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NMR in drug discovery on membrane proteins

Wirmer-Bartoschek, Julia ; Bartoschek, Stefan

Future Science Ltd ; 2012

In: Future Medicinal Chemistry Vol. 4, No. 7 ( 2012-05), p. 869-875

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In: Future Medicinal Chemistry, Future Science Ltd, Vol. 4, No. 7 ( 2012-05), p. 869-875

Abstract: Drug discovery on membrane proteins is still a difficult task, despite the recognized importance of membrane proteins as drug targets. Here, we present an overview of NMR methods available for structure-based drug design on membrane proteins. NMR spectroscopy is capable of identifying potential binders in screening and defining their relative binding constants, binding stoichiometry, conformation in the binding pocket and the relative binding orientation for binders of different series. Examples are given in the review highlighting the potential of NMR spectroscopy for future progress in drug discovery on membrane proteins.

Type of Medium: Online Resource

ISSN: 1756-8919 , 1756-8927

URL: Article

DOI: 10.4155/fmc.12.46

Language: English

Publisher: Future Science Ltd

Publication Date: 2012

SSG: 15,3

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Comprehensive Fragment Screening of the SARS‐CoV‐2 Proteome Explores Novel Chemical Space for Drug Development

Berg, Hannes ; Wirtz Martin, Maria A. ; Altincekic, Nadide ; [et al.]

Wiley ; 2022

In: Angewandte Chemie Vol. 134, No. 46 ( 2022-11-14)

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In: Angewandte Chemie, Wiley, Vol. 134, No. 46 ( 2022-11-14)

Abstract: SARS‐CoV‐2 (SCoV2) and its variants of concern pose serious challenges to the public health. The variants increased challenges to vaccines, thus necessitating for development of new intervention strategies including anti‐virals. Within the international Covid19‐NMR consortium, we have identified binders targeting the RNA genome of SCoV2. We established protocols for the production and NMR characterization of more than 80 % of all SCoV2 proteins. Here, we performed an NMR screening using a fragment library for binding to 25 SCoV2 proteins and identified hits also against previously unexplored SCoV2 proteins. Computational mapping was used to predict binding sites and identify functional moieties (chemotypes) of the ligands occupying these pockets. Striking consensus was observed between NMR‐detected binding sites of the main protease and the computational procedure. Our investigation provides novel structural and chemical space for structure‐based drug design against the SCoV2 proteome.

Type of Medium: Online Resource

ISSN: 0044-8249 , 1521-3757

URL: Issue

URL: Article

DOI: 10.1002/ange.v134.46

DOI: 10.1002/ange.202205858

RVK:

VA 2100

RVK:

VN 5020

Language: English

Publisher: Wiley

Publication Date: 2022

detail.hit.zdb_id: 505868-5

detail.hit.zdb_id: 506609-8

detail.hit.zdb_id: 514305-6

detail.hit.zdb_id: 505872-7

detail.hit.zdb_id: 1479266-7

detail.hit.zdb_id: 505867-3

detail.hit.zdb_id: 506259-7

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1H, 13C and 15N chemical shift assignment of the stem-loops 5b + c from the 5′-UTR of SARS-CoV-2

Mertinkus, Klara R. ; Grün, J. Tassilo ; Altincekic, Nadide ; [et al.]

Springer Science and Business Media LLC ; 2022

In: Biomolecular NMR Assignments Vol. 16, No. 1 ( 2022-04), p. 17-25

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In: Biomolecular NMR Assignments, Springer Science and Business Media LLC, Vol. 16, No. 1 ( 2022-04), p. 17-25

Abstract: The ongoing pandemic of the respiratory disease COVID-19 is caused by the SARS-CoV-2 (SCoV2) virus. SCoV2 is a member of the Betacoronavirus genus. The 30 kb positive sense, single stranded RNA genome of SCoV2 features 5′- and 3′-genomic ends that are highly conserved among Betacoronaviruses. These genomic ends contain structured cis -acting RNA elements, which are involved in the regulation of viral replication and translation. Structural information about these potential antiviral drug targets supports the development of novel classes of therapeutics against COVID-19. The highly conserved branched stem-loop 5 (SL5) found within the 5′-untranslated region (5′-UTR) consists of a basal stem and three stem-loops, namely SL5a, SL5b and SL5c. Both, SL5a and SL5b feature a 5′-UUUCGU-3′ hexaloop that is also found among Alphacoronaviruses. Here, we report the extensive 1 H, 13 C and 15 N resonance assignment of the 37 nucleotides (nts) long sequence spanning SL5b and SL5c (SL5b + c), as basis for further in-depth structural studies by solution NMR spectroscopy.

Type of Medium: Online Resource

ISSN: 1874-2718 , 1874-270X

URL: Article

DOI: 10.1007/s12104-021-10053-4

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2022

detail.hit.zdb_id: 2388861-1

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1H, 13C and 15N assignment of stem-loop SL1 from the 5'-UTR of SARS-CoV-2

Richter, Christian ; Hohmann, Katharina F. ; Toews, Sabrina ; [et al.]

