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Abstract
Glycoscience assembles all the scientific disciplines involved in studying various molecules and macromolecules containing carbohydrates and complex glycans. Such an ensemble involves one of the most extensive sets of molecules in quantity and occurrence since they occur in all microorganisms and higher organisms. Once the compositions and sequences of these molecules are established, the determination of their three-dimensional structural and dynamical features is a step toward understanding the molecular basis underlying their properties and functions. The range of the relevant computational methods capable of addressing such issues is anchored by the specificity of stereoelectronic effects from quantum chemistry to mesoscale modeling throughout molecular dynamics and mechanics and coarse-grained and docking calculations. The Review leads the reader through the detailed presentations of the applications of computational modeling. The illustrations cover carbohydrate-carbohydrate interactions, glycolipids, and N- and O-linked glycans, emphasizing their role in SARS-CoV-2. The presentation continues with the structure of polysaccharides in solution and solid-state and lipopolysaccharides in membranes. The full range of protein-carbohydrate interactions is presented, as exemplified by carbohydrate-active enzymes, transporters, lectins, antibodies, and glycosaminoglycan binding proteins. A final section features a list of 150 tools and databases to help address the many issues of structural glycobioinformatics.
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Affiliation(s)
- Serge Perez
- Centre de Recherche sur les Macromolecules Vegetales, University of Grenoble-Alpes, Centre National de la Recherche Scientifique, Grenoble F-38041, France
| | - Olga Makshakova
- FRC Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, Kazan 420111, Russia
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2
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Caron G, Digiesi V, Solaro S, Ermondi G. Flexibility in early drug discovery: focus on the beyond-Rule-of-5 chemical space. Drug Discov Today 2020; 25:621-627. [PMID: 31991117 DOI: 10.1016/j.drudis.2020.01.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/09/2020] [Accepted: 01/16/2020] [Indexed: 01/02/2023]
Abstract
Large and flexible compounds are of interest in pharmaceutical programs aimed at challenging protein targets that cannot be modulated by Rule of Five (Ro5)-compliant small molecules. Given their particular structural features, early drug discovery is now in charge of identifying which molecular descriptors should be used in the often called beyond-Rule-of-5 (bRo5) chemical space. Here, we focus on flexibility descriptors. First, we discuss the concept of flexibility and then focus on the number of rotatable bonds (NRot), the most common in silico descriptor. After identifying the pros and cons of NRot, we discuss how Kier's index Φ can replace NRot, and the limits of 3D descriptors. Finally, we show how a misuse of NRot and Φ can result in incorrect interpretations of the impact of flexibility in the bRo5 space and how flexibility has potential in the prospective design of orally bioavailable bRo5 drug candidates.
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Affiliation(s)
- Giulia Caron
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Quarello 15, 10135, Torino, Italy
| | - Vito Digiesi
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Quarello 15, 10135, Torino, Italy
| | - Sara Solaro
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Quarello 15, 10135, Torino, Italy
| | - Giuseppe Ermondi
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Quarello 15, 10135, Torino, Italy.
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3
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Wicker JP, Cooper RI. Beyond Rotatable Bond Counts: Capturing 3D Conformational Flexibility in a Single Descriptor. J Chem Inf Model 2016; 56:2347-2352. [PMID: 28024401 PMCID: PMC5271572 DOI: 10.1021/acs.jcim.6b00565] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Indexed: 11/29/2022]
Abstract
A new molecular descriptor, nConf20, based on chemical connectivity, is presented which captures the accessible conformational space of a molecule. Currently the best available two-dimensional descriptors for quantifying the flexibility of a particular molecule are the rotatable bond count (RBC) and the Kier flexibility index. We present a descriptor which captures this information by sampling the conformational space of a molecule using the RDKit conformer generator. Flexibility has previously been identified as a key feature in determining whether a molecule is likely to crystallize or not. For this application, nConf20 significantly outperforms previously reported single-variable classifiers and also assists rule-based analysis of black-box machine learning classification algorithms.
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Affiliation(s)
| | - Richard I. Cooper
- Chemical Crystallography, University of Oxford, Oxford OX1 3TA, U.K.
