Structure of a Cyclic Peptide as an Inhibitor of <i>Mycobacterium tuberculosis</i> Transcription: NMR and Molecular Dynamics Simulations
Background and Objectives: A novel antitubercular cyclic peptide, Cyclo(1,6)-Ac-CLYHFC-NH<sub>2</sub>, was designed to bind at the rifampicin (RIF) binding site on the RNA polymerase (RNAP) of <i>Mycobacterium tuberculosis</i> (MTB). This peptide inhibits RNA elongation in th...
Saved in:
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2024-11-01
|
| Series: | Pharmaceuticals |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1424-8247/17/11/1545 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1846152750504607744 |
|---|---|
| author | Filia Stephanie Usman Sumo Friend Tambunan Krzysztof Kuczera Teruna J. Siahaan |
| author_facet | Filia Stephanie Usman Sumo Friend Tambunan Krzysztof Kuczera Teruna J. Siahaan |
| author_sort | Filia Stephanie |
| collection | DOAJ |
| description | Background and Objectives: A novel antitubercular cyclic peptide, Cyclo(1,6)-Ac-CLYHFC-NH<sub>2</sub>, was designed to bind at the rifampicin (RIF) binding site on the RNA polymerase (RNAP) of <i>Mycobacterium tuberculosis</i> (MTB). This peptide inhibits RNA elongation in the MTB transcription initiation assay in the nanomolar range, which can halt the MTB transcription initiation complex, similar to RIF. Therefore, determining the solution conformation of this peptide is useful in improving the peptide’s binding affinity to the RNAP. Methods: Here, the solution structure of Cyclo(1,6)-Ac-CLYHFC-NH<sub>2</sub> was determined by two-dimensional (2D) NMR experiments and NMR-restrained molecular dynamic (MD) simulations. Results: All protons of Cyclo(1,6)-Ac-CLYHFC-NH<sub>2</sub> were assigned using TOCSY and NOE NMR spectroscopy. The NOE cross-peak intensities were used to calculate interproton distances within the peptide. The J<sub>NH-HCα</sub> coupling constants were used to determine the possible Phi angles within the peptide. The interproton distances and calculated Phi angles from NMR were used in NMR-restrained MD simulations. The NOE spectra showed NH-to-NH cross-peaks at Leu2-to-Tyr3 and Tyr3-to-His4, indicating a βI-turn formation at the Cys1-Leu2-Tyr3-His4 sequence. Conclusions: The NMR-restrained MD simulations showed several low-energy conformations that were congruent with the NMR data. Finally, the conformation of this peptide will be used to design derivatives that can better inhibit RNAP activity. |
| format | Article |
| id | doaj-art-ed3f3bc70b47477a96633f72aa10897d |
| institution | Kabale University |
| issn | 1424-8247 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Pharmaceuticals |
| spelling | doaj-art-ed3f3bc70b47477a96633f72aa10897d2024-11-26T18:17:34ZengMDPI AGPharmaceuticals1424-82472024-11-011711154510.3390/ph17111545Structure of a Cyclic Peptide as an Inhibitor of <i>Mycobacterium tuberculosis</i> Transcription: NMR and Molecular Dynamics SimulationsFilia Stephanie0Usman Sumo Friend Tambunan1Krzysztof Kuczera2Teruna J. Siahaan3Department of Pharmaceutical Chemistry, School of Pharmacy, The University of Kansas, Lawrence, KS 66047, USADepartment of Chemistry, University of Indonesia, Depok 16424, IndonesiaDepartment of Chemistry, The University of Kansas, Lawrence, KS 66045, USADepartment of Pharmaceutical Chemistry, School of Pharmacy, The University of Kansas, Lawrence, KS 66047, USABackground and Objectives: A novel antitubercular cyclic peptide, Cyclo(1,6)-Ac-CLYHFC-NH<sub>2</sub>, was designed to bind at the rifampicin (RIF) binding site on the RNA polymerase (RNAP) of <i>Mycobacterium