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Mahgoub RE, Mohamed FE, Alzyoud L, Ali BR, Ferreira J, Rabeh WM, AlNeyadi SS, Atatreh N, Ghattas MA. The Discovery of Small Allosteric and Active Site Inhibitors of the SARS-CoV-2 Main Protease via Structure-Based Virtual Screening and Biological Evaluation. Molecules 2022; 27:molecules27196710. [PMID: 36235244 PMCID: PMC9572942 DOI: 10.3390/molecules27196710] [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: 08/31/2022] [Revised: 10/05/2022] [Accepted: 10/07/2022] [Indexed: 11/16/2022] Open
Abstract
The main protease enzyme (Mpro) of SARS-CoV-2 is one of the most promising targets for COVID-19 treatment. Accordingly, in this work, a structure-based virtual screening of 3.8 million ligand libraries was carried out. After rigorous filtering, docking, and post screening assessments, 78 compounds were selected for biological evaluation, 3 of which showed promising inhibition of the Mpro enzyme. The obtained hits (CB03, GR04, and GR20) had reasonable potencies with Ki values in the medium to high micromolar range. Interestingly, while our most potent hit, GR20, was suggested to act via a reversible covalent mechanism, GR04 was confirmed as a noncompetitive inhibitor that seems to be one of a kind when compared to the other allosteric inhibitors discovered so far. Moreover, all three compounds have small sizes (~300 Da) with interesting fittings in their relevant binding sites, and they possess lead-like characteristics that can introduce them as very attractive candidates for the future development of COVID-19 treatments.
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Affiliation(s)
- Radwa E. Mahgoub
- College of Pharmacy, Al Ain University, Abu Dhabi 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 64141, United Arab Emirates
| | - Feda E. Mohamed
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain 15551, United Arab Emirates
| | - Lara Alzyoud
- College of Pharmacy, Al Ain University, Abu Dhabi 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 64141, United Arab Emirates
| | - Bassam R. Ali
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain 15551, United Arab Emirates
- Zayed Centre for Health Sciences, United Arab Emirates University, Al-Ain 15551, United Arab Emirates
| | - Juliana Ferreira
- Science Division, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Wael M. Rabeh
- Science Division, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Shaikha S. AlNeyadi
- Department of Chemistry, College of Science, United Arab Emirates University, Al-Ain 15551, United Arab Emirates
| | - Noor Atatreh
- College of Pharmacy, Al Ain University, Abu Dhabi 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 64141, United Arab Emirates
| | - Mohammad A. Ghattas
- College of Pharmacy, Al Ain University, Abu Dhabi 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 64141, United Arab Emirates
- Correspondence: ; Tel.: +971-26133275
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Etukala JR, Yadav JS. Synthesis of 1-(phenylsulfanyl/phenoxy)-3H-naptho[1,2,3-de]quinoline-2,7-diones. HETEROATOM CHEMISTRY 2008. [DOI: 10.1002/hc.20399] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Yu KL, Wang XA, Civiello RL, Trehan AK, Pearce BC, Yin Z, Combrink KD, Gulgeze HB, Zhang Y, Kadow KF, Cianci CW, Clarke J, Genovesi EV, Medina I, Lamb L, Wyde PR, Krystal M, Meanwell NA. Respiratory syncytial virus fusion inhibitors. Part 3: Water-soluble benzimidazol-2-one derivatives with antiviral activity in vivo. Bioorg Med Chem Lett 2005; 16:1115-22. [PMID: 16368233 DOI: 10.1016/j.bmcl.2005.11.109] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2005] [Revised: 11/24/2005] [Accepted: 11/28/2005] [Indexed: 10/25/2022]
Abstract
The introduction of acidic and basic functionality into the side chains of respiratory syncytial virus (RSV) fusion inhibitors was examined in an effort to identify compounds suitable for evaluation in vivo in the cotton rat model of RSV infection following administration as a small particle aerosol. The acidic compounds 2r, 2u, 2v, 2w, 2z, and 2aj demonstrated potent antiviral activity in cell culture and exhibited efficacy in the cotton rat comparable to ribavirin. In a BALB/c mouse model, the oxadiazolone 2aj reduced virus titers following subcutaneous dosing, whilst the ester 2az and amide 2aab exhibited efficacy following oral administration. These results established the potential of this class of RSV fusion inhibitors to interfere with infection in vivo following topical or systemic administration.
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Affiliation(s)
- Kuo-Long Yu
- Department of Chemistry, The Bristol-Myers Squibb Pharmaceutical Research Institute, 5, Research Parkway, Wallingford, CT 06492, USA
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Yu KL, Zhang Y, Civiello RL, Trehan AK, Pearce BC, Yin Z, Combrink KD, Gulgeze HB, Wang XA, Kadow KF, Cianci CW, Krystal M, Meanwell NA. Respiratory syncytial virus inhibitors. Part 2: Benzimidazol-2-one derivatives. Bioorg Med Chem Lett 2004; 14:1133-7. [PMID: 14980651 DOI: 10.1016/j.bmcl.2003.12.072] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2003] [Revised: 12/14/2003] [Accepted: 12/18/2003] [Indexed: 11/30/2022]
Abstract
Structure-activity relationships for a series of benzimidazol-2-one-based inhibitors of respiratory syncytial virus are described. These studies focused on structural variation of the benzimidazol-2-one substituent, a vector inaccessible in a series of benzotriazole derivatives on which 2 is based, and revealed a broad tolerance for substituent size and functionality.
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Affiliation(s)
- Kuo-Long Yu
- Department of Chemistry, The Bristol-Myers Squibb Pharmaceutical Research Institute, 5 Research Parkway, Wallingford, CT 06492, USA
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Yu KL, Zhang Y, Civiello RL, Kadow KF, Cianci C, Krystal M, Meanwell NA. Fundamental structure-activity relationships associated with a new structural class of respiratory syncytial virus inhibitor. Bioorg Med Chem Lett 2003; 13:2141-4. [PMID: 12798322 DOI: 10.1016/s0960-894x(03)00383-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Structure-activity relationships surrounding the dialkylamino side chain of a series of benzotriazole-derived inhibitors of respiratory syncytial virus fusion based on the screening lead 1a were examined. The results indicate that the topology of the side chain is important but the terminus element offers considerable latitude to modulate physical properties.
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Affiliation(s)
- Kuo Long Yu
- Department of Chemistry, The Bristol-Myers Squibb Pharmaceutical Research Institute, 5, Research Parkway, 06492, Wallingford, CT, USA
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Abstract
Respiratory syncytial virus (RSV) infection is the leading cause of lower respiratory tract infection in infants and young children. Premature infants and infants with underlying lung disease are at increased risk for severe RSV infection in the first 1 - 2 years of life. Monthly prophylaxis with palivizumab (Synagis) during RSV season has been proven safe and effective in this population and these effects have persisted over the 4 years since the drug was approved by the US FDA in 1998. Issues remain regarding the optimal candidates for palivizumab prophylaxis and whether additional groups of high-risk individuals, for example infants with congenital heart disease or cystic fibrosis, and immunocompromised hosts, might benefit from such preventive therapy. It is possible that palivizumab in combination with antiviral or anti-inflammatory agents might also prove to be beneficial in the treatment of RSV disease. Newer monoclonal antibodies to RSV in development may offer the potential for less frequent dosing, increased efficacy and a role in treatment of RSV disease, but pending further evaluation of such products palivizumab provides significant protection for high-risk infants against a major pathogen.
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Affiliation(s)
- Leonard R Krilov
- Pediatric Infectious Diseases, Winthrop University Hospital, Mineola, NY 11501, USA.
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