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Ismat F, Tariq A, Shaheen A, Ullah R, Raheem K, Muddassar M, Mahboob S, Abbas W, Iqbal M, Rahman M. Inhibition of NS2B-NS3 protease from all four serotypes of dengue virus by punicalagin, punicalin and ellagic acid identified from Punica granatum. J Biomol Struct Dyn 2024:1-16. [PMID: 38373021 DOI: 10.1080/07391102.2024.2314258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 01/29/2024] [Indexed: 02/20/2024]
Abstract
Despite a major threat to the public health in tropical and subtropical regions, dengue virus (DENV) infections are untreatable. Therefore, efforts are needed to investigate cost-effective therapeutic agents that could cure DENV infections in future. The NS2B-NS3 protease encoded by the genome of DENV is considered a critical target for the development of anti-dengue drugs. The objective of the current study was to find out a specific inhibitor of the NS2B-NS3 proteases from all four serotypes of DENV. To begin with, nine plant extracts with a medicinal history were evaluated for their role in inhibiting the NS2B-NS3 proteases by Fluorescence Resonance Energy Transfer (FRET) assay. Among the tested extracts, Punica granatum was found to be the most effective one. The metabolic profiling of this extract revealed the presence of several active compounds, including ellagic acid, punicalin and punicalagin, which are well-established antiviral agents. Further evaluation of IC50 values of these three antiviral molecules revealed punicalagin as the most potent anti-NS2B-NS3 protease drug with IC50 of 0.91 ± 0.10, 0.75 ± 0.05, 0.42 ± 0.03, 1.80 ± 0.16 µM against proteases from serotypes 1, 2, 3 and 4, respectively. The docking studies demonstrated that these compounds interacted at the active site of the enzyme, mainly with His and Ser residues. Molecular dynamics simulations analysis also showed the structural stability of the NS2B-NS3 proteases in the presence of punicalagin. In summary, this study concludes that the punicalagin can act as an effective inhibitor against NS2B-NS3 proteases from all four serotypes of DENV.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Fouzia Ismat
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Anam Tariq
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Aqsa Shaheen
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
- Department of Biochemistry and Biotechnology, University of Gujrat, Hafiz Hayat Campus, Gujrat, Pakistan
| | - Raheem Ullah
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Kayode Raheem
- Department of Bioscience, COMSATS University Islamabad, Islamabad, Pakistan
| | - Muhammad Muddassar
- Department of Bioscience, COMSATS University Islamabad, Islamabad, Pakistan
| | - Sadia Mahboob
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Wasim Abbas
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Mazhar Iqbal
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Moazur Rahman
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
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2
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Giri-Rachman EA, Effendy VV, Azmi MHS, Yamahoki N, Stephanie R, Agustiyanti DF, Wisnuwardhani PH, Angelina M, Rubiyana Y, Aditama R, Ningrum RA, Wardiana A, Fibriani A. The SARS-CoV-2 M pro Dimer-Based Screening System: A Synthetic Biology Tool for Identifying Compounds with Dimerization Inhibitory Potential. ACS Synth Biol 2024; 13:509-520. [PMID: 38316139 PMCID: PMC10877612 DOI: 10.1021/acssynbio.3c00446] [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: 07/23/2023] [Revised: 12/11/2023] [Accepted: 12/20/2023] [Indexed: 02/07/2024]
Abstract
The COVID-19 endemic remains a global concern. The search for effective antiviral candidates is still needed to reduce disease risk. However, the availability of high biosafety level laboratory facilities for drug screening is limited in number. To address this issue, a screening system that could be utilized at lower biosafety levels remains essential. This study aimed to develop a novel SARS-CoV-2 main protease (Mpro) dimer-based screening system (DBSS) utilizing synthetic biology in Escherichia coli BL21(DE3). We linked the SARS-CoV-2 Mpro with the DNA-binding domain of AraC regulatory protein, which regulates the reporter gene expression. Protein modeling and molecular docking showed that saquinavir could bind to AraC-Mpro both in its monomer and dimer forms. The constructed DBSS assay indicated the screening system could detect saquinavir inhibitory activity at a concentration range of 4-10 μg/mL compared to the untreated control (P ≤ 0.05). The Vero E6 cell assay validated the DBSS result that saquinavir at 4-10 μg/mL exhibited antiviral activity against SARS-CoV-2. Our DBSS could be used for preliminary screening of numerous drug candidates that possess a dimerization inhibitor activity of SARS-CoV-2 Mpro and also minimize the use of a high biosafety level laboratory.
