Complexity in molecular recognition

Grunenberg, Jörg

doi:10.1039/c1cp20097f

Cited by 23 publications

(21 citation statements)

References 66 publications

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“…These endpoints were nevertheless characterized by elaborate scans of the relevant conformational hyper surface. Further, since in cases of high chemical similarity, our assumption is that the enthalpy governs the recognition process anyway [ 34 – 35 ]. We thus further assumed a constant entropic contribution to the Gibbs–Helmholtz equation for all candidates, focusing on the realistic description of all enthalpic contributions.…”

Section: Overall Strategymentioning

confidence: 99%

Effective in silico prediction of new oxazolidinone antibiotics: force field simulations of the antibiotic–ribosome complex supervised by experiment and electronic structure methods

Grunenberg

Licari

2016

Beilstein J. Org. Chem.

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SummaryWe propose several new and promising antibacterial agents for the treatment of serious Gram-positive infections. Our predictions rely on force field simulations, supervised by first principle calculations and available experimental data. Different force fields were tested in order to reproduce linezolid's conformational space in terms of a) the isolated and b) the ribosomal bound state. In a first step, an all-atom model of the bacterial ribosome consisting of nearly 1600 atoms was constructed and evaluated. The conformational space of 30 different ribosomal/oxazolidinone complexes was scanned by stochastic methods, followed by an evaluation of their enthalpic penalties or rewards and the mechanical strengths of the relevant hydrogen bonds (relaxed force constants; compliance constants). The protocol was able to reproduce the experimentally known enantioselectivity favoring the S-enantiomer. In a second step, the experimentally known MIC values of eight linezolid analogues were used in order to crosscheck the robustness of our model. In a final step, this benchmarking led to the prediction of several new and promising lead compounds. Synthesis and biological evaluation of the new compounds are on the way.

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Section: Overall Strategymentioning

confidence: 99%

Effective in silico prediction of new oxazolidinone antibiotics: force field simulations of the antibiotic–ribosome complex supervised by experiment and electronic structure methods

Grunenberg

Licari

2016

Beilstein J. Org. Chem.

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“…This unique operational mode of SPs has great potential to make direct experimental observations and help answer more fundamental questions on the physical dynamics of proteins and the opportunities to explore the mutual interaction between biological components and surfaces. [ 42 ] Such operational mode may also offer the real possibility of many new applications, such as, the experimental real‐time study of single bimolecular binding kinetics, detection of ultra‐low concentration (below the fM level) of proteins and small molecules for the early diagnosis of various diseases. [ 43,44 ]…”

Section: Discussionmentioning

confidence: 99%

Generation of a Conjoint Surface Plasmon by an Infrared Nano‐Antenna Array

Allsop

Mou

Neal

et al. 2020

Advanced Photonics Research

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Localized surface plasmons (LSP) excited by optical fields have many potential applications resulting from their ability in detecting ultra‐small, ambient refractive index change. Current methods using surface nano‐patterning by means of lithography have given rise to LSP of limited propagation and interaction lengths, meaning that practical applications remain challenging. This article describes a new all‐optical method of generating LSP by means of a carefully fabricated low‐dimensional nano‐structured material using a direct‐write photochemical lithography. It is shown that the resulting array of localized SPs combine or “Conjoin” to have an unprecedented large interaction length, via coupled evanescent fields, giving rise to superior spectral sensitivities; several orders of magnitude better than those quoted elsewhere and reaching 6 × 103 nm RIU−1 in the aqueous regime and 104 nm RIU−1 in the gaseous regime. Numerical modeling is performed that shows this design of plasmonic platform is capable of producing sensitivities of 105–106 nm RIU−1. It is believed the results achieved in this investigation show that a unique conjoint SP operational mode will significantly impact areas of interest, such as single molecular dynamics, drug delivery systems, etc.

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“…The efficiency of this method was tested on both the covalent (see, e.g.,R efs. [94,95] and references therein) and noncovalent [96][97][98][99][100] bonds. In the following discussion, we use the relaxedf orce constants( RFCs), that is, the inverse values of compliance constants C ij calculated from Equation (1) (see Computational Methodology), to estimate the strength of the glycosidicbond.…”

Section: Glycosidic Bond Strength In Ai and Bi Dna-likeconformers Of mentioning

confidence: 99%

Substituting CF₂for O4′ in Components of Nucleic Acids: Towards Systems with Reduced Propensity to Form Abasic Lesions

Yurenko

Novotný

Sklenář

et al. 2015

Chemistry A European J

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Intrinsic structural features and energetics of nucleotides containing variously fluorinated sugars as potential building blocks of DNA duplexes and quadruplexes are explored systematically using the modern methods of density functional theory (DFT) and quantum chemical topology (QCT). Our results suggest that fluorination at the 2'-β or 2'-α,β positions somewhat stabilizes in vacuo the AI relative to the BI conformations. In contrast, substitution of the CF2 group for the O4' atom (O4'-CF2 modification) leads to a preference of the BI relative to AI DNA-like conformers. All the studied modifications result in a noticeable increase in the stability of the glycosidic bond [estimated by the relaxed force constants (RFC) approach], with particularly encouraging results for the O4'-CF2 derivative. Consequently, the O4'-CF2 modified systems are suggested and explored as promising scaffolds for the development of duplex and quadruplex structures with reduced propensity to form abasic lesions and to undergo DNA damage.

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Complexity in molecular recognition

Cited by 23 publications

References 66 publications

Effective in silico prediction of new oxazolidinone antibiotics: force field simulations of the antibiotic–ribosome complex supervised by experiment and electronic structure methods

Effective in silico prediction of new oxazolidinone antibiotics: force field simulations of the antibiotic–ribosome complex supervised by experiment and electronic structure methods

Generation of a Conjoint Surface Plasmon by an Infrared Nano‐Antenna Array

Substituting CF₂for O4′ in Components of Nucleic Acids: Towards Systems with Reduced Propensity to Form Abasic Lesions

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Complexity in molecular recognition

Cited by 23 publications

References 66 publications

Effective in silico prediction of new oxazolidinone antibiotics: force field simulations of the antibiotic–ribosome complex supervised by experiment and electronic structure methods

Effective in silico prediction of new oxazolidinone antibiotics: force field simulations of the antibiotic–ribosome complex supervised by experiment and electronic structure methods

Generation of a Conjoint Surface Plasmon by an Infrared Nano‐Antenna Array

Substituting CF2for O4′ in Components of Nucleic Acids: Towards Systems with Reduced Propensity to Form Abasic Lesions

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Substituting CF₂for O4′ in Components of Nucleic Acids: Towards Systems with Reduced Propensity to Form Abasic Lesions