Protein—ligand structure determination with the NMR molecular replacement tool, NMR2

Orts, Julien; Riek, Roland

doi:10.1007/s10858-020-00324-y

Cited by 9 publications

(7 citation statements)

References 44 publications

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“…

A precision of

% dictates the value of upper limit and lower limit distance restraints with the upper limit distance restraint being (

(extracted distance) and the lower limit distance restraint being (

(extracted distance).

A target function (TF) of less than 2 Å

within

is considered a successful structure determination .

The total number of degenerate lowest energy conformers is the number of distinct orientations of the ligand within the binding pocket that were obtained with a CYANA target function (TF) of 0 Å

from

calculations.…”

Section: Resultsmentioning

confidence: 99%

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An improved, time-efficient approach to extract accurate distance restraints for NMR² structure calculation

et al. 2022

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Abstract. Exact nuclear Overhauser enhancement (eNOE) yields highly accurate, ensemble averaged 1H–1H distance restraints with an accuracy of up to 0.1 Å for the multi-state structure determination of proteins as well as for nuclear magnetic resonance molecular replacement (NMR2) to determine the structure of the protein–ligand interaction site in a time-efficient manner. However, in the latter application, the acquired eNOEs lack the obtainable precision of 0.1 Å because of the asymmetrical nature of the filtered nuclear Overhauser enhancement spectroscopy (NOESY) experiment used in NMR2. This error is further propagated to the eNOE equations used to fit and extract the distance restraints. In this work, a new analysis method is proposed to obtain inter-molecular distance restraints from the filtered NOESY spectrum more accurately and intuitively by dividing the NOE cross peak by the corresponding diagonal peak of the ligand. The method termed diagonal-normalised eNOEs was tested on the data acquired by Torres et al. (2020) on the complex of PIN1 and a small, weak-binding phenylimidazole fragment. NMR2 calculations performed using the distances derived from diagonal-normalised eNOEs yielded the right orientation of the fragment in the binding pocket and produced a structure that more closely resembles the benchmark X-ray structure (2XP6) (Potter et al., 2010) with an average heavy-atom root-mean-square deviation (RMSD) of 1.681 Å with respect to it, when compared to the one produced with traditional NMR2 with an average heavy atom RMSD of 3.628 Å. This is attributed to the higher precision of the evaluated distance restraints.

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“…

A precision of

% dictates the value of upper limit and lower limit distance restraints with the upper limit distance restraint being (

(extracted distance) and the lower limit distance restraint being (

(extracted distance).

A target function (TF) of less than 2 Å

within

is considered a successful structure determination .

The total number of degenerate lowest energy conformers is the number of distinct orientations of the ligand within the binding pocket that were obtained with a CYANA target function (TF) of 0 Å

from

calculations.…”

Section: Resultsmentioning

confidence: 99%

“…Using

, Orts et al were able to solve the structure of various complexes accurately (up to 1 Å) within a few days of measurement and analysis. The

structure calculation workflow is detailed in and relies on acquiring precise inter-molecular distance restraints.…”

Section: Introductionmentioning

confidence: 99%

An improved, time-efficient approach to extract accurate distance restraints for NMR² structure calculation

et al. 2022

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“…Protein deuteration will also improve the quality of the NOE data. The NOE data should be processed and analyzed according to the previously reported protocols and fed to the N MR 2 software ( N MR 2 software v1 from Orts et al [ 29 ], Zurich, Switzerland). Priority should be given to the fragments having the highest topological parameters r l and r w .…”

Section: Discussionmentioning

confidence: 99%

A Benchmark Study of Protein–Fragment Complex Structure Calculations with NMR2

Torres,

Stadler,

Kwiatkowski

et al. 2023

IJMS

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Protein–fragment complex structures are particularly sought after in medicinal chemistry to rationally design lead molecules. These structures are usually derived using X-ray crystallography, but the failure rate is non-neglectable. NMR is a possible alternative for the calculation of weakly interacting complexes. Nevertheless, the time-consuming protein signal assignment step remains a barrier to its routine application. NMR Molecular Replacement (NMR2) is a versatile and rapid method that enables the elucidation of a protein–ligand complex structure. It has been successfully applied to peptides, drug-like molecules, and more recently to fragments. Due to the small size of the fragments, ca < 300 Da, solving the structures of the protein–fragment complexes is particularly challenging. Here, we present the expected performances of NMR2 when applied to protein–fragment complexes. The NMR2 approach has been benchmarked with the SERAPhic fragment library to identify the technical challenges in protein–fragment NMR structure calculation. A straightforward strategy is proposed to increase the method’s success rate further. The presented work confirms that NMR2 is an alternative method to X-ray crystallography for solving protein–fragment complex structures.

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“…Lastly, choosing a proper input structure is required which can be either X-ray or NMR structures in apo form, with another bound ligand, or a homolog to the protein of interest. Then the NMR 2 program analyzes for all possible partial assignments (such as methyl groups of a protein) and calculates the complex structures for all options [ 403 , 404 ]. This method was already successfully used to resolve complex structures in case of slow and fast exchange ligands [ 403 , 404 , 405 , 406 ].…”

Section: Nmr Methods For Drug Discovery and Drug Developmentmentioning

confidence: 99%

NMR as a “Gold Standard” Method in Drug Design and Discovery

et al. 2020

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Studying disease models at the molecular level is vital for drug development in order to improve treatment and prevent a wide range of human pathologies. Microbial infections are still a major challenge because pathogens rapidly and continually evolve developing drug resistance. Cancer cells also change genetically, and current therapeutic techniques may be (or may become) ineffective in many cases. The pathology of many neurological diseases remains an enigma, and the exact etiology and underlying mechanisms are still largely unknown. Viral infections spread and develop much more quickly than does the corresponding research needed to prevent and combat these infections; the present and most relevant outbreak of SARS-CoV-2, which originated in Wuhan, China, illustrates the critical and immediate need to improve drug design and development techniques. Modern day drug discovery is a time-consuming, expensive process. Each new drug takes in excess of 10 years to develop and costs on average more than a billion US dollars. This demonstrates the need of a complete redesign or novel strategies. Nuclear Magnetic Resonance (NMR) has played a critical role in drug discovery ever since its introduction several decades ago. In just three decades, NMR has become a “gold standard” platform technology in medical and pharmacology studies. In this review, we present the major applications of NMR spectroscopy in medical drug discovery and development. The basic concepts, theories, and applications of the most commonly used NMR techniques are presented. We also summarize the advantages and limitations of the primary NMR methods in drug development.

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Protein—ligand structure determination with the NMR molecular replacement tool, NMR2

Cited by 9 publications

References 44 publications

An improved, time-efficient approach to extract accurate distance restraints for NMR² structure calculation

An improved, time-efficient approach to extract accurate distance restraints for NMR² structure calculation

A Benchmark Study of Protein–Fragment Complex Structure Calculations with NMR2

NMR as a “Gold Standard” Method in Drug Design and Discovery

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Protein—ligand structure determination with the NMR molecular replacement tool, NMR2

Cited by 9 publications

References 44 publications

An improved, time-efficient approach to extract accurate distance restraints for NMR2 structure calculation

An improved, time-efficient approach to extract accurate distance restraints for NMR2 structure calculation

A Benchmark Study of Protein–Fragment Complex Structure Calculations with NMR2

NMR as a “Gold Standard” Method in Drug Design and Discovery

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Product

Resources

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An improved, time-efficient approach to extract accurate distance restraints for NMR² structure calculation

An improved, time-efficient approach to extract accurate distance restraints for NMR² structure calculation