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Choudhary S, Nehul S, Singh A, Panda PK, Kumar P, Sharma GK, Tomar S. Unraveling antiviral efficacy of multifunctional immunomodulatory triterpenoids against SARS-COV-2 targeting main protease and papain-like protease. IUBMB Life 2024; 76:228-241. [PMID: 38059400 DOI: 10.1002/iub.2793] [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: 03/15/2023] [Accepted: 10/20/2023] [Indexed: 12/08/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may be over, but its variants continue to emerge, and patients with mild symptoms having long COVID is still under investigation. SARS-CoV-2 infection leading to elevated cytokine levels and suppressed immune responses set off cytokine storm, fatal systemic inflammation, tissue damage, and multi-organ failure. Thus, drug molecules targeting the SARS-CoV-2 virus-specific proteins or capable of suppressing the host inflammatory responses to viral infection would provide an effective antiviral therapy against emerging variants of concern. Evolutionarily conserved papain-like protease (PLpro) and main protease (Mpro) play an indispensable role in the virus life cycle and immune evasion. Direct-acting antivirals targeting both these viral proteases represent an attractive antiviral strategy that is also expected to reduce viral inflammation. The present study has evaluated the antiviral and anti-inflammatory potential of natural triterpenoids: azadirachtin, withanolide_A, and isoginkgetin. These molecules inhibit the Mpro and PLpro proteolytic activities with half-maximal inhibitory concentrations (IC50) values ranging from 1.42 to 32.7 μM. Isothermal titration calorimetry (ITC) analysis validated the binding of these compounds to Mpro and PLpro. As expected, the two compounds, withanolide_A and azadirachtin, exhibit potent anti-SARS-CoV-2 activity in cell-based assays, with half-maximum effective concentration (EC50) values of 21.73 and 31.19 μM, respectively. The anti-inflammatory roles of azadirachtin and withanolide_A when assessed using HEK293T cells, were found to significantly reduce the levels of CXCL10, TNFα, IL6, and IL8 cytokines, which are elevated in severe cases of COVID-19. Interestingly, azadirachtin and withanolide_A were also found to rescue the decreased type-I interferon response (IFN-α1). The results of this study clearly highlight the role of triterpenoids as effective antiviral molecules that target SARS-CoV-2-specific enzymes and also host immune pathways involved in virus-mediated inflammation.
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Affiliation(s)
- Shweta Choudhary
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, India
| | - Sanketkumar Nehul
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, India
| | - Ankur Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, India
| | - Prasan Kumar Panda
- Department of Internal Medicine (Division of Infectious diseases), All India Institute of Medical Sciences (AIIMS), Rishikesh, India
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, India
| | - Gaurav Kumar Sharma
- Centre for Animal Disease Research and Diagnosis (CADRAD), Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India
| | - Shailly Tomar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, India
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Nunes JA, de Araújo RSA, da Silva FN, Cytarska J, Łączkowski KZ, Cardoso SH, Mendonça-Júnior FJB, da Silva-Júnior EF. Coumarin-Based Compounds as Inhibitors of Tyrosinase/Tyrosine Hydroxylase: Synthesis, Kinetic Studies, and In Silico Approaches. Int J Mol Sci 2023; 24:5216. [PMID: 36982292 PMCID: PMC10048804 DOI: 10.3390/ijms24065216] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/22/2023] [Accepted: 03/01/2023] [Indexed: 03/11/2023] Open
Abstract
Cancer represents the main cause of morbidity and mortality worldwide, constituting a serious health problem. In this context, melanoma represents the most aggressive and fatal type of skin cancer, with death rates increasing every year. Scientific efforts have been addressed to the development of inhibitors targeting the tyrosinase enzyme as potential anti-melanoma agents due to the importance of this enzyme in melanogenesis biosynthesis. Coumarin-based compounds have shown potential activity as anti-melanoma agents and tyrosinase inhibitors. In this study, coumarin-based derivatives were designed, synthesized, and experimentally evaluated upon tyrosinase. Compound FN-19, a coumarin-thiosemicarbazone analog, exhibited potent anti-tyrosinase activity, with an IC50 value of 42.16 ± 5.16 µM, being more active than ascorbic acid and kojic acid, both reference inhibitors. The kinetic study showed that FN-19 acts as a mixed inhibitor. Still, for this compound, molecular dynamics (MD) simulations were performed to determine the stability of the complex with tyrosinase, generating RMSD, RMSF, and interaction plots. Additionally, docking studies were performed to elucidate the binding pose at the tyrosinase, suggesting that the hydroxyl group of coumarin derivative performs coordinate bonds (bidentate) with the copper(II) ions at distances ranging from 2.09 to 2.61 Å. Then, MM/PBSA calculations revealed that van der Waals interactions are the most relevant intermolecular forces for complex stabilization. Furthermore, it was observed that FN-19 has a binding energy (ΔEMM) value similar to tropolone, a tyrosinase inhibitor. Therefore, the data obtained in this study will be useful for designing and developing novel coumarin-based analogs targeting the tyrosinase enzyme.
