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Metibemu DS, Adeyinka OS, Falode J, Crown O, Ogungbe IV. Inhibitors of the Structural and Nonstructural Proteins of Alphaviruses. ACS Infect Dis 2024. [PMID: 38992989 DOI: 10.1021/acsinfecdis.4c00254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
The Alphavirus genus includes viruses that cause encephalitis due to neuroinvasion and viruses that cause arthritis due to acute and chronic inflammation. There is no approved therapeutic for alphavirus infections, but significant efforts are ongoing, more so in recent years, to develop vaccines and therapeutics for alphavirus infections. This review article highlights some of the major advances made so far to identify small molecules that can selectively target the structural and the nonstructural proteins in alphaviruses with the expectation that persistent investigation of an increasingly expanding chemical space through a variety of structure-based design and high-throughput screening strategies will yield candidate drugs for clinical studies. While most of the works discussed are still in the early discovery to lead optimization stages, promising avenues remain for drug development against this family of viruses.
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Affiliation(s)
- Damilohun Samuel Metibemu
- Chemistry and Biotechnology Science and Engineering Programs, The University of Alabama in Huntsville, 301 Sparkman Drive, Huntsville, Alabama 35899, United States
| | - Olawale Samuel Adeyinka
- Chemistry and Biotechnology Science and Engineering Programs, The University of Alabama in Huntsville, 301 Sparkman Drive, Huntsville, Alabama 35899, United States
| | - John Falode
- Chemistry and Biotechnology Science and Engineering Programs, The University of Alabama in Huntsville, 301 Sparkman Drive, Huntsville, Alabama 35899, United States
| | - Olamide Crown
- Chemistry and Biotechnology Science and Engineering Programs, The University of Alabama in Huntsville, 301 Sparkman Drive, Huntsville, Alabama 35899, United States
| | - Ifedayo Victor Ogungbe
- Chemistry and Biotechnology Science and Engineering Programs, The University of Alabama in Huntsville, 301 Sparkman Drive, Huntsville, Alabama 35899, United States
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2
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Merten EM, Sears JD, Leisner TM, Hardy PB, Ghoshal A, Hossain MA, Asressu KH, Brown PJ, Stashko MA, Herring L, Mordant AL, Webb TS, Mills CA, Barker NK, Streblow ZJ, Perveen S, Arrowsmith C, Arnold JJ, Cameron CE, Streblow DN, Moorman NJ, Heise M, Willson TM, Popov K, Pearce KH. Discovery of a cell-active chikungunya virus nsP2 protease inhibitor using a covalent fragment-based screening approach. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586341. [PMID: 38562906 PMCID: PMC10983941 DOI: 10.1101/2024.03.22.586341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that has been responsible for numerous large-scale outbreaks in the last twenty years. Currently, there are no FDA-approved therapeutics for any alphavirus infection. CHIKV non-structural protein 2 (nsP2), which contains a cysteine protease domain, is essential for viral replication, making it an attractive target for a drug discovery campaign. Here, we optimized a CHIKV nsP2 protease (nsP2pro) biochemical assay for the screening of a 6,120-compound cysteine-directed covalent fragment library. Using a 50% inhibition threshold, we identified 153 hits (2.5% hit rate). In dose-response follow up, RA-0002034, a covalent fragment that contains a vinyl sulfone warhead, inhibited CHIKV nsP2pro with an IC 50 of 58 ± 17 nM, and further analysis with time-dependent inhibition studies yielded a k inact /K I of 6.4 x 10 3 M -1 s -1 . LC-MS/MS analysis determined that RA-0002034 covalently modified the catalytic cysteine in a site-specific manner. Additionally, RA-0002034 showed no significant off-target reactivity against a panel of cysteine proteases. In addition to the potent biochemical inhibition of CHIKV nsP2pro activity and exceptional selectivity, RA-0002034 was tested in cellular models of alphavirus infection and effectively inhibited viral replication of both CHIKV and related alphaviruses. This study highlights the discovery and characterization of the chemical probe RA-0002034 as a promising hit compound from covalent fragment-based screening for development toward a CHIKV or pan-alphavirus therapeutic. Significance Statement Chikungunya virus is one of the most prominent and widespread alphaviruses and has caused explosive outbreaks of arthritic disease. Currently, there are no FDA-approved drugs to treat disease caused by chikungunya virus or any other alphavirus-caused infection. Here, we report the discovery of a covalent small molecule inhibitor of chikungunya virus nsP2 protease activity and viral replication of four diverse alphaviruses. This finding highlights the utility of covalent fragment screening for inhibitor discovery and represents a starting point towards the development of alphavirus therapeutics targeting nsP2 protease.
