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Gervasoni S, Manelfi C, Adobati S, Talarico C, Biswas AD, Pedretti A, Vistoli G, Beccari AR. Target Prediction by Multiple Virtual Screenings: Analyzing the SARS-CoV-2 Phenotypic Screening by the Docking Simulations Submitted to the MEDIATE Initiative. Int J Mol Sci 2023; 25:450. [PMID: 38203621 PMCID: PMC10779154 DOI: 10.3390/ijms25010450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/15/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
Phenotypic screenings are usually combined with deconvolution techniques to characterize the mechanism of action for the retrieved hits. These studies can be supported by various computational analyses, although docking simulations are rarely employed. The present study aims to assess if multiple docking calculations can prove successful in target prediction. In detail, the docking simulations submitted to the MEDIATE initiative are utilized to predict the viral targets involved in the hits retrieved by a recently published cytopathic screening. Multiple docking results are combined by the EFO approach to develop target-specific consensus models. The combination of multiple docking simulations enhances the performances of the developed consensus models (average increases in EF1% value of 40% and 25% when combining three and two docking runs, respectively). These models are able to propose reliable targets for about half of the retrieved hits (31 out of 59). Thus, the study emphasizes that docking simulations might be effective in target identification and provide a convincing validation for the collaborative strategies that inspire the MEDIATE initiative. Disappointingly, cross-target and cross-program correlations suggest that common scoring functions are not specific enough for the simulated target.
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Affiliation(s)
- Silvia Gervasoni
- Dipartimento di Scienze Farmaceutiche, Università Degli Studi di Milano, Via Mangiagalli, 25, I-20133 Milano, Italy; (S.G.); (S.A.); (A.P.)
- Department of Physics, Università di Cagliari, I-09042 Monserrato, Italy
| | - Candida Manelfi
- EXSCALATE, Dompé Farmaceutici S.p.A., Via Tommaso De Amicis, 95, I-80131 Napoli, Italy; (C.M.); (C.T.); (A.D.B.); (A.R.B.)
| | - Sara Adobati
- Dipartimento di Scienze Farmaceutiche, Università Degli Studi di Milano, Via Mangiagalli, 25, I-20133 Milano, Italy; (S.G.); (S.A.); (A.P.)
| | - Carmine Talarico
- EXSCALATE, Dompé Farmaceutici S.p.A., Via Tommaso De Amicis, 95, I-80131 Napoli, Italy; (C.M.); (C.T.); (A.D.B.); (A.R.B.)
| | - Akash Deep Biswas
- EXSCALATE, Dompé Farmaceutici S.p.A., Via Tommaso De Amicis, 95, I-80131 Napoli, Italy; (C.M.); (C.T.); (A.D.B.); (A.R.B.)
| | - Alessandro Pedretti
- Dipartimento di Scienze Farmaceutiche, Università Degli Studi di Milano, Via Mangiagalli, 25, I-20133 Milano, Italy; (S.G.); (S.A.); (A.P.)
| | - Giulio Vistoli
- Dipartimento di Scienze Farmaceutiche, Università Degli Studi di Milano, Via Mangiagalli, 25, I-20133 Milano, Italy; (S.G.); (S.A.); (A.P.)
| | - Andrea R. Beccari
- EXSCALATE, Dompé Farmaceutici S.p.A., Via Tommaso De Amicis, 95, I-80131 Napoli, Italy; (C.M.); (C.T.); (A.D.B.); (A.R.B.)
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Hajji H, Alaqarbeh M, Lakhlifi T, Ajana MA, Alsakhen N, Bouachrine M. Computational approach investigation bioactive molecules from Saussurea Costus plant as SARS-CoV-2 main protease inhibitors using reverse docking, molecular dynamics simulation, and pharmacokinetic ADMET parameters. Comput Biol Med 2022; 150:106209. [PMID: 36257276 PMCID: PMC9554895 DOI: 10.1016/j.compbiomed.2022.106209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 09/23/2022] [Accepted: 10/09/2022] [Indexed: 11/17/2022]
Abstract
SARS-COV-2 virus causes (COVID-19) disease; it has become a global pandemic since 2019 and has negatively affected all aspects of human life. Scientists have made great efforts to find a reliable cure, vaccine, or treatment for this emerging disease. Efforts have been directed towards using medicinal plants as alternative medicines, as the active chemical compounds in them have been discovered as potential antiviral or anti-inflammatory agents. In this research, the potential of Saussurea costus (S. Costus) or QUST Al Hindi chemical consistent as potential antiviral agents was investigated by using computational methods such as Reverse Docking, ADMET, and Molecular Dynamics with different proteases COVID-19 such as PDB: 2GZ9; 6LU7; 7AOL, 6Y2E, 6Y84. The results of Reverse Docking the complex between 6LU7 proteases and Cynaropicrin compound being the best complex, as the same result, is achieved by molecular dynamics. Also, the toxicity testing result from ADMET method proved that the complex is the least toxic and the safest possible drug. In addition, 6LU7-Cynaropicrin complex obeyed Lipinski rule; it formed ≤5 H-bond donors and ≤10 H bond acceptors, MW < 500 Daltons, and octanol/water partition coefficient <5.