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Buevich AV. Atropisomerization of 8-Membered Dibenzolactam: Experimental NMR and Theoretical DFT Study. J Org Chem 2015; 81:485-501. [DOI: 10.1021/acs.joc.5b02321] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alexei V. Buevich
- Merck Research Laboratories,
Discovery and Preclinical Sciences, Process and Analytical Chemistry, NMR Structure Elucidation, Kenilworth, New Jersey 07033, United States
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5
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Sacan A, Ekins S, Kortagere S. Applications and limitations of in silico models in drug discovery. Methods Mol Biol 2012; 910:87-124. [PMID: 22821594 DOI: 10.1007/978-1-61779-965-5_6] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Drug discovery in the late twentieth and early twenty-first century has witnessed a myriad of changes that were adopted to predict whether a compound is likely to be successful, or conversely enable identification of molecules with liabilities as early as possible. These changes include integration of in silico strategies for lead design and optimization that perform complementary roles to that of the traditional in vitro and in vivo approaches. The in silico models are facilitated by the availability of large datasets associated with high-throughput screening, bioinformatics algorithms to mine and annotate the data from a target perspective, and chemoinformatics methods to integrate chemistry methods into lead design process. This chapter highlights the applications of some of these methods and their limitations. We hope this serves as an introduction to in silico drug discovery.
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Affiliation(s)
- Ahmet Sacan
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, USA
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Kortagere S, Lill M, Kerrigan J. Role of computational methods in pharmaceutical sciences. Methods Mol Biol 2012; 929:21-48. [PMID: 23007425 DOI: 10.1007/978-1-62703-050-2_3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Over the past two decades computational methods have eased up the financial and experimental burden of early drug discovery process. The in silico methods have provided support in terms of databases, data mining of large genomes, network analysis, systems biology on the bioinformatics front and structure-activity relationship, similarity analysis, docking, and pharmacophore methods for lead design and optimization. This review highlights some of the applications of bioinformatics and chemoinformatics methods that have enriched the field of drug discovery. In addition, the review also provided insights into the use of free energy perturbation methods for efficiently computing binding energy. These in silico methods are complementary and can be easily integrated into the traditional in vitro and in vivo methods to test pharmacological hypothesis.
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Affiliation(s)
- Sandhya Kortagere
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA.
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7
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Bhadbhade MM, Kishore R. Intramolecular CH···O Hydrogen-bond mediated stabilization of a Cis-DPro imide-bond in a stereocontrolled heterochiral model peptide. Biopolymers 2011; 97:73-82. [DOI: 10.1002/bip.21705] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 07/21/2011] [Indexed: 11/06/2022]
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8
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Li Manni G, Barone G, Duca D, Murzin DY. Systematic conformational search analysis of the SRR and RRR epimers of 7-hydroxymatairesinol. J PHYS ORG CHEM 2010. [DOI: 10.1002/poc.1595] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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9
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Xia J, Margulis CJ. Computational Study of the Conformational Structures of Saccharides in Solution Based on J Couplings and the “Fast Sugar Structure Prediction Software”. Biomacromolecules 2009; 10:3081-8. [DOI: 10.1021/bm900756q] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Junchao Xia
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242
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Xia J, Margulis C. A tool for the prediction of structures of complex sugars. JOURNAL OF BIOMOLECULAR NMR 2008; 42:241-256. [PMID: 18953494 DOI: 10.1007/s10858-008-9279-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2008] [Accepted: 09/11/2008] [Indexed: 05/27/2023]
Abstract
In two recent back to back articles(Xia et al., J Chem Theory Comput 3:1620-1628 and 1629-1643, 2007a, b) we have started to address the problem of complex oligosaccharide conformation and folding. The scheme previously presented was based on exhaustive searches in configuration space in conjunction with Nuclear Overhauser Effect (NOE) calculations and the use of a complex rotameric library that takes branching into account. NOEs are extremely useful for structural determination but only provide information about short range interactions and ordering. Instead, the measurement of residual dipolar couplings (RDC), yields information about molecular ordering or folding that is long range in nature. In this article we show the results obtained by incorporation RDC calculations into our prediction scheme. Using this new approach we are able to accurately predict the structure of six human milk sugars: LNF-1, LND-1, LNF-2, LNF-3, LNnT and LNT. Our exhaustive search in dihedral configuration space combined with RDC and NOE calculations allows for highly accurate structural predictions that, because of the non-ergodic nature of these molecules on a time scale compatible with molecular dynamics simulations, are extremely hard to obtain otherwise (Almond et al., Biochemistry 43:5853-5863, 2004). Molecular dynamics simulations in explicit solvent using as initial configurations the structures predicted by our algorithm show that the histo-blood group epitopes in these sugars are relatively rigid and that the whole family of oligosaccharides derives its conformational variability almost exclusively from their common linkage (beta-D: -GlcNAc-(1-->3)-beta-D: -Gal) which can exist in two distinct conformational states. A population analysis based on the conformational variability of this flexible glycosidic link indicates that the relative population of the two distinct states varies for different human milk oligosaccharides.