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Cao V, Loeanurit N, Hengphasatporn K, Hairani R, Wacharachaisurapol N, Prompila N, Wittayalertpanya S, Shigeta Y, Khotavivattana T, Chavasiri W, Boonyasuppayakorn S. The 8-bromobaicalein alleviated chikungunya-induced musculoskeletal inflammation and reduced the viral load in healthy adult mice. Emerg Microbes Infect 2023; 12:2270074. [PMID: 37842770 PMCID: PMC10653753 DOI: 10.1080/22221751.2023.2270074] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 10/05/2023] [Indexed: 10/17/2023]
Abstract
Chikungunya virus is a re-emerging arbovirus that has caused epidemic outbreaks in recent decades. Patients in older age groups with high viral load and severe immunologic response during acute infection are likely to develop chronic arthritis and severe joint pain. Currently, no antiviral drug is available. Previous studies suggested that a flavone derivative, 8-bromobaicalein, was a potential dengue and Zika replication inhibitor in a cell-based system targeting flaviviral polymerase. Here we characterized that 8-bromobaicalein inhibited chikungunya virus replication with EC50 of 0.49 ± 0.11 µM in Vero cells. The molecular target predicted at viral nsP1 methyltransferase using molecular binding and fragment molecular orbital calculation. Additionally, oral administration of 250 mg/kg twice daily treatment alleviated chikungunya-induced musculoskeletal inflammation and reduced viral load in healthy adult mice. Pharmacokinetic analysis indicated that the 250 mg/kg administration maintained the compound level above EC99.9 for 12 h. Therefore, 8-bromobaicalein should be a potential candidate for further development as a pan-arboviral drug.
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Affiliation(s)
- Van Cao
- Center of Excellence in Applied Medical Virology, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Interdisciplinary Program in Microbiology, Graduate School, Chulalongkorn University, Bangkok, Thailand
- DaNang University of Medical Technology and Pharmacy, DaNang, Vietnam
| | - Naphat Loeanurit
- Center of Excellence in Applied Medical Virology, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | | | - Rita Hairani
- Center of Excellence in Natural Products Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Noppadol Wacharachaisurapol
- Clinical Pharmakokinetics and Pharmacogenomics Research Unit, Department of Pharmacology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Nantaporn Prompila
- Chula Pharmacokinetic Research Center, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Supeecha Wittayalertpanya
- Clinical Pharmakokinetics and Pharmacogenomics Research Unit, Department of Pharmacology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Chula Pharmacokinetic Research Center, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Tanatorn Khotavivattana
- Center of Excellence in Natural Products Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Warinthorn Chavasiri
- Center of Excellence in Natural Products Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Siwaporn Boonyasuppayakorn
- Center of Excellence in Applied Medical Virology, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Vaccine Research and Development, Chulalongkorn University (Chula-VRC), Bangkok, Thailand
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4
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Puhl AC, Fernandes RS, Godoy AS, Gil LHVG, Oliva G, Ekins S. The protein disulfide isomerase inhibitor 3-methyltoxoflavin inhibits Chikungunya virus. Bioorg Med Chem 2023; 83:117239. [PMID: 36940609 PMCID: PMC10150329 DOI: 10.1016/j.bmc.2023.117239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/07/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023]
Abstract
Chikungunya virus (CHIKV) is the etiological agent of chikungunya fever, a (re)emerging arbovirus infection, that causes severe and often persistent arthritis, as well as representing a serious health concern worldwide for which no antivirals are currently available. Despite efforts over the last decade to identify and optimize new inhibitors or to reposition existing drugs, no compound has progressed to clinical trials for CHIKV and current prophylaxis is based on vector control, which has shown limited success in containing the virus. Our efforts to rectify this situation were initiated by screening 36 compounds using a replicon system and ultimately identified the natural product derivative 3-methyltoxoflavin with activity against CHIKV using a cell-based assay (EC50 200 nM, SI = 17 in Huh-7 cells). We have additionally screened 3-methyltoxoflavin against a panel of 17 viruses and showed that it only additionally demonstrated inhibition of the yellow fever virus (EC50 370 nM, SI = 3.2 in Huh-7 cells). We have also showed that 3-methyltoxoflavin has excellent in vitro human and mouse microsomal metabolic stability, good solubility and high Caco-2 permeability and it is not likely to be a P-glycoprotein substrate. In summary, we demonstrate that 3-methyltoxoflavin has activity against CHIKV, good in vitro absorption, distribution, metabolism and excretion (ADME) properties as well as good calculated physicochemical properties and may represent a valuable starting point for future optimization to develop inhibitors for this and other related viruses.