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Affiliation(s)
- Jéssica Alves Nunes
- Biological and Molecular Chemistry Research Group, Institute of Chemistry and Biotechnology, Federal University of Alagoas, AC Simões Campus, Lourival Melo Mota Avenue, s/n, Maceió 57072-970, Alagoas, Brazil (E.F.d.S.-J.)
| | - Rodrigo Santos Aquino de Araújo
- Laboratory of Synthesis and Drug Delivery, Department of Biological Sciences, State University of Paraíba, João Pessoa 58429-500, Paraíba, Brazil
| | - Fabrícia Nunes da Silva
- Laboratory of Organic and Medicinal Synthesis, Federal University of Alagoas, Campus Arapiraca, Manoel Severino Barbosa Avenue, Arapiraca 57309-005, Alagoas, Brazil
| | - Joanna Cytarska
- Department of Chemical Technology and Pharmaceuticals, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Jurasza 2, 85-089 Bydgoszcz, Poland
| | - Krzysztof Z. Łączkowski
- Department of Chemical Technology and Pharmaceuticals, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Jurasza 2, 85-089 Bydgoszcz, Poland
| | - Sílvia Helena Cardoso
- Laboratory of Organic and Medicinal Synthesis, Federal University of Alagoas, Campus Arapiraca, Manoel Severino Barbosa Avenue, Arapiraca 57309-005, Alagoas, Brazil
| | | | - Edeildo Ferreira da Silva-Júnior
- Biological and Molecular Chemistry Research Group, Institute of Chemistry and Biotechnology, Federal University of Alagoas, AC Simões Campus, Lourival Melo Mota Avenue, s/n, Maceió 57072-970, Alagoas, Brazil (E.F.d.S.-J.)
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Antonopoulou I, Sapountzaki E, Rova U, Christakopoulos P. Inhibition of the main protease of SARS-CoV-2 (M pro) by repurposing/designing drug-like substances and utilizing nature's toolbox of bioactive compounds. Comput Struct Biotechnol J 2022; 20:1306-1344. [PMID: 35308802 PMCID: PMC8920478 DOI: 10.1016/j.csbj.2022.03.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 12/14/2022] Open
Abstract
The emergence of the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has resulted in a long pandemic, with numerous cases and victims worldwide and enormous consequences on social and economic life. Although vaccinations have proceeded and provide a valuable shield against the virus, the approved drugs are limited and it is crucial that further ways to combat infection are developed, that can also act against potential mutations. The main protease (Mpro) of the virus is an appealing target for the development of inhibitors, due to its importance in the viral life cycle and its high conservation among different coronaviruses. Several compounds have shown inhibitory potential against Mpro, both in silico and in vitro, with few of them also having entered clinical trials. These candidates include: known drugs that have been repurposed, molecules specifically designed based on the natural substrate of the protease or on structural moieties that have shown high binding affinity to the protease active site, as well as naturally derived compounds, either isolated or in plant extracts. The aim of this work is to collectively present the results of research regarding Mpro inhibitors to date, focusing on the function of the compounds founded by in silico simulations and further explored by in vitro and in vivo assays. Creating an extended portfolio of promising compounds that may block viral replication by inhibiting Mpro and by understanding involved structure-activity relationships, could provide a basis for the development of effective solutions against SARS-CoV-2 and future related outbreaks.
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Affiliation(s)
| | | | - Ulrika Rova
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, SE-97187 Luleå, Sweden
| | - Paul Christakopoulos
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, SE-97187 Luleå, Sweden
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Mousivand M, Bagherzadeh K, Anfossi L, Javan-Nikkhah M. Key criteria for engineering mycotoxin binding aptamers via computational simulations: Aflatoxin B1 as a case study. Biotechnol J 2021; 17:e2100280. [PMID: 34800084 DOI: 10.1002/biot.202100280] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 11/16/2021] [Accepted: 11/16/2021] [Indexed: 12/30/2022]
Abstract
Due to the difficulties in monoclonal antibody production specific to mycotoxins, aptameric probes have been considered as suitable alternatives. The low efficiency of the SELEX procedure in screening high affinity aptamers for binding mycotoxins as small molecules can be significantly improved through computational techniques. Previously, we designed five new aptamers to aflatoxin B1 (AFB1) based on a known aptamer sequence (Patent: PCT/CA2010/001 292, Apt1) through a genetic algorithm-based in silico maturation strategy and experimentally measured their affinity to the target toxin. Here, integrated molecular dynamic simulation (MDs) studies with molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) analysis to clarify the binding modes, critical interacting nucleic bases and energy component contributions in the six AFB1-binding aptamers. The aptamer F20, which was selected in the first work, showed the best free binding energy and complex stability compared to other aptamers. The trajectory analysis revealed that AFB1 recognized F20 through the groove binding mode along with precise shape complementarity. The MD simulation results revealed that dynamic water intermediate interactions also play a key role in promoting complex stability. According to the MM-PBSA calculations, van der Waals contacts were identified as dominant energy components in all complexes. Interestingly, a high consistency is observed between the experimentally obtained binding affinities of the six aptamers with their free energy solvation. The computational findings, confirmed via previous experiments, highlighted the binding modes, the dynamic hydration of complex components and the total free interacting energy as the crucial criteria in discovering high functional aptameric probes.
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Affiliation(s)
- Maryam Mousivand
- Microbial Biotechnology Department, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization, Department of Plant Protection, College of Agricultural Sciences and Engineering, University of Tehran, Karaj, Iran
| | - Kowsar Bagherzadeh
- Stem Cell and Regenerative Medicine Research Center, Iran University of Medical Sciences, Eye Research Center, the Five Senses Health Institute, Rassoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Laura Anfossi
- Department of Chemistry, University of Turin, Department of Plant Protection, College of Agricultural Sciences and Engineering, University of Tehran, Turin, Italy
| | - Mohammad Javan-Nikkhah
- Microbial Biotechnology Department, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization, Department of Plant Protection, College of Agricultural Sciences and Engineering, University of Tehran, Karaj, Iran
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