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Affiliation(s)
| | - Vergio V. Effendy
- School
of Life Sciences and Technology, Institut
Teknologi Bandung, Bandung 40132, Indonesia
| | - Muhammad H. S. Azmi
- School
of Life Sciences and Technology, Institut
Teknologi Bandung, Bandung 40132, Indonesia
| | - Nicholas Yamahoki
- School
of Life Sciences and Technology, Institut
Teknologi Bandung, Bandung 40132, Indonesia
| | - Rebecca Stephanie
- School
of Life Sciences and Technology, Institut
Teknologi Bandung, Bandung 40132, Indonesia
| | - Dian F. Agustiyanti
- Research
Center for Genetic Engineering, Indonesian
National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
| | - Popi H. Wisnuwardhani
- Research
Center for Genetic Engineering, Indonesian
National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
| | - Marissa Angelina
- Research
Center for Pharmaceutical Ingredients and Traditional Medicine, Indonesian National Research and Innovation Agency
(BRIN), Serpong 15314, Indonesia
| | - Yana Rubiyana
- Research
Center for Genetic Engineering, Indonesian
National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
| | - Reza Aditama
- Biochemistry
Research Group, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Bandung 40132, Indonesia
| | - Ratih A. Ningrum
- Research
Center for Genetic Engineering, Indonesian
National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
| | - Andri Wardiana
- Research
Center for Genetic Engineering, Indonesian
National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
| | - Azzania Fibriani
- School
of Life Sciences and Technology, Institut
Teknologi Bandung, Bandung 40132, Indonesia
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3
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Khalili NSD, Khawory MH, Salin NH, Zakaria II, Hariono M, Mikhaylov AA, Kamarulzaman EE, A Wahab H, Supratman U, Nurul Azmi M. Synthesis and biological activity of imidazole phenazine derivatives as potential inhibitors for NS2B-NS3 dengue protease. Heliyon 2024; 10:e24202. [PMID: 38293469 PMCID: PMC10825487 DOI: 10.1016/j.heliyon.2024.e24202] [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: 10/03/2023] [Revised: 01/04/2024] [Accepted: 01/04/2024] [Indexed: 02/01/2024] Open
Abstract
A series of new imidazole-phenazine derivatives were synthesized via a two-step process. The condensation of 2,3-diaminophenazine and benzaldehyde derivatives proceeds with intermediate formation of an aniline Schiff base, which undergoes subsequent cyclodehydrogenation in situ. The structures of the synthesized compounds were characterized by 1D and 2D NMR, FTIR and HRMS. A total of thirteen imidazole phenazine derivatives were synthesized and validated for their inhibitory activity as anti-dengue agents by an in vitro DENV2 NS2B-NS3 protease assay using a fluorogenic Boc-Gly-Arg-Arg-AMC substrate. Two para-substituted imidazole phenazines, 3e and 3k, were found to be promising lead molecules for novel NS2B-NS3 protease inhibitors with IC50 of 54.8 μM and 71.9 μM, respectively, compared to quercetin as a control (IC50 104.8 μM). The in silico study was performed using AutoDock Vina to identify the binding energy and conformation of 3e and 3k with the active site of the DENV2 NS2B-NS3 protease Wichapong model. The results indicate better binding properties of 3e and 3k with calculated binding energies of -8.5 and -8.4 kcal mol-1, respectively, compared to the binding energy of quercetin of -7.2 kcal mol-1, which corroborates well with the experimental observations.