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Affiliation(s)
- Ana C. Puhl
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC 27606, USA
| | - Rafaela S. Fernandes
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, SP, 13563-120, Brazil
| | - Andre S. Godoy
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, SP, 13563-120, Brazil
| | - Laura H. V. G. Gil
- Department of Virology, Oswaldo Cruz Foundation, Aggeu Magalhães Institute, Av. Prof. Moraes Rego, s/n - Cidade Universitaria, Recife, PE, 50670-420, Brazil
| | - Glaucius Oliva
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, SP, 13563-120, Brazil
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC 27606, USA
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Skidmore AM, Bradfute SB. The life cycle of the alphaviruses: From an antiviral perspective. Antiviral Res 2023; 209:105476. [PMID: 36436722 PMCID: PMC9840710 DOI: 10.1016/j.antiviral.2022.105476] [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: 06/20/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022]
Abstract
The alphaviruses are a widely distributed group of positive-sense, single stranded, RNA viruses. These viruses are largely arthropod-borne and can be found on all populated continents. These viruses cause significant human disease, and recently have begun to spread into new populations, such as the expansion of Chikungunya virus into southern Europe and the Caribbean, where it has established itself as endemic. The study of alphaviruses is an active and expanding field, due to their impacts on human health, their effects on agriculture, and the threat that some pose as potential agents of biological warfare and terrorism. In this systematic review we will summarize both historic knowledge in the field as well as recently published data that has potential to shift current theories in how alphaviruses are able to function. This review is comprehensive, covering all parts of the alphaviral life cycle as well as a brief overview of their pathology and the current state of research in regards to vaccines and therapeutics for alphaviral disease.
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Affiliation(s)
- Andrew M Skidmore
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, 915 Camino de Salud, IDTC Room 3245, Albuquerque, NM, 87131, USA.
| | - Steven B Bradfute
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, 915 Camino de Salud, IDTC Room 3330A, Albuquerque, NM, 87131, USA.
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Pelliccia S, Cerchia C, Esposito F, Cannalire R, Corona A, Costanzi E, Kuzikov M, Gribbon P, Zaliani A, Brindisi M, Storici P, Tramontano E, Summa V. Easy access to α-ketoamides as SARS-CoV-2 and MERS M pro inhibitors via the PADAM oxidation route. Eur J Med Chem 2022; 244:114853. [PMID: 36332546 PMCID: PMC9575579 DOI: 10.1016/j.ejmech.2022.114853] [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] [Received: 07/29/2022] [Revised: 10/11/2022] [Accepted: 10/11/2022] [Indexed: 11/28/2022]
Abstract
SARS-CoV-2 caused worldwide the current outbreak called COVID-19. Despite multiple countermeasures implemented, there is an urgent global need for new potent and efficient antiviral drugs against this pathogen. In this context, the main protease (Mpro) of SARS-CoV-2 is an essential viral enzyme and plays a pivotal role in viral replication and transcription. Its specific cleavage of polypeptides after a glutamine residue has been considered as a key element to design novel antiviral drugs. Herein, we reported the design, synthesis and structure-activity relationships of novel α-ketoamides as covalent reversible inhibitors of Mpro, exploiting the PADAM oxidation route. The reported compounds showed μM to nM activities in enzymatic and in the antiviral cell-based assays against SARS-CoV-2 Mpro. In order to assess inhibitors’ binding mode, two co-crystal structures of SARS-CoV-2 Mpro in complex with our inhibitors were solved, which confirmed the covalent binding of the keto amide moiety to the catalytic Cys145 residue of Mpro. Finally, in order to interrogate potential broad-spectrum properties, we assessed a selection of compounds against MERS Mpro where they showed nM inhibitory potency, thus highlighting their potential as broad-spectrum coronavirus inhibitors.
