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Romeo I, Prandi IG, Giombini E, Gruber CEM, Pietrucci D, Borocci S, Abid N, Fava A, Beccari AR, Chillemi G, Talarico C. The Spike Mutants Website: A Worldwide Used Resource against SARS-CoV-2. Int J Mol Sci 2022; 23:13082. [PMID: 36361870 PMCID: PMC9654198 DOI: 10.3390/ijms232113082] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/24/2022] [Accepted: 10/24/2022] [Indexed: 07/22/2023] Open
Abstract
A large number of SARS-CoV-2 mutations in a short period of time has driven scientific research related to vaccines, new drugs, and antibodies to combat the new variants of the virus. Herein, we present a web portal containing the structural information, the tridimensional coordinates, and the molecular dynamics trajectories of the SARS-CoV-2 spike protein and its main variants. The Spike Mutants website can serve as a rapid online tool for investigating the impact of novel mutations on virus fitness. Taking into account the high variability of SARS-CoV-2, this application can help the scientific community when prioritizing molecules for experimental assays, thus, accelerating the identification of promising drug candidates for COVID-19 treatment. Below we describe the main features of the platform and illustrate the possible applications for speeding up the drug discovery process and hypothesize new effective strategies to overcome the recurrent mutations in SARS-CoV-2 genome.
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Affiliation(s)
- Isabella Romeo
- Dipartimento di Scienze della Salute, Università Magna Græcia di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy
- Net4Science Academic Spin-Off, Università Magna Graecia di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy
| | - Ingrid Guarnetti Prandi
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy
| | - Emanuela Giombini
- Laboratory of Virology, INMI Lazzaro Spallanzani IRCCS, Via Portuense 292, 00149 Roma, Italy
| | | | - Daniele Pietrucci
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), CNR, 70126 Bari, Italy
| | - Stefano Borocci
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy
- Laboratory of Transmissible Diseases and Biological Active Substances LR99ES27, Faculty of Pharmacy, University of Monastir, Rue Ibn Sina, Monastir 5000, Tunisia
| | - Nabil Abid
- Laboratory of Transmissible Diseases and Biological Active Substances LR99ES27, Faculty of Pharmacy, University of Monastir, Rue Ibn Sina, Monastir 5000, Tunisia
- High Institute of Biotechnology of Monastir, Department of Molecular and Cellular Biology, University of Monastir, Monastir 5000, Tunisia
| | - Anna Fava
- Dompé Farmaceutici SpA, Via Tommaso De Amicis, 95, 80131 Napoli, Italy
| | - Andrea R. Beccari
- Dompé Farmaceutici SpA, Via Tommaso De Amicis, 95, 80131 Napoli, Italy
| | - Giovanni Chillemi
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy
| | - Carmine Talarico
- Dompé Farmaceutici SpA, Via Tommaso De Amicis, 95, 80131 Napoli, Italy
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Chromenone derivatives as a versatile scaffold with dual mode of inhibition of HIV-1 reverse transcriptase-associated Ribonuclease H function and integrase activity. Eur J Med Chem 2019; 182:111617. [PMID: 31442684 DOI: 10.1016/j.ejmech.2019.111617] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 08/09/2019] [Accepted: 08/10/2019] [Indexed: 12/31/2022]
Abstract
A number of compounds targeting different processes of the Human Immunodeficiency Virus type 1 (HIV-1) life cycle have been developed in the continuing fight against AIDS. Coumarin-based molecules already proved to act as HIV-1 Protease (PR) or Integrase (IN) inhibitors and also to target HIV-1 reverse transcriptase (RT), blocking the DNA-dependent DNA-polymerase activity or the RNA-dependent DNA-polymerase activity working as common NNRTIs. In the present study, with the aim to exploit a coumarin-based scaffold to achieve the inhibition of multiple viral coded enzymatic functions, novel 4-hydroxy-2H, 5H-pyrano (3, 2-c) chromene-2, 5-dione derivatives were synthesized. The modeling studies calculated the theoretical binding affinity of the synthesized compounds on both HIV-1 IN and RT-associated Ribonuclease H (RNase H) active sites, which was confirmed by biological assays. Our results provide a basis for the identification of dual HIV-1 IN and RT RNase H inhibitors compounds.
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