Springer Science and Business Media LLC ; 2021

In: Biomolecular NMR Assignments Vol. 15, No. 2 ( 2021-10), p. 467-474

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In: Biomolecular NMR Assignments, Springer Science and Business Media LLC, Vol. 15, No. 2 ( 2021-10), p. 467-474

Abstract: The stem-loop (SL1) is the 5'-terminal structural element within the single-stranded SARS-CoV-2 RNA genome. It is formed by nucleotides 7–33 and consists of two short helical segments interrupted by an asymmetric internal loop. This architecture is conserved among Betacoronaviruses. SL1 is present in genomic SARS-CoV-2 RNA as well as in all subgenomic mRNA species produced by the virus during replication, thus representing a ubiquitous cis -regulatory RNA with potential functions at all stages of the viral life cycle. We present here the 1 H, 13 C and 15 N chemical shift assignment of the 29 nucleotides-RNA construct 5_SL1, which denotes the native 27mer SL1 stabilized by an additional terminal G-C base-pair.

Type of Medium: Online Resource

ISSN: 1874-2718 , 1874-270X

URL: Article

DOI: 10.1007/s12104-021-10047-2

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2021

detail.hit.zdb_id: 2388861-1

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Comprehensive Fragment Screening of the SARS‐CoV‐2 Proteome Explores Novel Chemical Space for Drug Development

Berg, Hannes ; Wirtz Martin, Maria A. ; Altincekic, Nadide ; [et al.]

Wiley ; 2022

In: Angewandte Chemie International Edition Vol. 61, No. 46 ( 2022-11-14)

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In: Angewandte Chemie International Edition, Wiley, Vol. 61, No. 46 ( 2022-11-14)

Type of Medium: Online Resource

ISSN: 1433-7851 , 1521-3773

URL: Issue

URL: Article

DOI: 10.1002/anie.v61.46

DOI: 10.1002/anie.202205858

RVK:

VA 2100

Language: English

Publisher: Wiley

Publication Date: 2022

detail.hit.zdb_id: 2011836-3

detail.hit.zdb_id: 123227-7

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The COVID19‐NMR Consortium: A Public Report on the Impact of this New Global Collaboration

Duchardt‐Ferner, Elke ; Ferner, Jan ; Fürtig, Boris ; [et al.]

Wiley ; 2023

In: Angewandte Chemie International Edition Vol. 62, No. 14 ( 2023-03-27)

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In: Angewandte Chemie International Edition, Wiley, Vol. 62, No. 14 ( 2023-03-27)

Abstract: The outbreak of COVID‐19 in December 2019 required the formation of international consortia for a coordinated scientific effort to understand and combat the virus. In this Viewpoint Article, we discuss how the NMR community has gathered to investigate the genome and proteome of SARS‐CoV‐2 and tested them for binding to low‐molecular‐weight binders. External factors including extended lockdowns due to the global pandemic character of the viral infection triggered the transition from locally focused collaborative research conducted within individual research groups to digital exchange formats for immediate discussion of unpublished results and data analysis, sample sharing, and coordinated research between more than 50 groups from 18 countries simultaneously. We discuss key lessons that might pertain after the end of the pandemic and challenges that we need to address.

Type of Medium: Online Resource

ISSN: 1433-7851 , 1521-3773

URL: Issue

URL: Article

DOI: 10.1002/anie.v62.14

DOI: 10.1002/anie.202217171

RVK:

VA 2100

Language: English

Publisher: Wiley

Publication Date: 2023

detail.hit.zdb_id: 2011836-3

detail.hit.zdb_id: 123227-7

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Exploring the Druggability of Conserved RNA Regulatory Elements in the SARS‐CoV‐2 Genome

Sreeramulu, Sridhar ; Richter, Christian ; Berg, Hannes ; [et al.]

Wiley ; 2021

In: Angewandte Chemie International Edition Vol. 60, No. 35 ( 2021-08-23), p. 19191-19200

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In: Angewandte Chemie International Edition, Wiley, Vol. 60, No. 35 ( 2021-08-23), p. 19191-19200

Abstract: SARS‐CoV‐2 contains a positive single‐stranded RNA genome of approximately 30 000 nucleotides. Within this genome, 15 RNA elements were identified as conserved between SARS‐CoV and SARS‐CoV‐2. By nuclear magnetic resonance (NMR) spectroscopy, we previously determined that these elements fold independently, in line with data from in vivo and ex‐vivo structural probing experiments. These elements contain non‐base‐paired regions that potentially harbor ligand‐binding pockets. Here, we performed an NMR‐based screening of a poised fragment library of 768 compounds for binding to these RNAs, employing three different 1 H‐based 1D NMR binding assays. The screening identified common as well as RNA‐element specific hits. The results allow selection of the most promising of the 15 RNA elements as putative drug targets. Based on the identified hits, we derive key functional units and groups in ligands for effective targeting of the RNA of SARS‐CoV‐2.