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Affiliation(s)
- Sveva Pelliccia
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131, Naples, Italy,Corresponding author
| | - Carmen Cerchia
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131, Naples, Italy
| | - Francesca Esposito
- Dipartimento di Scienze della Vita e dell'Ambiente, Cittadella Universitaria di Monserrato, Cagliari, Monserrato, SS-554, Italy
| | - Rolando Cannalire
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131, Naples, Italy
| | - Angela Corona
- Dipartimento di Scienze della Vita e dell'Ambiente, Cittadella Universitaria di Monserrato, Cagliari, Monserrato, SS-554, Italy
| | - Elisa Costanzi
- Protein Facility, Elettra - Sincrotrone Trieste S.C.p.A., SS 14 - km 163, 5 in AREA Science Park, Trieste, Basovizza, 34149, Italy
| | - Maria Kuzikov
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, Hamburg, 22525, Germany,Department of Life Sciences and Chemistry, Jacobs University Bremen, 28759, Bremen, Germany,Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, Hamburg, 22525, Germany,Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, Hamburg, 22525, Germany,Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Margherita Brindisi
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131, Naples, Italy
| | - Paola Storici
- Protein Facility, Elettra - Sincrotrone Trieste S.C.p.A., SS 14 - km 163, 5 in AREA Science Park, Trieste, Basovizza, 34149, Italy
| | - Enzo Tramontano
- Dipartimento di Scienze della Vita e dell'Ambiente, Cittadella Universitaria di Monserrato, Cagliari, Monserrato, SS-554, Italy
| | - Vincenzo Summa
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131, Naples, Italy,Corresponding author
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MBZM-N-IBT, a Novel Small Molecule, Restricts Chikungunya Virus Infection by Targeting nsP2 Protease Activity In Vitro, In Vivo, and Ex Vivo. Antimicrob Agents Chemother 2022; 66:e0046322. [PMID: 35766508 PMCID: PMC9295557 DOI: 10.1128/aac.00463-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The increase in disease incidences and persistent Chikungunya virus (CHIKV)-induced arthritis have been a huge burden on public health globally. In the absence of specific antivirals or vaccines, it is essential to continue efforts to develop effective anti-CHIKV strategies. Our previous study showing the in vitro anti-CHIKV potential of a novel molecule 1-[(2-methylbenzimidazol-1-yl) methyl]-2-oxo-indolin-3-ylidene] amino] thiourea (MBZM-N-IBT) encouraged us to further validate its efficacy. Here, the effect of MBZM-N-IBT was evaluated in vitro in RAW 264.7 cells, in vivo in C57BL/6 mice, and ex vivo in human peripheral blood mononuclear cells (hPBMCs). The study demonstrated that CHIKV infection was efficiently abrogated in RAW 264.7 cells (IC50 = 22.34 μM) with significant inhibition in viral proteins. The inhibition was effective in the postentry step, and MBZM-N-IBT predominately interfered in the early stages of CHIKV life cycle. It was further supported when the protease activity of CHIKV-nsP2 was hindered by the compound. Moreover, it diminished the CHIKV-induced inflammatory responses in vitro through significant downregulation of all the major mitogen-activated protein kinases (MAPKs), NF-κB, cyclooxygenase (COX)-2, and cytokines. Furthermore, MBZM-N-IBT restricted CHIKV infection and inflammation in vivo, leading to reduced clinical scores and complete survival of C57BL/6 mice. Additionally, it has been noticed that the CHIKV infection was reduced remarkably in hPBMC-derived monocyte-macrophage populations ex vivo by the compound. In conclusion, it can be suggested that this novel compound MBZM-N-IBT has been demonstrated to be a potential anti-CHIKV molecule in vitro, in vivo, and ex vivo and fulfilled all the criteria to investigate further for successful treatment of CHIKV infection.
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Muniz LS, da Rocha Pita SS. In silico studies revealed interaction mechanisms of benzylidene–acrylohydrazide derivatives and nsP2 CHIKV. NEW J CHEM 2022. [DOI: 10.1039/d1nj05593c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Here we studied benzylidene–acrylohydrazide derivatives via ADMET properties and docking analysis in the hope that they will be useful chemical moieties against the Chikungunya virus.
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Affiliation(s)
- Larissa Silva Muniz
- Laboratory of Bioinformatics and Molecular Modeling (LaBiMM), Pharmacy College, Federal University of Bahia (UFBA), Rua Barão de Jeremoabo, 147, Salvador, 40170-115, Bahia, Brazil
| | - Samuel Silva da Rocha Pita
- Laboratory of Bioinformatics and Molecular Modeling (LaBiMM), Pharmacy College, Federal University of Bahia (UFBA), Rua Barão de Jeremoabo, 147, Salvador, 40170-115, Bahia, Brazil
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