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Stagnoli S, Macari G, Corsi P, Capone B, Vidaurrazaga A, Ereño-Orbea J, Ardá A, Polticelli F, Jiménez-Barbero J, Abrescia NGA, Coluzza I. Targeting the Spike: Repurposing Mithramycin and Dihydroergotamine to Block SARS-CoV-2 Infection. ACS OMEGA 2023; 8:43490-43499. [PMID: 38027314 PMCID: PMC10666140 DOI: 10.1021/acsomega.3c02921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 09/15/2023] [Indexed: 12/01/2023]
Abstract
The urgency to find complementary therapies to current SARS-CoV-2 vaccines, whose effectiveness is preserved over time and not compromised by the emergence of new and emerging variants, has become a critical health challenge. We investigate the possibility of jamming the opening of the Receptor Binding Domain (RBD) of the spike protein of SARS-CoV-2 with small compounds. Through in silico screening, we identified two potential candidates that would lock the Receptor Binding Domain (RBD) in a closed configuration, preventing the virus from infecting the host cells. We show that two drugs already approved by the FDA, mithramycin and dihydroergotamine, can block infection using concentrations in the μM range in cell-based assays. Further STD-NMR experiments support dihydroergotamine's direct interaction with the spike protein. Overall, our results indicate that repurposing of these compounds might lead to potential clinical drug candidates for the treatment of SARS-CoV-2 infection.
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Affiliation(s)
- Soledad Stagnoli
- Structure
and Cell Biology of Viruses Lab, Center
for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research
and Technology Alliance (BRTA), 48160 Derio, Spain
| | - Gabriele Macari
- Department
of Sciences, University of Rome Tre, 00154 Rome, Italy
| | - Pietro Corsi
- Department
of Sciences, University of Rome Tre, 00154 Rome, Italy
| | - Barbara Capone
- Department
of Sciences, University of Rome Tre, 00154 Rome, Italy
| | - Ander Vidaurrazaga
- Structure
and Cell Biology of Viruses Lab, Center
for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research
and Technology Alliance (BRTA), 48160 Derio, Spain
| | - June Ereño-Orbea
- Chemical
Glycobiology Laboratory, CIC bioGUNE, BRTA, 48160 Derio, Spain
- IKERBASQUE,
Basque Foundation for Science, 48009 Bilbao, Spain
| | - Ana Ardá
- Chemical
Glycobiology Laboratory, CIC bioGUNE, BRTA, 48160 Derio, Spain
| | - Fabio Polticelli
- Department
of Sciences, University of Rome Tre, 00154 Rome, Italy
- National
Institute of Nuclear Physics, Roma Tre Section, 00154 Rome, Italy
| | - Jesús Jiménez-Barbero
- Chemical
Glycobiology Laboratory, CIC bioGUNE, BRTA, 48160 Derio, Spain
- IKERBASQUE,
Basque Foundation for Science, 48009 Bilbao, Spain
- Centro
de
Investigación Biomédica En Red de Enfermedades Respiratorias.
(CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Department
of Organic & Inorganic Chemistry, Faculty
of Science and Technology University of the Basque Country, EHU-UPV, 48940 Leioa, Spain
| | - Nicola GA Abrescia
- Structure
and Cell Biology of Viruses Lab, Center
for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research
and Technology Alliance (BRTA), 48160 Derio, Spain
- IKERBASQUE,
Basque Foundation for Science, 48009 Bilbao, Spain
- Centro
de Investigación Biomédica en Red de Enfermedades Hepáticas
y Digestivas (CIBERehd), Instituto de Salud
Carlos III, 28029 Madrid, Spain
| | - Ivan Coluzza
- IKERBASQUE,
Basque Foundation for Science, 48009 Bilbao, Spain
- Computational
Soft Matter and Biophysics Lab, Basque Center
for Materials, Applications and Nanostructures (BCMaterials), Buil. Martina Casiano, Pl. 3 Parque
Científico UPV/EHU Barrio Sarriena, 48940 Leioa, Spain
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Sánchez IE, Galpern EA, Garibaldi MM, Ferreiro DU. Molecular Information Theory Meets Protein Folding. J Phys Chem B 2022; 126:8655-8668. [PMID: 36282961 DOI: 10.1021/acs.jpcb.2c04532] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We propose an application of molecular information theory to analyze the folding of single domain proteins. We analyze results from various areas of protein science, such as sequence-based potentials, reduced amino acid alphabets, backbone configurational entropy, secondary structure content, residue burial layers, and mutational studies of protein stability changes. We found that the average information contained in the sequences of evolved proteins is very close to the average information needed to specify a fold ∼2.2 ± 0.3 bits/(site·operation). The effective alphabet size in evolved proteins equals the effective number of conformations of a residue in the compact unfolded state at around 5. We calculated an energy-to-information conversion efficiency upon folding of around 50%, lower than the theoretical limit of 70%, but much higher than human-built macroscopic machines. We propose a simple mapping between molecular information theory and energy landscape theory and explore the connections between sequence evolution, configurational entropy, and the energetics of protein folding.
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Affiliation(s)
- Ignacio E Sánchez
- Facultad de Ciencias Exactas y Naturales, Laboratorio de Fisiología de Proteínas, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos AiresCP1428, Argentina
| | - Ezequiel A Galpern
- Facultad de Ciencias Exactas y Naturales, Laboratorio de Fisiología de Proteínas, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos AiresCP1428, Argentina
| | - Martín M Garibaldi
- Facultad de Ciencias Exactas y Naturales, Laboratorio de Fisiología de Proteínas, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos AiresCP1428, Argentina
| | - Diego U Ferreiro
- Facultad de Ciencias Exactas y Naturales, Laboratorio de Fisiología de Proteínas, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos AiresCP1428, Argentina
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