tuberculosis</i> (MTB). This peptide inhibits RNA elongation in the MTB transcription initiation assay in the nanomolar range, which can halt the MTB transcription initiation complex, similar to RIF. Therefore, determining the solution conformation of this peptide is useful in improving the peptide’s binding affinity to the RNAP. Methods: Here, the solution structure of Cyclo(1,6)-Ac-CLYHFC-NH<sub>2</sub> was determined by two-dimensional (2D) NMR experiments and NMR-restrained molecular dynamic (MD) simulations. Results: All protons of Cyclo(1,6)-Ac-CLYHFC-NH<sub>2</sub> were assigned using TOCSY and NOE NMR spectroscopy. The NOE cross-peak intensities were used to calculate interproton distances within the peptide. The J<sub>NH-HCα</sub> coupling constants were used to determine the possible Phi angles within the peptide. The interproton distances and calculated Phi angles from NMR were used in NMR-restrained MD simulations. The NOE spectra showed NH-to-NH cross-peaks at Leu2-to-Tyr3 and Tyr3-to-His4, indicating a βI-turn formation at the Cys1-Leu2-Tyr3-His4 sequence. Conclusions: The NMR-restrained MD simulations showed several low-energy conformations that were congruent with the NMR data. Finally, the conformation of this peptide will be used to design derivatives that can better inhibit RNAP activity.https://www.mdpi.com/1424-8247/17/11/1545cyclic peptide conformationmolecular dynamics simulationmRNA polymerase inhibitor<i>Mycobacterium tuberculosis</i>nuclear magnetic resonance |
| spellingShingle | Filia Stephanie Usman Sumo Friend Tambunan Krzysztof Kuczera Teruna J. Siahaan Structure of a Cyclic Peptide as an Inhibitor of <i>Mycobacterium tuberculosis</i> Transcription: NMR and Molecular Dynamics Simulations Pharmaceuticals cyclic peptide conformation molecular dynamics simulation mRNA polymerase inhibitor <i>Mycobacterium tuberculosis</i> nuclear magnetic resonance |
| title | Structure of a Cyclic Peptide as an Inhibitor of <i>Mycobacterium tuberculosis</i> Transcription: NMR and Molecular Dynamics Simulations |
| title_full | Structure of a Cyclic Peptide as an Inhibitor of <i>Mycobacterium tuberculosis</i> Transcription: NMR and Molecular Dynamics Simulations |
| title_fullStr | Structure of a Cyclic Peptide as an Inhibitor of <i>Mycobacterium tuberculosis</i> Transcription: NMR and Molecular Dynamics Simulations |
| title_full_unstemmed | Structure of a Cyclic Peptide as an Inhibitor of <i>Mycobacterium tuberculosis</i> Transcription: NMR and Molecular Dynamics Simulations |
| title_short | Structure of a Cyclic Peptide as an Inhibitor of <i>Mycobacterium tuberculosis</i> Transcription: NMR and Molecular Dynamics Simulations |
| title_sort | structure of a cyclic peptide as an inhibitor of i mycobacterium tuberculosis i transcription nmr and molecular dynamics simulations |
| topic | cyclic peptide conformation molecular dynamics simulation mRNA polymerase inhibitor <i>Mycobacterium tuberculosis</i> nuclear magnetic resonance |
| url | https://www.mdpi.com/1424-8247/17/11/1545 |
| work_keys_str_mv | AT filiastephanie structureofacyclicpeptideasaninhibitorofimycobacteriumtuberculosisitranscriptionnmrandmoleculardynamicssimulations AT usmansumofriendtambunan structureofacyclicpeptideasaninhibitorofimycobacteriumtuberculosisitranscriptionnmrandmoleculardynamicssimulations AT krzysztofkuczera structureofacyclicpeptideasaninhibitorofimycobacteriumtuberculosisitranscriptionnmrandmoleculardynamicssimulations AT terunajsiahaan structureofacyclicpeptideasaninhibitorofimycobacteriumtuberculosisitranscriptionnmrandmoleculardynamicssimulations |