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Wonpil Im – One of the best experts on this subject based on the ideXlab platform.

  • Stalis: A Computational Method for Template‐Based Ab Initio Ligand Design
    Journal of Computational Chemistry, 2019
    Co-Authors: Wonpil Im
    Abstract:

    : Proteins interact with small molecules through specific molecular recognition, which is central to essential biological functions in living systems. Therefore, understanding such interactions is crucial for basic sciences and drug discovery. Here, we present Structure template-based ab initio Ligand design solution (Stalis), a knowledge-based approach that uses structure templates from the Protein Data Bank libraries of whole Ligands and their fragments and generates a set of molecules (virtual Ligands) whose structures represent the pocket shape and chemical features of a given target binding site. Our benchmark performance evaluation shows that Ligand structure-based virtual screening using virtual Ligands from Stalis outperforms a receptor structure-based virtual screening using AutoDock Vina, demonstrating reliable overall screening performance applicable to computational high-throughput screening. However, virtual Ligands from Stalis are worse in recognizing active compounds at the small fraction of a rank-ordered list of screened library compounds than crystal Ligands, due to the low resolution of the virtual Ligand structures. In conclusion, Stalis can facilitate drug discovery research by designing virtual Ligands that can be used for fast Ligand structure-based virtual screening. Moreover, Stalis provides actual three-dimensional Ligand structures that likely bind to a target protein, enabling to gain structural insight into potential Ligands. Stalis can be an efficient computational platform for high-throughput Ligand design for fundamental biological study and drug discovery research at the proteomic level. © 2019 Wiley Periodicals, Inc.

  • Computer-Aided Drug Design Utilizing Structure Templates Identified by Local Structure Alignment
    Biophysical Journal, 2013
    Co-Authors: Wonpil Im
    Abstract:

    With a rapid increase in the number of high-resolution proteinLigand structures, the known proteinLigand structures can be used to gain insights into how a Ligand binds in a target protein. Based on the fact that the structurally similar binding sites share information about their Ligands, we have developed a local structure alignment tool, G-LoSA (Graph-based Local Structure Alignment). Using G-LoSA, the known proteinLigand binding-site structure library is searched to detect local structures with similar geometry and physicochemical properties to a query structure regardless of sequence continuity and protein fold. Then, the Ligands in the identified complexes are used as templates to predict a binding site and a Ligand structure for the target protein. The performance of G-LoSA is validated against benchmark targets. G-LoSA is able to not only predict the Ligand binding sites with high accuracy but also identify a single template Ligand that is highly similar to the target Ligand. In addition, our benchmark analyses show that an assembly of structural fragments from multiple template Ligands can be used to design novel Ligand structures specific to the target protein. This study clearly indicates that local-structure based binding-site prediction and Ligand modeling have potential for de novo Ligand design.

  • Identification of Ligand Templates using Local Structure Alignment for Structure-Based Drug Design
    Journal of Chemical Information and Modeling, 2012
    Co-Authors: Wonpil Im
    Abstract:

    With a rapid increase in the number of high-resolution proteinLigand structures, the known proteinLigand structures can be used to gain insight into Ligand-binding modes in a target protein. On the basis of the fact that the structurally similar binding sites share information about their Ligands, we have developed a local structure alignment tool, G-LoSA (graph-based local structure alignment). The known proteinLigand binding-site structure library is searched by G-LoSA to detect binding-site structures with similar geometry and physicochemical properties to a query binding-site structure regardless of sequence continuity and protein fold. Then, the Ligands in the identified complexes are used as templates (i.e., template Ligands) to predict/design a Ligand for the target protein. The performance of G-LoSA is validated against 76 benchmark targets from the Astex diverse set. Using the currently available proteinLigand structure library, G-LoSA is able to identify a single template Ligand (from a nonh…

Dieter Vogt – One of the best experts on this subject based on the ideXlab platform.