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Affiliation(s)
- Junchao Xia
- Department of Chemistry, University of Iowa, Iowa City 52242, USA
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11
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Xia J, Daly RP, Chuang FC, Parker L, Jensen JH, Margulis CJ. Sugar Folding: A Novel Structural Prediction Tool for Oligosaccharides and Polysaccharides 2. J Chem Theory Comput 2007; 3:1629-43. [DOI: 10.1021/ct700034q] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Junchao Xia
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, and Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Ryan P. Daly
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, and Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Feng-Chuan Chuang
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, and Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Laura Parker
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, and Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Jan H. Jensen
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, and Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Claudio J. Margulis
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, and Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
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Cioci G, Rivet A, Koca J, Pérez S. Conformational analysis of complex oligosaccharides: the CICADA approach to the uromodulin O-glycans. Carbohydr Res 2004; 339:949-59. [PMID: 15010302 DOI: 10.1016/j.carres.2003.12.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2003] [Accepted: 12/12/2003] [Indexed: 11/26/2022]
Abstract
Uromodulin is the pregnancy-associated Tamm-Horsfall glycoprotein, with the enhanced ability to inhibit T-cell proliferation. Pregnancy-associated structural changes mainly occur in the O-glycosylation of this glycoprotein. These include up to 12 glycan structures, made up of an unusual core type 2 sequence terminated with one, two, or three sialyl Lewis(x) sequences; this type of O-glycans could serve as E- and P-selectin ligands. The present work focuses on the most complex one; a tetradecamer made up of a type 2 core carrying three sialyl Lewis(x) branches. Five different monosaccharides are assembled by 14 glycosidic linkages. The conformational behavior of the constituting disaccharide segments was evaluated using the flexible residue procedure of the MM3 molecular mechanics procedure. For each disaccharide, the adiabatic energy surface, along with the local energy minima were established. All these results were used for the generation, prior to complete optimization of the tetradecamer. This was followed by a complete exploration of conformational hyperspace throughout the use of the single coordinate method as implemented in the CICADA program. Despite the potential flexibility of the tetradecasaccharide, only four conformational families occur, accounting for more than 95% of the total low energy conformations. For each family, the molecular properties (electrostatic, lipophilicity, and hydrogen potential) were studied. The shape of the tetradecasaccharide is best described as a flat ribbon, flanked by three branches having terminal sialyl residues. Two of the branches interact through nonbonded interactions, bringing further energy stabilization, and limiting the conformational flexibility of the sialyl residues. Only one branch maintains the original conformational features of sialyl Lewis(x). This O-glycan can be seen as a fascinating example of 'dendrimeric' structure, where the spatial arrangement of three S-Le(x) epitopes may favor its complementary 'presentations' for the interactions with E- and P-selectins.
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Affiliation(s)
- Gianluca Cioci
- Centre de Recherches sur les Macromolécules Végétales, CNRS and Joseph Fourier University, IFR 2607, BP#53, F-38041 Grenoble, France.
