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Caruso IP, dos Santos Almeida V, do Amaral MJ, de Andrade GC, de Araújo GR, de Araújo TS, de Azevedo JM, Barbosa GM, Bartkevihi L, Bezerra PR, dos Santos Cabral KM, de Lourenço IO, Malizia-Motta CL, de Luna Marques A, Mebus-Antunes NC, Neves-Martins TC, de Sá JM, Sanches K, Santana-Silva MC, Vasconcelos AA, da Silva Almeida M, de Amorim GC, Anobom CD, Da Poian AT, Gomes-Neto F, Pinheiro AS, Almeida FC. Insights into the specificity for the interaction of the promiscuous SARS-CoV-2 nucleocapsid protein N-terminal domain with deoxyribonucleic acids. Int J Biol Macromol 2022; 203:466-480. [PMID: 35077748 PMCID: PMC8783401 DOI: 10.1016/j.ijbiomac.2022.01.121] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 12/23/2022]
Abstract
The SARS-CoV-2 nucleocapsid protein (N) is a multifunctional promiscuous nucleic acid-binding protein, which plays a major role in nucleocapsid assembly and discontinuous RNA transcription, facilitating the template switch of transcriptional regulatory sequences (TRS). Here, we dissect the structural features of the N protein N-terminal domain (N-NTD) and N-NTD plus the SR-rich motif (N-NTD-SR) upon binding to single and double-stranded TRS DNA, as well as their activities for dsTRS melting and TRS-induced liquid-liquid phase separation (LLPS). Our study gives insights on the specificity for N-NTD(-SR) interaction with TRS. We observed an approximation of the triple-thymidine (TTT) motif of the TRS to β-sheet II, giving rise to an orientation difference of ~25° between dsTRS and non-specific sequence (dsNS). It led to a local unfavorable energetic contribution that might trigger the melting activity. The thermodynamic parameters of binding of ssTRSs and dsTRS suggested that the duplex dissociation of the dsTRS in the binding cleft is entropically favorable. We showed a preference for TRS in the formation of liquid condensates when compared to NS. Moreover, our results on DNA binding may serve as a starting point for the design of inhibitors, including aptamers, against N, a possible therapeutic target essential for the virus infectivity.
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Affiliation(s)
- Icaro Putinhon Caruso
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), São José do Rio Preto, Brazil; Rio BioNMR Network, Rio de Janeiro, Brazil.
| | - Vitor dos Santos Almeida
- National Center of Nuclear Magnetic Resonance (CNRMN), CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil,Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Mariana Juliani do Amaral
- Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil,Protein Advanced Biochemistry (PAB), CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil,Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Guilherme Caldas de Andrade
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil,National Center of Nuclear Magnetic Resonance (CNRMN), CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil,Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Gabriela Rocha de Araújo
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil,National Center of Nuclear Magnetic Resonance (CNRMN), CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil,Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Talita Stelling de Araújo
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil,Protein Advanced Biochemistry (PAB), CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil,Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Jéssica Moreira de Azevedo
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil,Protein Advanced Biochemistry (PAB), CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil,Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Glauce Moreno Barbosa
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil,National Center of Nuclear Magnetic Resonance (CNRMN), CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil,Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Leonardo Bartkevihi
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil,National Center of Nuclear Magnetic Resonance (CNRMN), CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil,Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Peter Reis Bezerra
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil,National Center of Nuclear Magnetic Resonance (CNRMN), CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil,Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Katia Maria dos Santos Cabral
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil,Protein Advanced Biochemistry (PAB), CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil,Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Isabella Otênio de Lourenço
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), São José do Rio Preto, Brazil,Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Clara L.F. Malizia-Motta
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil,Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Aline de Luna Marques
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil,Multidisciplinary Center for Research in Biology (NUMPEX), Campus Duque de Caxias Federal University of Rio de Janeiro, Duque de Caxias, Brazil,Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Nathane Cunha Mebus-Antunes
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil,Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Thais Cristtina Neves-Martins
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil,Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Jéssica Maróstica de Sá
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), São José do Rio Preto, Brazil,Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Karoline Sanches
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), São José do Rio Preto, Brazil,Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Marcos Caique Santana-Silva
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil,Multidisciplinary Center for Research in Biology (NUMPEX), Campus Duque de Caxias Federal University of Rio de Janeiro, Duque de Caxias, Brazil,Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Ariana Azevedo Vasconcelos
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil,National Center of Nuclear Magnetic Resonance (CNRMN), CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil,Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Marcius da Silva Almeida
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil,Protein Advanced Biochemistry (PAB), CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil,Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Gisele Cardoso de Amorim
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil,Multidisciplinary Center for Research in Biology (NUMPEX), Campus Duque de Caxias Federal University of Rio de Janeiro, Duque de Caxias, Brazil,Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Cristiane Dinis Anobom
- National Center of Nuclear Magnetic Resonance (CNRMN), CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil,Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil,Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Andrea T. Da Poian
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil,Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Francisco Gomes-Neto
- National Center of Nuclear Magnetic Resonance (CNRMN), CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil,Laboratory of Toxinology, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil,Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Anderson S. Pinheiro
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil,Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Fabio C.L. Almeida
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil,National Center of Nuclear Magnetic Resonance (CNRMN), CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil,Rio BioNMR Network, Rio de Janeiro, Brazil,Correspondence to: F.C.L. Almeida, National Center of Nuclear Magnetic Resonance (CNRMN), CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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Ortlieb LO, Caruso ÍP, Mebus-Antunes NC, Da Poian AT, Petronilho EDC, Figueroa-Villar JD, Nascimento CJ, Almeida FCL. Searching for drug leads targeted to the hydrophobic cleft of dengue virus capsid protein. J Enzyme Inhib Med Chem 2021; 37:287-298. [PMID: 34894959 PMCID: PMC8667904 DOI: 10.1080/14756366.2021.2004591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
We synthesised and screened 18 aromatic derivatives of guanylhydrazones and oximes aromatic for their capacity to bind to dengue virus capsid protein (DENVC). The intended therapeutic target was the hydrophobic cleft of DENVC, which is a region responsible for its anchoring in lipid droplets in the infected cells. The inhibition of this process completely suppresses virus infectivity. Using NMR, we describe five compounds able to bind to the α1-α2 interface in the hydrophobic cleft. Saturation transfer difference experiments showed that the aromatic protons of the ligands are important for the interaction with DENVC. Fluorescence binding isotherms indicated that the selected compounds bind at micromolar affinities, possibly leading to binding-induced conformational changes. NMR-derived docking calculations of ligands showed that they position similarly in the hydrophobic cleft. Cytotoxicity experiments and calculations of in silico drug properties suggest that these compounds may be promising candidates in the search for antivirals targeting DENVC.
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Affiliation(s)
- Liliane O Ortlieb
- Department of Chemistry, Military Institute of Engineering (IME), Rio de Janeiro, Brazil.,Institute of Medical Biochemistry Leopoldo de Meis (IBqM) and National Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Ícaro P Caruso
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM) and National Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.,Multiuser Center for Biomolecular Innovation (CMIB) and Department of Physics, Institute of Biosciences, Letters and Exact Sciences (IBILCE), São Paulo State University (UNESP), São José do Rio Preto, Brazil
| | - Nathane C Mebus-Antunes
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Andrea T Da Poian
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Elaine da C Petronilho
- Department of Chemistry, Military Institute of Engineering (IME), Rio de Janeiro, Brazil
| | | | - Claudia J Nascimento
- Department of Natural Sciences, Institute of Biosciences, Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Brazil
| | - Fabio C L Almeida
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM) and National Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
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