  • Amide versus amine Ligand paradigm in the direct amination of alcohols with Ru-PNP complexes
    Catalysis Science & Technology, 2018
    Co-Authors: Dennis Pingen, Jong-hoo Choi, Henry Allen, George Murray, Prasad Ganji, Piet Van Leeuwen, Martin Prechtl, Dieter Vogt
    Abstract:

    The catalytic activity of a series of Ru-PNP pincer Ligand complexes was studied in the direct amination of alcohols with ammonia. It turned out that all complexes of PNP Ligands bearing a secondary amine showed no activity in this hydrogen-shuttling reaction sequence, while all complexes of homologous Ligands bearing a tertiary aminamine gave active catalysts. Further comparative studies on catalysts bearing an acridine-based PNP pincer Ligand and a PNP Ligand of the Xantphos family provided valuable mechanistic insight that led to the design of a highly active catalyst. It appears that in the group of Ligands studied here only Ligands that do not form stable Ru-amido complexes are active alcohol amination catalysts.

Matthew C. Beard – One of the best experts on this subject based on the ideXlab platform.

  • Designing Janus Ligand Shells on PbS Quantum Dots using LigandLigand Cooperativity.
    ACS nano, 2019
    Co-Authors: Noah D. Bronstein, Marissa S. Martinez, Daniel M. Kroupa, Nicholas P. Brawand, Arthur J. Nozik, Alan Sellinger, Giulia Galli, Márton Vörös, Matthew C. Beard
    Abstract:

    We present a combined experimental and theoretical study of LigandLigand cooperativity during X-type carboxylate-to-carboxylate Ligand exchange reactions on PbS quantum dot surfaces. We find that the Ligand dipole moment (varied through changing the substituents on the benzene ring of cinnamic acid derivatives) impacts the Ligand-exchange isotherms; in particular, Ligands with large electron withdrawing character result in a sharper transition from an oleate-dominated Ligand shell to a cinnamate-dominated Ligand shell. We developed a two-dimensional lattice model to simulate the Ligand-exchange isotherms that accounts for the difference in Ligand binding energy as well as LigandLigand cooperativity. Our model shows that Ligands with larger LigandLigand coupling energy exhibit sharper isotherms indicating an order-disorder phase transition. Finally, we developed an anisotropic Janus Ligand shell by taking advantage of the LigandLigand cooperative Ligand exchanges. We monitored the Janus Ligand shell using 19F nuclear magnetic resoresonance, showing that when the LigandLigand coupling energy falls within the order region of the phase diagram, Janus Ligand shells can be constructed.

  • Designing Janus Ligand Shells on PbS Quantum Dots using LigandLigand Cooperativity
    , 2019
    Co-Authors: Noah D. Bronstein, Marissa S. Martinez, Daniel M. Kroupa, Márton Vörös, Nicholas P. Brawand, Arthur J. Nozik, Alan Sellinger, Giulia Galli, Matthew C. Beard
    Abstract:

    We present a combined experimental and theoretical study of LigandLigand cooperativity during X-type carboxylate-to-carboxylate Ligand exchange reactions on PbS quantum dot surfaces. We find that the Ligand dipole moment (varied through changing the substituents on the benzene ring of cinnamic acid derivatives) impacts the Ligand-exchange isotherms; in particular, Ligands with large electron withdrawing character result in a sharper transition from an oleate-dominated Ligand shell to a cinnamate-dominated Ligand shell. We developed a two-dimensional lattice model to simulate the Ligand-exchange isotherms that accounts for the difference in Ligand binding energy as well as LigandLigand cooperativity. Our model shows that Ligands with larger LigandLigand coupling energy exhibit sharper isotherms indicating an order–disorder phase transition. Finally, we developed an anisotropic Janus Ligand shell by taking advantage of the LigandLigand cooperative Ligand exchanges. We monitored the Janus Ligand shell using 19F nuclear magnetic resoresonance, showing that when the LigandLigand coupling energy falls within the order region of the phase diagram, Janus Ligand shells can be constructed

Purdie Mark – One of the best experts on this subject based on the ideXlab platform.

  • Expansion of the Ligand Knowledge Base for Chelating P,P-Donor Ligands (LKB-PP).
    Organometallics, 2012
    Co-Authors: Jesús Jover, Natalie Fey, Jeremy N. Harvey, Guy C. Lloyd-jones, A. Guy Orpen, Gareth J. J. Owen-smith, Paul M. Murray, David R. J. Hose, Robert Osborne, Purdie Mark
    Abstract:

    We have expanded the Ligand knowledge base for bidentate P,P- and P,N-donor Ligands (LKB-PP, Organometallics 2008, 27, 1372–1383) by 208 Ligands and introduced an additional steric descriptor (nHe8). This expanded knowledge base now captures information on 334 bidentate Ligands and has been processed with principal compcomponent analysis (PCA) of the descriptors to produce a detailed map of bidentate Ligand space, which better captures Ligand variation and has been used for the analysis of Ligand properties.