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Affiliation(s)
- Nur Sarah Dyana Khalili
- Malaysian Institute of Pharmaceuticals and Nutraceuticals, National Institutes of Biotechnology Malaysia, Gelugor, Pulau Pinang, Malaysia
- Natural Products and Synthesis Organic Research Laboratory (NPSO), School of Chemical Sciences, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia
| | - Muhammad Hidhir Khawory
- Malaysian Institute of Pharmaceuticals and Nutraceuticals, National Institutes of Biotechnology Malaysia, Gelugor, Pulau Pinang, Malaysia
| | - Nurul Hanim Salin
- Malaysian Institute of Pharmaceuticals and Nutraceuticals, National Institutes of Biotechnology Malaysia, Gelugor, Pulau Pinang, Malaysia
| | - Iffah Izzati Zakaria
- Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, 43000 Kajang, Selangor, Malaysia
| | - Maywan Hariono
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia
| | - Andrey A. Mikhaylov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., Moscow, 117997, Russia
| | - Ezatul Ezleen Kamarulzaman
- Malaysian Institute of Pharmaceuticals and Nutraceuticals, National Institutes of Biotechnology Malaysia, Gelugor, Pulau Pinang, Malaysia
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia
| | - Habibah A Wahab
- Malaysian Institute of Pharmaceuticals and Nutraceuticals, National Institutes of Biotechnology Malaysia, Gelugor, Pulau Pinang, Malaysia
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia
| | - Unang Supratman
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, 45363 Jatinangor, Indonesia
| | - Mohamad Nurul Azmi
- Natural Products and Synthesis Organic Research Laboratory (NPSO), School of Chemical Sciences, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia
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Fibriani A, Taharuddin AAP, Yamahoki N, Stephanie R, Laurelia J, Agustiyanti DF, Wisnuwardhani PH, Angelina M, Rubiyana Y, Ningrum RA, Wardiana A, Desriani D, Iskandar F, Permatasari FA, Giri-Rachman EA. Porphyrin-derived carbon dots for an enhanced antiviral activity targeting the CTD of SARS-CoV-2 nucleocapsid. J Genet Eng Biotechnol 2023; 21:93. [PMID: 37801271 PMCID: PMC10558421 DOI: 10.1186/s43141-023-00548-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 09/20/2023] [Indexed: 10/07/2023]
Abstract
BACKGROUND Since effective antiviral drugs for COVID-19 are still limited in number, the exploration of compounds that have antiviral activity against SARS-CoV-2 is in high demand. Porphyrin is potentially developed as a COVID-19 antiviral drug. However, its low solubility in water restricts its clinical application. Reconstruction of porphyrin into carbon dots is expected to possess better solubility and bioavailability as well as lower biotoxicity. METHODS AND RESULTS In this study, we investigated the antiviral activity of porphyrin and porphyrin-derived carbon dots against SARS-CoV-2. Through the in silico analysis and assessment using a novel drug screening platform, namely dimer-based screening system, we demonstrated the capability of the antivirus candidates in inhibiting the dimerization of the C-terminal domain of SARS-CoV-2 Nucleocapsid. It was shown that porphyrin-derived carbon dots possessed lower cytotoxicity on Vero E6 cells than porphyrin. Furthermore, we also assessed their antiviral activity on the SARS-CoV-2-infected Vero E6 cells. The transformation of porphyrin into carbon dots substantially augmented its performance in disrupting SARS-CoV-2 propagation in vitro. CONCLUSIONS Therefore, this study comprehensively demonstrated the potential of porphyrin-derived carbon dots to be developed further as a promisingly safe and effective COVID-19 antiviral drug.
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Affiliation(s)
- Azzania Fibriani
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, 40132, Indonesia.