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Affiliation(s)
- Halima Hajji
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, University Moulay Ismail, Meknes, Morocco
| | - Marwa Alaqarbeh
- National Agricultural Research Center, Al-Baqa, 19381, Jordan.
| | - Tahar Lakhlifi
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, University Moulay Ismail, Meknes, Morocco
| | - Mohammed Aziz Ajana
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, University Moulay Ismail, Meknes, Morocco
| | - Nada Alsakhen
- Department of Chemistry, Faculty of Science, The Hashemite University, Zarqa, Jordan
| | - Mohammed Bouachrine
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, University Moulay Ismail, Meknes, Morocco; Superior School of Technology - Khenifra (EST-Khenifra), University of Sultan Moulay Sliman, PB 170, Khenifra, 54000, Morocco.
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Drewry DH, Potjewyd FM, Bayati A, Smith JL, Dickmander RJ, Howell S, Taft-Benz S, Min SM, Hossain MA, Heise M, McPherson PS, Moorman NJ, Axtman AD. Identification and Utilization of a Chemical Probe to Interrogate the Roles of PIKfyve in the Lifecycle of β-Coronaviruses. J Med Chem 2022; 65:12860-12882. [PMID: 36111834 PMCID: PMC9574855 DOI: 10.1021/acs.jmedchem.2c00697] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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From a designed library of indolyl pyrimidinamines, we
identified
a highly potent and cell-active chemical probe (17) that
inhibits phosphatidylinositol-3-phosphate 5-kinase (PIKfyve). Comprehensive
evaluation of inhibitor selectivity confirmed that this PIKfyve probe
demonstrates excellent kinome-wide selectivity. A structurally related
indolyl pyrimidinamine (30) was characterized as a negative
control that lacks PIKfyve inhibitory activity and exhibits exquisite
selectivity when profiled broadly. Chemical probe 17 disrupts
multiple phases of the lifecycle of β-coronaviruses: viral replication
and viral entry. The diverse antiviral roles of PIKfyve have not been
previously probed comprehensively in a single study or using the same
compound set. Our scaffold is a distinct chemotype that lacks the
canonical morpholine hinge-binder of classical lipid kinase inhibitors
and has a non-overlapping kinase off-target profile with known PIKfyve
inhibitors. Our chemical probe set can be used by the community to
further characterize the role of PIKfyve in virology.
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Affiliation(s)
- David H. Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Frances M. Potjewyd
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Armin Bayati
- Structural Genomics Consortium, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Jeffery L. Smith
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Rebekah J. Dickmander
- UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, North Carolina 27599, United States
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Stefanie Howell
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Sharon Taft-Benz
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, North Carolina 27599, United States
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Sophia M. Min
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Mohammad Anwar Hossain
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Mark Heise
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, North Carolina 27599, United States
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Peter S. McPherson
- Structural Genomics Consortium, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Nathaniel J. Moorman
- UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, North Carolina 27599, United States
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Alison D. Axtman
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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Jukič M, Kores K, Janežič D, Bren U. Repurposing of Drugs for SARS-CoV-2 Using Inverse Docking Fingerprints. Front Chem 2021; 9:757826. [PMID: 35028304 PMCID: PMC8748264 DOI: 10.3389/fchem.2021.757826] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 11/12/2021] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 or SARS-CoV-2 is a virus that belongs to the Coronaviridae family. This group of viruses commonly causes colds but possesses a tremendous pathogenic potential. In humans, an outbreak of SARS caused by the SARS-CoV virus was first reported in 2003, followed by 2012 when the Middle East respiratory syndrome coronavirus (MERS-CoV) led to an outbreak of Middle East respiratory syndrome (MERS). Moreover, COVID-19 represents a serious socioeconomic and global health problem that has already claimed more than four million lives. To date, there are only a handful of therapeutic options to combat this disease, and only a single direct-acting antiviral, the conditionally approved remdesivir. Since there is an urgent need for active drugs against SARS-CoV-2, the strategy of drug repurposing represents one of the fastest ways to achieve this goal. An in silico drug repurposing study using two methods was conducted. A structure-based virtual screening of the FDA-approved drug database on SARS-CoV-2 main protease was performed, and the 11 highest-scoring compounds with known 3CLpro activity were identified while the methodology was used to report further 11 potential and completely novel 3CLpro inhibitors. Then, inverse molecular docking was performed on the entire viral protein database as well as on the Coronaviridae family protein subset to examine the hit compounds in detail. Instead of target fishing, inverse docking fingerprints were generated for each hit compound as well as for the five most frequently reported and direct-acting repurposed drugs that served as controls. In this way, the target-hitting space was examined and compared and we can support the further biological evaluation of all 11 newly reported hits on SARS-CoV-2 3CLpro as well as recommend further in-depth studies on antihelminthic class member compounds. The authors acknowledge the general usefulness of this approach for a full-fledged inverse docking fingerprint screening in the future.
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Affiliation(s)
- Marko Jukič
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Koper, Slovenia
| | - Katarina Kores
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
| | - Dušanka Janežič
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Koper, Slovenia
| | - Urban Bren
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Koper, Slovenia
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