  • Expansion of the Ligand Knowledge Base for Monodentate P-Donor Ligands (LKB-P)†
    Organometallics, 2010
    Co-Authors: Jesús Jover, Natalie Fey, Jeremy N. Harvey, Guy C. Lloyd-jones, A. Guy Orpen, Gareth J. J. Owen-smith, Paul M. Murray, David R. J. Hose, Robert Osborne, Purdie Mark
    Abstract:

    We have expanded the Ligand knowledge base for monodentate P-donor Ligands (LKB-P, Chem. Eur. J. 2006, 12, 291−302) by 287 Ligands and added descriptors derived from computational results on a gold complex [AuClL]. This expansion to 348 Ligands captures known Ligand space for this class of monodentate two-electron donor Ligands well, and we have used principal compcomponent analysis (PCA) of the descriptors to derive an improved map of Ligand space. Potential applications of this map, including the visualization of Ligand similarities/differences and trends in experimental data, as well as the design of Ligand test sets for high-throughput screening and the identification of Ligands for reaction optimization, are discussed. Descriptors of Ligand properties can also be used in regression models for the interpretation and prediction of available response data, and here we explore such models for both experimental and calculated data, highlighting the advantages of large training sets that sample Ligand space well.

Piet W. N. M. Van Leeuwen – One of the best experts on this subject based on the ideXlab platform.

  • Wide bite angle amine, arsine and phosphine Ligands in rhodium- and platinum/tin-catalysed hydroformylation
    Journal of the Chemical Society Dalton Transactions, 2000
    Co-Authors: Lars A. Van Der Veen, Peter K. Keeven, Paul C. J. Kamer, Piet W. N. M. Van Leeuwen
    Abstract:

    New wide bite angle amine, arsine and mixed phosphineamine and phosphinearsine Ligands based on xanthene backbones were synthesized. The co-ordination chemistry and the catalytic performance of these Ligands were compared to those of the parent phosphine Ligands. The amine based xanthene Ligands do not form rhodium–hydride complexes and therefore give very poor rhodium hydroformylation catalysts. The catalytic performance of the xantarsine and the mixed xantphosarsine Ligands is comparable with that of the xantphos Ligands and they form similar (Ligand)Rh(CO)2H and [(Ligand)Rh(CO)2]2 complexes. In the platinum/tin-catalysed hydroformylation the xantarsine and the mixed xantphosarsine Ligands proved to be superior to the xantphos Ligands. The remarkably high selectivity and activity that is displayed by the mixed xantphosarsine Ligand is explained by its wide natural bite angle and the formation of cis co-ordinated platinum complexes.

  • wide bite angle amine arsine and phosphine Ligands in rhodium and platinum tin catalysed hydroformylation
    Journal of The Chemical Society-dalton Transactions, 2000
    Co-Authors: Lars A. Van Der Veen, Peter K. Keeven, Paul C. J. Kamer, Piet W. N. M. Van Leeuwen
    Abstract:

    New wide bite angle amine, arsine and mixed phosphineamine and phosphinearsine Ligands based on xanthene backbones were synthesized. The co-ordination chemistry and the catalytic performance of these Ligands were compared to those of the parent phosphine Ligands. The amine based xanthene Ligands do not form rhodium–hydride complexes and therefore give very poor rhodium hydroformylation catalysts. The catalytic performance of the xantarsine and the mixed xantphosarsine Ligands is comparable with that of the xantphos Ligands and they form similar (Ligand)Rh(CO)2H and [(Ligand)Rh(CO)2]2 complexes. In the platinum/tin-catalysed hydroformylation the xantarsine and the mixed xantphosarsine Ligands proved to be superior to the xantphos Ligands. The remarkably high selectivity and activity that is displayed by the mixed xantphosarsine Ligand is explained by its wide natural bite angle and the formation of cis co-ordinated platinum complexes.