- Research Center for Nanoscience and Nanotechnology, Institut Teknologi Bandung, Bandung, 40132, Indonesia.
| | | | - Nicholas Yamahoki
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, 40132, Indonesia
| | - Rebecca Stephanie
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, 40132, Indonesia
| | - Jessica Laurelia
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, 40132, Indonesia
| | - Dian Fitria Agustiyanti
- Research Center for Genetic Engineering, Indonesian National Research and Innovation Agency (BRIN), Cibinong, 16911, Indonesia
| | - Popi Hadi Wisnuwardhani
- Research Center for Genetic Engineering, Indonesian National Research and Innovation Agency (BRIN), Cibinong, 16911, Indonesia
| | - Marissa Angelina
- Research Center for Pharmaceutical Ingredients and Traditional Medicine, Indonesian National Research and Innovation Agency (BRIN), Serpong, 15314, Indonesia
| | - Yana Rubiyana
- Research Center for Genetic Engineering, Indonesian National Research and Innovation Agency (BRIN), Cibinong, 16911, Indonesia
| | - Ratih Asmana Ningrum
- Research Center for Genetic Engineering, Indonesian National Research and Innovation Agency (BRIN), Cibinong, 16911, Indonesia
| | - Andri Wardiana
- Research Center for Genetic Engineering, Indonesian National Research and Innovation Agency (BRIN), Cibinong, 16911, Indonesia
| | - Desriani Desriani
- Research Center for Genetic Engineering, Indonesian National Research and Innovation Agency (BRIN), Cibinong, 16911, Indonesia
| | - Ferry Iskandar
- Research Center for Nanoscience and Nanotechnology, Institut Teknologi Bandung, Bandung, 40132, Indonesia
- Department of Physics, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Bandung, 40132, Indonesia
- Collaboration Research Center for Advanced Energy Materials, National Research and Innovation Agency-Institut Teknologi, Bandung, Bandung, 40132, Indonesia
| | - Fitri Aulia Permatasari
- Department of Physics, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Bandung, 40132, Indonesia
- Collaboration Research Center for Advanced Energy Materials, National Research and Innovation Agency-Institut Teknologi, Bandung, Bandung, 40132, Indonesia
- Research Center for Chemistry, National Research and Innovation Agency (BRIN), Serpong, 15314, Indonesia
| | - Ernawati Arifin Giri-Rachman
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, 40132, Indonesia
- Research Center for Nanoscience and Nanotechnology, Institut Teknologi Bandung, Bandung, 40132, Indonesia
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5
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Maus H, Müller P, Meta M, Hoba SN, Hammerschmidt SJ, Zimmermann RA, Zimmer C, Fuchs N, Schirmeister T, Barthels F. Next Generation of Fluorometric Protease Assays: 7-Nitrobenz-2-oxa-1,3-diazol-4-yl-amides (NBD-Amides) as Class-Spanning Protease Substrates. Chemistry 2023; 29:e202301855. [PMID: 37313627 DOI: 10.1002/chem.202301855] [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: 06/12/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/15/2023]
Abstract
Fluorometric assays are one of the most frequently used methods in medicinal chemistry. Over the last 50 years, the reporter molecules for the detection of protease activity have evolved from first-generation colorimetric p-nitroanilides, through FRET substrates, and 7-amino-4-methyl coumarin (AMC)-based substrates. The aim of further substrate development is to increase sensitivity and reduce vulnerability to assay interferences. Herein, we describe a new generation of substrates for protease assays based on 7-nitrobenz-2-oxa-1,3-diazol-4-yl-amides (NBD-amides). In this study, we synthesized and tested substrates for 10 different proteases from the serine-, cysteine-, and metalloprotease classes. Enzyme- and substrate-specific parameters as well as the inhibitory activity of literature-known inhibitors confirmed their suitability for application in fluorometric assays. Hence, we were able to present NBD-based alternatives for common protease substrates. In conclusion, these NBD substrates are not only less susceptible to common assay interference, but they are also able to replace FRET-based substrates with the requirement of a prime site amino acid residue.