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Clément MJ, Imberty A, Phalipon A, Pérez S, Simenel C, Mulard LA, Delepierre M. Conformational studies of the O-specific polysaccharide of Shigella flexneri 5a and of four related synthetic pentasaccharide fragments using NMR and molecular modeling. J Biol Chem 2003; 278:47928-36. [PMID: 12925526 DOI: 10.1074/jbc.m308259200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
As part of a program for the development of synthetic vaccines against the pathogen Shigella flexneri, we used a combination of NMR and molecular modeling methods to study the conformations of the O-specific polysaccharide (O-SP) of S. flexneri 5a and of four related synthetic pentasaccharide fragments. The NMR study, based on the analysis of 1H and 13C chemical shifts, the evaluation of inter-residue distances, and the measurement of one- and three-bond heteronuclear coupling constants, showed that the conformation of one of the four pentasaccharides is similar to that of the native O-SP in solution. Interestingly, inhibition enzyme-linked immunosorbent assay demonstrated that a protective monoclonal antibody specific for S. flexneri 5a has a greater affinity for this pentasaccharide than for the others. We carried out a complete conformational search on the pentasaccharides using the CICADA algorithm interfaced with MM3 force field. We calculated Boltzmann-averaged inter-residue distances and 3JC,H coupling constants for the different conformational families and compared the results with NMR data for all pentasaccharides. Our experimental data are consistent with only one conformational family. We also used molecular modeling data to build models of the O-SP with the molecular builder program POLYS. The models that are in agreement with NMR data adopt right-handed 3-fold helical structures in which the branched glucosyl residue points outwards.
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Affiliation(s)
- Marie-Jeanne Clément
- Unité de RMN des Biomolécules, URA CNRS 2185, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris, Cedex 15, France
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14
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Fadrná E, Koca J. Conformational flexibility of two RNA trimers explored by computational tools and database search. J Biomol Struct Dyn 2003; 20:715-32. [PMID: 12643774 DOI: 10.1080/07391102.2003.10506888] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Two RNA sequences, AAA and AUG, were studied by the conformational search program CICADA and by molecular dynamics (MD) in the framework of the AMBER force field, and also via thorough PDB database search. CICADA was used to provide detailed information about conformers and conformational interconversions on the energy surfaces of the above molecules. Several conformational families were found for both sequences. Analysis of the results shows differences, especially between the energy of the single families, and also in flexibility and concerted conformational movement. Therefore, several MD trajectories (altogether 16 ns) were run to obtain more details about both the stability of conformers belonging to different conformational families and about the dynamics of the two systems. Results show that the trajectories strongly depend on the starting structure. When the MD start from the global minimum found by CICADA, they provide a stable run, while MD starting from another conformational family generates a trajectory where several different conformational families are visited. The results obtained by theoretical methods are compared with the thorough database search data. It is concluded that all except for the highest energy conformational families found in theoretical result also appear in experimental data. Registry numbers: adenylyl-(3' --> 5')-adenylyl-(3' --> 5')-adenosine [917-44-2] adenylyl-(3' --> 5')-uridylyl-(3' --> 5')-guanosine [3494-35-7].
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Affiliation(s)
- Eva Fadrná
- National Centre for Biomolecular Research, Department of Organic Chemistry, Faculty of Science, Masaryk University, Kotlrsk 2, 611 37 Brno, Czech Republic.
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15
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Imberty A, Pérez S. Structure, conformation, and dynamics of bioactive oligosaccharides: theoretical approaches and experimental validations. Chem Rev 2000; 100:4567-88. [PMID: 11749358 DOI: 10.1021/cr990343j] [Citation(s) in RCA: 212] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- A Imberty
- Centre de Recherches sur les Macromolécules Végétales (CERMAV-CNRS, affiliated with Joseph Fourier Université), 601 rue de la Chimie, BP 53, F-38041 Grenoble Cedex 9
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16
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Picard C, Gruza J, Derouet C, Renard CM, Mazeau K, Koca J, Imberty A, Hervé Du Penhoat C. A conformational study of the xyloglucan oligomer, XXXG, by NMR spectroscopy and molecular modeling. Biopolymers 2000; 54:11-26. [PMID: 10799977 DOI: 10.1002/(sici)1097-0282(200007)54:1<11::aid-bip20>3.0.co;2-d] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A structural study of the XXXG xyloglucan heptasaccharide (X = alpha-D-Xylp(1 --> 6)-beta-D-Glcp and G = beta-D-Glcp) isolated from apple fruit has been undertaken with nmr and molecular mechanics methods. Quantitative 400 MHz nmr data including nuclear Overhauser effect spectroscopy (NOESY) volumes were recorded at both 6 and 20 degrees C. In spite of severe overlapping of resonances, it was possible to estimate summed NOEs for the majority of the anomeric and glucosyl methylene protons. An ensemble-average population of preferred geometries has been established with the CICADA conformational searching algorithm associated with the MM3 force field. Comparison of the theoretical data obtained by back-calculation of the NOESY volumes from the ensemble-average distance matrix program and motional models based on the Stokes-Einstein-Debye relation satisfactorily reproduce the experimental data. Conformational averaging about the mainchain glycosidic linkages includes both the syn and anti conformers and a minor gauche-gauche population is highly probable. The theoretical data overestimate the syn preference of the Glc(c) --> Glc(b) linkage as well as the Glc(c) GT rotamer population. Finally, both the motional models and the conformational search indicate a fairly rigid backbone and greater flexiblity for the xylose side chains.