Type of Medium: Online Resource

ISSN: 1433-7851 , 1521-3773

URL: Issue

URL: Article

DOI: 10.1002/anie.v60.35

DOI: 10.1002/anie.202103693

RVK:

VA 2100

Language: English

Publisher: Wiley

Publication Date: 2021

detail.hit.zdb_id: 2011836-3

detail.hit.zdb_id: 123227-7

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1H, 13C, 15N and 31P chemical shift assignment for stem-loop 4 from the 5′-UTR of SARS-CoV-2

Vögele, Jennifer ; Ferner, Jan-Peter ; Altincekic, Nadide ; [et al.]

Springer Science and Business Media LLC ; 2021

In: Biomolecular NMR Assignments Vol. 15, No. 2 ( 2021-10), p. 335-340

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In: Biomolecular NMR Assignments, Springer Science and Business Media LLC, Vol. 15, No. 2 ( 2021-10), p. 335-340

Abstract: The SARS-CoV-2 virus is the cause of the respiratory disease COVID-19. As of today, therapeutic interventions in severe COVID-19 cases are still not available as no effective therapeutics have been developed so far. Despite the ongoing development of a number of effective vaccines, therapeutics to fight the disease once it has been contracted will still be required. Promising targets for the development of antiviral agents against SARS-CoV-2 can be found in the viral RNA genome. The 5′- and 3′-genomic ends of the 30 kb SCoV-2 genome are highly conserved among Betacoronaviruses and contain structured RNA elements involved in the translation and replication of the viral genome. The 40 nucleotides (nt) long highly conserved stem-loop 4 (5_SL4) is located within the 5′-untranslated region (5′-UTR) important for viral replication. 5_SL4 features an extended stem structure disrupted by several pyrimidine mismatches and is capped by a pentaloop. Here, we report extensive 1 H, 13 C, 15 N and 31 P resonance assignments of 5_SL4 as the basis for in-depth structural and ligand screening studies by solution NMR spectroscopy.

Type of Medium: Online Resource

ISSN: 1874-2718 , 1874-270X

URL: Article

DOI: 10.1007/s12104-021-10026-7

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2021

detail.hit.zdb_id: 2388861-1

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Das COVID19‐NMR‐Konsortium: Ein öffentlicher Bericht über den Einfluss dieser neuen globalen Kollaboration

Duchardt‐Ferner, Elke ; Ferner, Jan ; Fürtig, Boris ; [et al.]

Wiley ; 2023

In: Angewandte Chemie Vol. 135, No. 14 ( 2023-03-27)

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In: Angewandte Chemie, Wiley, Vol. 135, No. 14 ( 2023-03-27)

Abstract: Der Ausbruch von COVID‐19 im Dezember 2019 erforderte eine Koordination wissenschaftlicher Beiträge zum Verständnis und zur Bekämpfung des Virus und führte so zur Bildung internationaler Forschungskonsortien. In diesem Viewpoint Article erläutern wir, wie sich die NMR‐Community versammelt hat, um sowohl das Genom als auch das Proteom von SARS‐CoV‐2 strukturell zu untersuchen und für beide die Bindung an niedermolekulare Verbindungen zu testen. Externe Faktoren, einschließlich längerfristiger Lockdowns aufgrund der Pandemie, begünstigten den Übergang von lokaler, auf einzelne Forschungsgruppen ausgerichteter Verbundforschung hin zu hochkoordinierter Forschung mit über 50 Gruppen aus 18 Ländern, die durch digitale Austauschformate unmittelbar gemeinsam Daten analysierten und unveröffentlichte Ergebnisse diskutierten und darüber hinaus Proben untereinander teilten. Wir diskutieren hier einige wichtige Lehren, die nach dem Ende der Pandemie gezogen werden sollten, und Herausforderungen, die es anzugehen gilt.

Type of Medium: Online Resource

ISSN: 0044-8249 , 1521-3757

URL: Issue

URL: Article

DOI: 10.1002/ange.v135.14

DOI: 10.1002/ange.202217171

RVK:

VA 2100

RVK:

VN 5020

Language: English

Publisher: Wiley

Publication Date: 2023

detail.hit.zdb_id: 505868-5

detail.hit.zdb_id: 506609-8

detail.hit.zdb_id: 514305-6

detail.hit.zdb_id: 505872-7

detail.hit.zdb_id: 1479266-7

detail.hit.zdb_id: 505867-3

detail.hit.zdb_id: 506259-7

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Correction to ‘Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy’

Wacker, Anna ; Weigand, Julia E ; Akabayov, Sabine R ; [et al.]

Oxford University Press (OUP) ; 2021

In: Nucleic Acids Research Vol. 49, No. 12 ( 2021-07-09), p. 7204-7205

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In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 49, No. 12 ( 2021-07-09), p. 7204-7205

Type of Medium: Online Resource

ISSN: 0305-1048 , 1362-4962

URL: Article

DOI: 10.1093/nar/gkab568

RVK:

WA 15000

Language: English

Publisher: Oxford University Press (OUP)

Publication Date: 2021

detail.hit.zdb_id: 1472175-2

SSG: 12

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