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Affiliation(s)
- Hannah Maus
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
| | - Patrick Müller
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
| | - Mergim Meta
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
| | - Sabrina N Hoba
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
| | - Stefan J Hammerschmidt
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
| | - Robert A Zimmermann
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
| | - Collin Zimmer
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
| | - Natalie Fuchs
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
| | - Fabian Barthels
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
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6
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Salin NH, Hariono M, Khalili NSD, Zakaria II, Saqallah FG, Mohamad Taib MNA, Kamarulzaman EE, Wahab HA, Khawory MH. Computational study of nitro-benzylidene phenazine as dengue virus-2 NS2B-NS3 protease inhibitor. Front Mol Biosci 2022; 9:875424. [PMID: 36465554 PMCID: PMC9715268 DOI: 10.3389/fmolb.2022.875424] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 10/06/2022] [Indexed: 08/17/2023] Open
Abstract
According to the World Health Organisation (WHO), as of week 23 of 2022, there were more than 1,311 cases of dengue in Malaysia, with 13 deaths reported. Furthermore, there was an increase of 65.7% during the same period in 2021. Despite the increase in cumulative dengue incidence, there is no effective antiviral drug available for dengue treatment. This work aimed to evaluate several nitro-benzylidene phenazine compounds, especially those that contain 4-hydroxy-3,5-bis((2-(4-nitrophenyl)hydrazinylidene)-methyl)benzoate through pharmacophore queries selection method as potential dengue virus 2 (DENV2) NS2B-NS3 protease inhibitors. Herein, molecular docking was employed to correlate the energies of selected hits' free binding and their binding affinities. Pan assay interference compounds (PAINS) filter was also adopted to identify and assess the drug-likeness, toxicity, mutagenicity potentials, and pharmacokinetic profiles to select hit compounds that can be considered as lead DENV2 NS2B-NS3 protease inhibitors. Molecular dynamics assessment of two nitro-benzylidene phenazine derivatives bearing dinitro and hydroxy groups at the benzylidene ring showed their stability at the main binding pocket of DENV2 protease, where their MM-PBSA binding energies were between -22.53 and -17.01 kcal/mol. This work reports those two nitro-benzylidene phenazine derivatives as hits with 52-55% efficiency as antiviral candidates. Therefore, further optimisation is required to minimise the lead compounds' toxicity and mutagenicity.
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Affiliation(s)
- Nurul Hanim Salin
- Malaysian Institute of Pharmaceuticals and Nutraceuticals, National Institutes of Biotechnology Malaysia, Gelugor, Pulau Pinang, Malaysia
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor, Pulau Pinang, Malaysia
| | - Maywan Hariono
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor, Pulau Pinang, Malaysia
| | - Nur Sarah Dyana Khalili
- Malaysian Institute of Pharmaceuticals and Nutraceuticals, National Institutes of Biotechnology Malaysia, Gelugor, Pulau Pinang, Malaysia
- School of Chemical Sciences, Universiti Sains Malaysia, Gelugor, Pulau Pinang, Malaysia
| | - Iffah Izzati Zakaria
- Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Kajang, Selangor, Malaysia
| | - Fadi G. Saqallah
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor, Pulau Pinang, Malaysia
| | | | | | - Habibah A. Wahab
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor, Pulau Pinang, Malaysia
| | - Muhammad Hidhir Khawory
- Malaysian Institute of Pharmaceuticals and Nutraceuticals, National Institutes of Biotechnology Malaysia, Gelugor, Pulau Pinang, Malaysia
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7
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Durgam L, Guruprasad L. Computational studies on the design of NCI natural products as inhibitors to SARS-CoV-2 main protease. J Biomol Struct Dyn 2022; 41:3741-3751. [PMID: 35333147 DOI: 10.1080/07391102.2022.2054470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The pandemic coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in more than 5 million deaths globally. Currently there are no effective drugs available to treat COVID-19. The viral protease replication can be blocked by the inhibition of main protease that is encoded in polyprotein 1a and is therefore a potential protein target for drug discovery. We have carried out virtual screening of NCI natural compounds followed by molecular docking in order to identify hit molecules as probable SARS-CoV-2 main protease inhibitors. The molecular dynamics (MD) simulations of apo form in complex with N3, α-ketoamide and NCI natural products was used to validate the screened compounds. The MD simulations trajectories were analyzed using normal mode analysis and principal component analysis revealing dynamical nature of the protein. These findings aid in understanding the binding of natural products and molecular mechanisms of SARS-CoV-2 main protease inhibition.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Laxman Durgam