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Affiliation(s)
- C Picard
- Département de Chimie, URA 1679, Ecole Normale Supérieure, 24 Rue Lhomond, 75231 Paris Cedex 05, France
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Koca J, Ludin M, Pérez S, Imberty A. Single-coordinate-driving method for molecular docking: application to modeling of guest inclusion in cyclodextrin. J Mol Graph Model 2000; 18:108-18. [PMID: 10994514 DOI: 10.1016/s1093-3263(00)00042-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
An extension of the computer program CICADA has been developed that allows us to use the single-coordinate-driving (SCD) method for flexible molecular docking. The docking procedure is composed of three independent space rotations, three independent translations, and the torsions selected by the user. One of the coordinates is driven; the other coordinates are relaxed. This procedure follows low-energy wells on the potential energy surface of the entire system. The program allows us to dock more than one ligand molecule to the receptor. We ran two test examples, docking N,N-dimethylformamide into alpha-cyclodextrin and R-phenoxypropionic acid into beta-cyclodextrin. The test examples showed that the SCD approach is able to overcome high-energy barriers and to cover the entire box within which the search is performed. The limitations of molecular dynamics docking in comparison with our approach also are discussed. The philosophy of the newly developed approach is not only to find the best dock for the receptor-ligand(s) system, but also to describe all the important binding modes and provide a good starting point for studying the dynamics within the cavity during the docking process.
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Affiliation(s)
- J Koca
- Laboratory of Biomolecular Structure and Dynamics, Faculty of Science, Masaryk University, Brno, Czech Republic
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18
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Černohorský M, Kettou S, Koča J. VADER: New Software for Exploring Interconversions on Potential Energy Surfaces. ACTA ACUST UNITED AC 1999. [DOI: 10.1021/ci9804138] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Martin Černohorský
- Institute of Computer Science, Masaryk University, 602 00 Brno, Czech Republic, Department of Organic Chemistry, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic, and Laboratory of Biomolecular Structure and Dynamics, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic
| | - Sofiane Kettou
- Institute of Computer Science, Masaryk University, 602 00 Brno, Czech Republic, Department of Organic Chemistry, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic, and Laboratory of Biomolecular Structure and Dynamics, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic
| | - Jaroslav Koča
- Institute of Computer Science, Masaryk University, 602 00 Brno, Czech Republic, Department of Organic Chemistry, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic, and Laboratory of Biomolecular Structure and Dynamics, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic
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19
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Petrová P, Koča J, Imberty A. Potential Energy Hypersurfaces of Nucleotide Sugars: Ab Initio Calculations, Force-Field Parametrization, and Exploration of the Flexibility. J Am Chem Soc 1999. [DOI: 10.1021/ja983854g] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Pavla Petrová
- Contribution from the Laboratory of Biomolecular Structure and Dynamics and Department of Organic Chemistry, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic, and Centre de Recherches sur les Macromolécules Végétales-CNRS (affiliated with Université Joseph Fourier), BP 53, F-38041 Grenoble Cedex 9, France
| | - Jaroslav Koča
- Contribution from the Laboratory of Biomolecular Structure and Dynamics and Department of Organic Chemistry, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic, and Centre de Recherches sur les Macromolécules Végétales-CNRS (affiliated with Université Joseph Fourier), BP 53, F-38041 Grenoble Cedex 9, France
| | - Anne Imberty
- Contribution from the Laboratory of Biomolecular Structure and Dynamics and Department of Organic Chemistry, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic, and Centre de Recherches sur les Macromolécules Végétales-CNRS (affiliated with Université Joseph Fourier), BP 53, F-38041 Grenoble Cedex 9, France
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