A drug discovery toolbox for Nuclear Magnetic Resonance (NMR) characterization of ligands and their targets

LeBlanc, Regan M.; Mesleh, Michael F.

doi:10.1016/j.ddtec.2020.11.008

Cited by 6 publications

(4 citation statements)

References 74 publications

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“…Structural biology finds important applications in the field of drug research. NMR spectroscopy is an important technique in fragment-based drug-design − or in structure–activity relationship studies. ,, In-cell solution NMR studies can help in characterizing drug binding or drug engagement in cells, as we will show in this section. Solid-state NMR spectroscopy has had important contributions while using cellular samples or membrane extracts.…”

Section: What Benefits For Therapeutic Purposes?mentioning

confidence: 99%

In-Cell Structural Biology by NMR: The Benefits of the Atomic Scale

Theillet

2022

Chem. Rev.

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In-cell structural biology aims at extracting structural information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promises and is already providing new facts and outlooks of interest at both fundamental and applied levels. NMR spectroscopy has important contributions on this stage: it brings information on a broad variety of nuclei at the atomic scale, which ensures its great versatility and uniqueness. Here, we detail the methods, the fundamental knowledge and the applications in biomedical engineering related to in-cell NMR. We finally propose a brief overview of the main other techniques in the field (EPR, smFRET, cryo-ET…) to draw some advisable developments for in-cell NMR. In the era of large-scale screenings and deep learning, both accurate and qualitative experimental evidences are as essential as ever to understand the interior life of cells. In-cell structural biology by NMR spectroscopy can generate such a knowledge, and it does so at the atomic scale. This review is meant to deliver comprehensive but accessible information, with advanced technical details and reflections on the methods, the nature of the results and the future of the field. CONTENTS 5.1.1. In-cell EPR 5.1.2. In-cell FRET microscopy 5.1.3. Mass-spectrometry 5.1.4. Cryo-ET 5.2. The specific benefits of in-cell NMR 5.3. The future technical challenges of in-cell NMR 6. Conclusion Author Information

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Section: What Benefits For Therapeutic Purposes?mentioning

confidence: 99%

In-Cell Structural Biology by NMR: The Benefits of the Atomic Scale

Theillet

2022

Chem. Rev.

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“…This occurrence highlights that library quality control should also be performed in media used in experiments, over an experimentally relevant time-frame. This could be done concurrently with compound screening in the case of ligand detected NMR [25–26]. However, other common screening techniques such as SPR and thermal shift assays would not be able to detect compound degradation such as that presented here.…”

Section: Discussionmentioning

confidence: 99%

“…This could be done concurrently with compound screening in the case of ligand detected NMR [25][26]. However, other common screening techniques such as SPR and thermal shift assays…”

Section: Discussionmentioning

confidence: 99%

Fortuitousin vitrocompound degradation produces a tractable hit againstMycobacterium tuberculosisdethiobiotin synthetase: a cautionary tale of what goes in, does not always come out

Salaemae

Thompson

Gaiser³

et al. 2023

Preprint

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We previously reported potent ligands and inhibitors of Mycobacterium tuberculosis dethiobiotin synthetase (MtDTBS), a promising target for antituberculosis drug development (Schumannet al., ACS Chem Biol. 2021, 16, 2339-2347); here the unconventional origin of the fragment compound they were derived from is described for the first time. Compound1(9b-hydroxy-6b,7,8,9,9a,9b-hexahydrocyclopenta[3,4]cyclobuta[1,2-c]chromen-6(6aH)-one), identified byin silicofragment screen, was subsequently shown by surface plasmon resonance to have dose-responsive binding (KD0.6 mM). Clear electron density was revealed in the DAPA substrate binding pocket, when1was soaked intoMtDTBS crystals, but the density was inconsistent with the structure of1. Here we show the lactone of1hydrolyses to carboxylic acid2under basic conditions, including those of the crystallography soak, with subsequent ring-opening of the component cyclobutane ring to form cyclopentylacetic acid3. Crystals soaked directly with authentic3produced electron density that matched that of crystals soaked with presumed1, confirming the identity of the bound ligand. The synthetic utility of fortuitously formed3enabled subsequent compound development into nanomolar inhibitors. Our findings represent an example of chemical modification within drug discovery assays and demonstrate the value of high-resolution structural data in the fragment hit validation process.

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“…This occurrence highlights that library quality control should also be performed in media used in experiments over an experimentally relevant time frame. This could be done concurrently with compound screening in the case of ligand-detected NMR. , However, other common screening techniques, such as SPR and thermal shift assays, would not be able to detect compound degradation such as that presented here. Parallel analysis of promising hits under the same screening conditions, for example by NMR or LC/MS, may be beneficial in these cases.…”

Section: Discussionmentioning

confidence: 99%

Fortuitous In Vitro Compound Degradation Produces a Tractable Hit against Mycobacterium tuberculosis Dethiobiotin Synthetase: A Cautionary Tale of What Goes In Does Not Always Come Out

Salaemae,

Thompson,

Gaiser

et al. 2023

ACS Chem. Biol.

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We previously reported potent ligands and inhibitors of Mycobacterium tuberculosis dethiobiotin synthetase (MtDTBS), a promising target for antituberculosis drug development (Schumann et al., ACS Chem Biol. 2021, 16, 2339−2347; here, the unconventional origin of the fragment compound they were derived from is described for the first time. 7,8,9,9a,9bhexahydrocyclopenta[3,4]cyclobuta[1,2-c]chromen-6(6aH)-one), identified by an in silico fragment screen, was subsequently shown by surface plasmon resonance to have dose-responsive binding (K D = 0.6 mM). Clear electron density was revealed in the DAPA substrate binding pocket when 1 was soaked into MtDTBS crystals, but the density was inconsistent with the structure of 1. Here, we show that the lactone of 1 hydrolyzes to a carboxylic acid (2) under basic conditions, including those of the crystallography soak, with a subsequent ring opening of the component cyclobutane ring forming a cyclopentylacetic acid (3). Crystals soaked directly with authentic 3 produced an electron density that matched that of crystals soaked with presumed 1, confirming the identity of the bound ligand. The synthetic utility of fortuitously formed 3 enabled the subsequent compound development of nanomolar inhibitors. Our findings represent an example of chemical modification within drug discovery assays and demonstrate the value of high-resolution structural data in the fragment hit validation process.

show abstract

A drug discovery toolbox for Nuclear Magnetic Resonance (NMR) characterization of ligands and their targets

Cited by 6 publications

References 74 publications

In-Cell Structural Biology by NMR: The Benefits of the Atomic Scale

In-Cell Structural Biology by NMR: The Benefits of the Atomic Scale

Fortuitousin vitrocompound degradation produces a tractable hit againstMycobacterium tuberculosisdethiobiotin synthetase: a cautionary tale of what goes in, does not always come out

Fortuitous In Vitro Compound Degradation Produces a Tractable Hit against Mycobacterium tuberculosis Dethiobiotin Synthetase: A Cautionary Tale of What Goes In Does Not Always Come Out

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