD, Zhao Y. A priori assessment of the stereoelectronic profile of phosphines and phosphites. J Am Chem Soc. 2003; 125:4318.
  • [9]Gusev DG. Electronic and steric parameters of 76 N-heterocyclic carbenes in Ni(CO) 3 (NHC). Organometallics. 2009; 28:6458-61.
  • [10]Gusev DG. Donor properties of a series of two-electron ligands. Organometallics. 2009; 28:763-70.
  • [11]Foscato M, Venkatraman V, Occhipinti G, Alsberg BK, Jensen VR. Automated building of organometallic complexes from 3D fragments. J Chem Inf Model. 2014; 54:1919-31.
  • [12]Maldonado AG, Hageman JA, Mastroianni S, Rothenberg G. Backbone diversity analysis in catalyst design. Adv Synth Catal. 2009; 351:387-96.
  • [13]Chu Y, Heyndrickx W, Occhipinti G, Jensen VR, Alsberg BK. An evolutionary algorithm for de novo optimization of functional transition metal compounds. J Am Chem Soc. 2012; 134:8885-95.
  • [14]Occhipinti G, Bjorsvik HR, Jensen VR. Quantitative structure-activity relationships of ruthenium catalysts for olefin metathesis. J Am Chem Soc. 2006; 128:6952-64.
  • [15]Burello E, Rothenberg G. Topological mapping of bidentate ligands: a fast approach for screening homogeneous catalysts. Adv Synth Catal. 2005; 347:1969-77.
  • [16]Reymond J-L, van Deursen R, Blum LC, Ruddigkeit L. Chemical space as a source for new drugs. MedChemComm. 2010; 1:30-8.
  • [17]Fey N, Garland M, Hopewell JP, McMullin CL, Mastroianni S, Orpen AG et al.. Stable fluorophosphines: predicted and realized ligands for catalysis. Angew Chem Int Ed. 2012; 51:118-22.
  • [18]Fey N, Orpen AG, Harvey JN. Building ligand knowledge bases for organometallic chemistry: computational description of phosphorus(III)-donor ligands and the metal-phosphorus bond. Coord Chem Rev. 2009; 253:704-22.
  • [19]Tolman CA. Steric effects of phosphorus ligands in organometallic chemistry and homogeneous catalysis. Chem Rev. 1977; 77:313-48.
  • [20]Ivanenkov YA, Savchuk NP, Ekins S, Balakin KV. Computational mapping tools for drug discovery. Drug Discov Today. 2009; 14:767-75.
  • [21]Livingstone D. A practical guide to scientific data analysis. Wiley & Sons Ltd., Chichester, UK; 2009.
  • [22]Townend J. Practical statistics for environmental and biological scientists. John Wiley & Sons Ltd., Chichester; 2002.
  • [23]Fey N. The contribution of computational studies to organometallic catalysis: descriptors, mechanisms and models. Dalton Trans. 2010; 39:296-310.
  • [24]Hansch C, Leo A, Taft RW. A survey of Hammett substituent constants and resonance and field parameters. Chem Rev. 1991; 91:165-95.
  • [25]Aguado-Ullate S, Guasch L, Urbano-Cuadrado M, Bo C, Carbo JJ. 3D-QSPR models for predicting the enantioselectivity and the activity for asymmetric hydroformylation of styrene catalyzed by Rh-diphosphane. Catal Sci Techn. 2012; 2:1694-704.
  • [26]Harper KC, Bess EN, Sigman MS. Multidimensional steric parameters in the analysis of asymmetric catalytic reactions. Nature Chem. 2012; 4:366-74.
  • [27]Harper KC, Sigman MS. Predicting and optimizing asymmetric catalyst performance using the principles of experimental design and steric parameters. Proc. Nat. Acad. Sci. 2011; 108:2179-83.
  • [28]Jover J, Fey N, Harvey JN, Lloyd-Jones GC, Orpen AG, Owen-Smith GJJ et al.. Expansion of the ligand knowledge base for monodentate P-donor ligands (LKB-P). Organometallics. 2010; 29:6245-58.
  • [29]DiFranco SA, Maciulis NA, Staples RJ, Batrice RJ, Odom AL. Evaluation of donor and steric properties of anionic ligands on high valent transition metals. Inorg Chem. 2011; 51:1187-200.
  • [30]Fey N, Haddow MF, Harvey JN, McMullin CL, Orpen AG. A ligand knowledge base for carbenes (LKB-C): maps of ligand space. Dalton Trans. 2009:8183–96.
  • [31]Clavier H, Nolan SP. Percent buried volume for phosphine and N-heterocyclic carbene ligands: steric properties in organometallic chemistry. Chem Commun. 2010; 46:841-61.
  • [32]Nelson DJ, Nolan SP. Quantifying and understanding the electronic properties of N-heterocyclic carbenes. Chem Soc Rev. 2013; 42:6723-53.