- School of Chemistry, University of Hyderabad, Hyderabad, India
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8
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Rahman MM, Biswas S, Islam KJ, Paul AS, Mahato SK, Ali MA, Halim MA. Antiviral phytochemicals as potent inhibitors against NS3 protease of dengue virus. Comput Biol Med 2021; 134:104492. [PMID: 34022487 DOI: 10.1016/j.compbiomed.2021.104492] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 05/10/2021] [Accepted: 05/10/2021] [Indexed: 10/21/2022]
Abstract
Dengue, a mosquito-borne disease, has appeared as a major infectious disease globally. The virus requires its proteins to replicate and reproduce in the host cell. The NS3 protease converts the polyprotein to functional proteins with the help of the NS2B cofactor. Thus, NS3 protease is a promising target to develop antiviral inhibitors against the dengue virus. A systematic screening including ADMET properties, molecular docking, molecular dynamics (MD) simulation, binding free energy calculation, and QSAR studies is carried out to predict potent inhibitors against the NS3 protease. From the screening of 40 antiviral phytochemicals, ADMET properties analysis was used to screen out ligands that violate ADME rules and have probable toxicity. Cyanidin 3-Glucoside, Dithymoquinone, and Glabridin were predicted to be potent inhibitors against the NS3 protease according to their binding affinity. These ligands showed several noncovalent interactions, including hydrogen bond, hydrophobic interaction, electrostatic interaction, pi-sulfur interactions. The ligand-protein complexes were further scrutinized using 250 ns molecular dynamics simulation. The MM-PBSA binding free energy calculation was conducted to investigate their binding stability in dynamic conditions. The calculated pIC50(mM) value was predicted using the QSAR model with 89.91% goodness of fit. The predicted biologocal activity value for the ligands indicates they might have good potency.
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Affiliation(s)
- Md Mahbubur Rahman
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Sourav Biswas
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Kazi Jahidul Islam
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Archi Sundar Paul
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Shiplob Kumar Mahato
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Md Ackas Ali
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Mohammad A Halim
- Department of Physical Sciences, University of Arkansas-Fort Smith, Fort Smith, AR, USA.
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9
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Hariono M, Nuwarda RF, Yusuf M, Rollando R, Jenie RI, Al-Najjar B, Julianus J, Putra KC, Nugroho ES, Wisnumurti YK, Dewa SP, Jati BW, Tiara R, Ramadani RD, Qodria L, Wahab HA. Arylamide as Potential Selective Inhibitor for Matrix Metalloproteinase 9 (MMP9): Design, Synthesis, Biological Evaluation, and Molecular Modeling. J Chem Inf Model 2019; 60:349-359. [PMID: 31825614 DOI: 10.1021/acs.jcim.9b00630] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Previous studies have reported that compounds bearing an arylamide linked to a heterocyclic planar ring have successfully inhibited the hemopexin-like domain (PEX9) of matrix metalloproteinase 9 (MMP9). PEX9 has been suggested to be more selectively targeted than MMP9's catalytic domain in a degrading extracellular matrix under some pathologic conditions, especially in cancer. In this study, we aim to synthesize and evaluate 10 arylamide compounds as MMP9 inhibitors through an enzymatic assay as well as a cellular assay. The mechanism of inhibition for the most active compounds was investigated via molecular dynamics simulation (MD). Molecular docking was performed using AutoDock4.0 with PEX9 as the protein model to predict the binding of the designed compounds. The synthesis was carried out by reacting aniline derivatives with 3-bromopropanoyl chloride using pyridine as the catalyst at room temperature. The MMP9 assay was conducted using the FRET-based MMP9 kits protocol and gelatin zymography assay. The cytotoxicity assay was done using the MTT method, and the MD simulation was performed using AMBER16. Assay on MMP9 demonstrated activities of three compounds (2, 7, and 9) with more than 50% inhibition. Further inhibition on MMP9 expressed by 4T1 showed that two compounds (7 and 9) inhibited its gelatinolytic activity more than 50%. The cytotoxicity assay against 4T1 cells results in the inhibition of the cell growth with an EC50 of 125 μM and 132 μM for 7 and 9, respectively. The MD simulation explained a stable interaction of 7 and 9 in PEX9 at 100 ns with a free energy of binding of -8.03 kcal/mol and -6.41 kcal/mol, respectively. Arylamides have potential effects as selective MMP9 inhibitors in inhibiting breast cancer cell progression.
