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Neira JL, López-Redondo ML, Cámara-Artigas A, Marina A, Contreras A. Structure and dynamics of the cyanobacterial regulator SipA. Arch Biochem Biophys 2024; 754:109943. [PMID: 38395125 DOI: 10.1016/j.abb.2024.109943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/09/2024] [Accepted: 02/20/2024] [Indexed: 02/25/2024]
Abstract
The small, 78-residue long, regulator SipA interacts with the non-bleaching sensor histidine kinase (NblS). We have solved the solution structure of SipA on the basis of 990 nuclear Overhauser effect- (NOE-) derived distance constraints. The average pairwise root-mean-square deviation (RMSD) for the twenty best structures for the backbone residues, obtained by CYANA, was 1.35 ± 0.21 Å, and 1.90 ± 0.16 Å when all heavy atoms were considered (the target function of CYANA was 0.540 ± 0.08). The structure is that of a β-II class protein, basically formed by a five-stranded β-sheet composed of antiparallel strands following the arrangement: Gly6-Leu11 (β-strand 1), which packs against Leu66-Val69 (β-strand 5) on one side, and against Gly36-Thr42 (β-strand 2) on the other side; Trp50-Phe54 (β-strand 3); and Gly57-Leu60 (β-strand 4). The protein is highly mobile, as shown by measurements of R1, R2, NOE and ηxy relaxation parameters, with an average order parameter () of 0.70; this mobility encompasses movements in different time scales. We hypothesize that this high flexibility allows the interaction with other proteins (among them NblS), and it explains the large conformational stability of SipA.
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Affiliation(s)
- José L Neira
- IDIBE, Universidad Miguel Hernández, 03202, Elche, Alicante, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, 50018, Zaragoza, Spain.
| | - María Luisa López-Redondo
- Unidad Regulación de La Síntesis de Proteínas, Instituto de Biomedicina de Valencia (CSIC), 46010, Valencia, Spain
| | - Ana Cámara-Artigas
- Departamento de Química y Física, Research Center CIAIMBITAL, Universidad de Almería- CeiA3, 04120, Almería, Spain
| | - Alberto Marina
- Instituto de Biomedicina de Valencia (CSIC) and Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), 46010, Valencia, Spain
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Gargantilla M, Francés C, Adhav A, Forcada-Nadal A, Martínez-Gualda B, Martí-Marí O, López-Redondo ML, Melero R, Marco-Marín C, Gougeard N, Espinosa C, Rubio-del-Campo A, Ruiz-Partida R, Hernández-Sierra MD, Villamayor-Belinchón L, Bravo J, Llacer JL, Marina A, Rubio V, San-Félix A, Geller R, Pérez-Pérez MJ. C-2 Thiophenyl Tryptophan Trimers Inhibit Cellular Entry of SARS-CoV-2 through Interaction with the Viral Spike (S) Protein. J Med Chem 2023; 66:10432-10457. [PMID: 37471688 PMCID: PMC10424185 DOI: 10.1021/acs.jmedchem.3c00576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Indexed: 07/22/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19, by infecting cells via the interaction of its spike protein (S) with the primary cell receptor angiotensin-converting enzyme (ACE2). To search for inhibitors of this key step in viral infection, we screened an in-house library of multivalent tryptophan derivatives. Using VSV-S pseudoparticles, we identified compound 2 as a potent entry inhibitor lacking cellular toxicity. Chemical optimization of 2 rendered compounds 63 and 65, which also potently inhibited genuine SARS-CoV-2 cell entry. Thermofluor and microscale thermophoresis studies revealed their binding to S and to its isolated receptor binding domain (RBD), interfering with the interaction with ACE2. High-resolution cryoelectron microscopy structure of S, free or bound to 2, shed light on cell entry inhibition mechanisms by these compounds. Overall, this work identifies and characterizes a new class of SARS-CoV-2 entry inhibitors with clear potential for preventing and/or fighting COVID-19.
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Affiliation(s)
- Marta Gargantilla
- Instituto de Química
Médica (IQM, CSIC), c/Juan de la Cierva 3, Madrid 28006, Spain
| | - Clara Francés
- Institute for Integrative Systems Biology (I2SysBio), UV-CSIC, c/Catedrático Agustin Escardino,
9, Paterna 46980, Valencia, Spain
| | - Anmol Adhav
- Instituto de Biomedicina de Valencia (IBV, CSIC), c/Jaime Roig 11, Valencia 46010, Spain
| | - Alicia Forcada-Nadal
- Instituto de Biomedicina de Valencia (IBV, CSIC), c/Jaime Roig 11, Valencia 46010, Spain
- Group 739, Centro de Investigación
Biomédica en Red en Enfermedades Raras (CIBERER-ISCIII), Madrid 28049, Spain
| | | | - Olaia Martí-Marí
- Instituto de Química
Médica (IQM, CSIC), c/Juan de la Cierva 3, Madrid 28006, Spain
| | | | - Roberto Melero
- Centro
Nacional de Biotecnología (CNB, CSIC), c/Darwin 3, Madrid 28049, Spain
| | - Clara Marco-Marín
- Instituto de Biomedicina de Valencia (IBV, CSIC), c/Jaime Roig 11, Valencia 46010, Spain
- Group 739, Centro de Investigación
Biomédica en Red en Enfermedades Raras (CIBERER-ISCIII), Madrid 28049, Spain
| | - Nadine Gougeard
- Instituto de Biomedicina de Valencia (IBV, CSIC), c/Jaime Roig 11, Valencia 46010, Spain
- Group 739, Centro de Investigación
Biomédica en Red en Enfermedades Raras (CIBERER-ISCIII), Madrid 28049, Spain
| | - Carolina Espinosa
- Instituto de Biomedicina de Valencia (IBV, CSIC), c/Jaime Roig 11, Valencia 46010, Spain
| | | | - Rafael Ruiz-Partida
- Instituto de Biomedicina de Valencia (IBV, CSIC), c/Jaime Roig 11, Valencia 46010, Spain
| | | | | | - Jerónimo Bravo
- Instituto de Biomedicina de Valencia (IBV, CSIC), c/Jaime Roig 11, Valencia 46010, Spain
| | - José-Luis Llacer
- Instituto de Biomedicina de Valencia (IBV, CSIC), c/Jaime Roig 11, Valencia 46010, Spain
- Group 739, Centro de Investigación
Biomédica en Red en Enfermedades Raras (CIBERER-ISCIII), Madrid 28049, Spain
| | - Alberto Marina
- Instituto de Biomedicina de Valencia (IBV, CSIC), c/Jaime Roig 11, Valencia 46010, Spain
- Group 739, Centro de Investigación
Biomédica en Red en Enfermedades Raras (CIBERER-ISCIII), Madrid 28049, Spain
| | - Vicente Rubio
- Instituto de Biomedicina de Valencia (IBV, CSIC), c/Jaime Roig 11, Valencia 46010, Spain
- Group 739, Centro de Investigación
Biomédica en Red en Enfermedades Raras (CIBERER-ISCIII), Madrid 28049, Spain
| | - Ana San-Félix
- Instituto de Química
Médica (IQM, CSIC), c/Juan de la Cierva 3, Madrid 28006, Spain
| | - Ron Geller
- Institute for Integrative Systems Biology (I2SysBio), UV-CSIC, c/Catedrático Agustin Escardino,
9, Paterna 46980, Valencia, Spain
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