  • [33]Pickup OJS, Khazal I, Smith EJ, Whitwood AC, Lynam JM, Bolaky K et al.. Computational discovery of stable transition-metal vinylidene complexes. Organometallics. 2014; 33:1751-61.
  • [34]Fey N, Harvey JN, Lloyd-Jones GC, Murray P, Orpen AG, Osborne R et al.. Computational descriptors for chelating P, P- and P,N-donor ligands. Organometallics. 2008; 27:1372-83.
  • [35]Jover J, Fey N. Screening substituent and backbone effects on the properties of bidentate P, P-donor ligands (LKB-PPscreen). Dalton Trans. 2013; 42:172-81.
  • [36]Jover J, Fey N, Harvey JN, Lloyd-Jones GC, Orpen AG, Owen-Smith GJJ et al.. Expansion of the ligand knowledge base for chelating P, P-donor ligands (LKB-PP). Organometallics. 2012; 31:5302-6.
  • [37]Mathew J, Tinto T, Suresh CH. Quantitative assessment of the stereoelectronic profile of phosphine ligands. Inorg Chem. 2007; 46:10800-9.
  • [38]Burello E, Marion P, Galland J-C, Chamard A, Rothenberg G. Ligand descriptor analysis in nickel-catalysed hydrocyanation: a combined experimental and theoretical study. Adv Synth Catal. 2005; 347:803-10.
  • [39]Moseley JD, Murray PM. Ligand and solvent selection in challenging catalytic reactions. J Chem Technol Biotechnol. 2014; 89:623-32.
  • [40]Hageman JA, Westerhuis JA, Frühauf H-W, Rothenberg G. Design and assembly of virtual homogeneous catalyst libraries–towards in silico catalyst optimisation. Adv Synth Catal. 2006; 348:361-9.
  • [41]Burello E, Farrusseng D, Rothenberg G. Combinatorial explosion in homogeneous catalysis: screening 60,000 cross-coupling reactions. Adv Synth Catal. 2004; 346:1844-53.
  • [42]Maldonado AG, Rothenberg G. Predictive modeling in homogeneous catalysis: a tutorial. Chem Soc Rev. 2010; 39:1891-902.
  • [43]Burello E, Rothenberg G. Optimal heck cross-coupling catalysis: a pseudo-pharmaceutical approach. Adv Synth Catal. 2003; 345:1334-40.
  • [44]Foscato M, Occhipinti G, Venkatraman V, Alsberg BK, Jensen VR. Automated design of realistic organometallic molecules from fragments. J Chem Inf Model. 2014; 54:767-80.
  • [45]Medina-Franco JL. Interrogating novel areas of chemical space for drug discovery using chemoinformatics. Drug Dev Res. 2012; 73:430-8.
  • [46]Medina-Franco JL, Martinez-Mayorga K, Meurice N. Balancing novelty with confined chemical space in modern drug discovery. Expert Opin Drug Discovery. 2014; 9:151-65.
  • [47]Ursu O, Rayan A, Goldblum A, Oprea TI. Understanding drug-likeness. WIREs Comput Mol Sci. 2011; 1:760-81.
  • [48]Sukumar N, Krein MP, Prabhu G, Bhattacharya S, Sen S. Network measures for chemical library design. Drug Dev Res. 2014; 75:402-11.
  • [49]Deng Z-L, Du C-X, Li X, Hu B, Kuang Z-K, Wang R et al.. Exploring the biologically relevant chemical space for drug discovery. J Chem Inf Model. 2013; 53:2820-8.
  • [50]Lameijer E-W, Kok JN, Bäck T, Ijzerman AP. Mining a chemical database for fragment co-occurrence: discovery of “Chemical clichés”. J Chem Inf Model. 2006; 46:553-62.
  • [51]Langdon SR, Brown N, Blagg J. Scaffold diversity of exemplified medicinal chemistry space. J Chem Inf Model. 2011; 51:2174-85.
  • [52]Kim J, Kim H, Park SB. Privileged structures: efficient chemical “Navigators” toward unexplored biologically relevant chemical spaces. J Am Chem Soc. 2014; 136:14629-38.
  • [53]Ruddigkeit L, Blum LC, Reymond J-L. Visualization and virtual screening of the chemical universe database GDB-17. J Chem Inf Model. 2012; 53:56-65.
  • [54]Ruddigkeit L, Awale M, Reymond J-L. Expanding the fragrance chemical space for virtual screening. J Cheminf. 2014; 6:27. BioMed Central Full Text
  • [55]Reymond J-L, Awale M. Exploring chemical space for drug discovery using the chemical Universe database. ACS Chem Neurosci. 2012; 3:649-57.
  • [56]Stauffer SR, Hartwig JF. Fluorescence Resonance Energy Transfer (FRET) as a high-throughput assay for coupling reactions. Arylation of amines as a case study. J Am Chem Soc. 2003; 125:6977-85.
  文献评价指标  
  下载次数:98次 浏览次数:18次