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Affiliation(s)
- Maywan Hariono
- Faculty of Pharmacy , Sanata Dharma University , Depok, Sleman 55282 , Yogyakarta , Indonesia
| | - Rina F Nuwarda
- Faculty of Pharmacy , Padjadjaran University , Jatinangor, Sumedang 45363 , West Java , Indonesia
| | - Muhammad Yusuf
- Chemistry Department, Faculty of Mathematics and Natural Sciences , Padjadjaran University , Jatinangor, Sumedang 45363 , West Java , Indonesia
| | - Rollando Rollando
- Pharmacy Program, Faculty of Science and Technology , Ma Chung University , Malang 65151 , Indonesia
| | - Riris I Jenie
- Cancer Chemoprevention Research Center, Faculty of Pharmacy , Gadjah Mada University , Sekip Utara 55281 , Yogyakarta , Indonesia
| | - Belal Al-Najjar
- Faculty of Pharmacy and Medical Sciences , AlAhliyya Amman University , Amman 19328 , Jordan
| | - Jeffry Julianus
- Faculty of Pharmacy , Sanata Dharma University , Depok, Sleman 55282 , Yogyakarta , Indonesia
| | - Kevin C Putra
- Faculty of Pharmacy , Sanata Dharma University , Depok, Sleman 55282 , Yogyakarta , Indonesia
| | - Ervan S Nugroho
- Faculty of Pharmacy , Sanata Dharma University , Depok, Sleman 55282 , Yogyakarta , Indonesia
| | - Yohanes K Wisnumurti
- Faculty of Pharmacy , Sanata Dharma University , Depok, Sleman 55282 , Yogyakarta , Indonesia
| | - Sangga P Dewa
- Faculty of Pharmacy , Sanata Dharma University , Depok, Sleman 55282 , Yogyakarta , Indonesia
| | - Benedictus W Jati
- Faculty of Pharmacy , Sanata Dharma University , Depok, Sleman 55282 , Yogyakarta , Indonesia
| | - Reynaldo Tiara
- Faculty of Pharmacy , Sanata Dharma University , Depok, Sleman 55282 , Yogyakarta , Indonesia
| | - Ratna D Ramadani
- Cancer Chemoprevention Research Center, Faculty of Pharmacy , Gadjah Mada University , Sekip Utara 55281 , Yogyakarta , Indonesia
| | - Lailatul Qodria
- Cancer Chemoprevention Research Center, Faculty of Pharmacy , Gadjah Mada University , Sekip Utara 55281 , Yogyakarta , Indonesia
| | - Habibah A Wahab
- Pharmaceutical Technology Department, School of Pharmaceutical Sciences and USM-RIKEN Centre for Ageing Science (URICAS) , Universiti Sains Malaysia , 11800 Minden , Pulau Pinang , Malaysia
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