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Discovery of C-12 dithiocarbamate andrographolide analogues as inhibitors of SARS-CoV-2 main protease: In vitro and in silico studies. Comput Struct Biotechnol J 2022; 20:2784-2797. [PMID: 35677603 PMCID: PMC9167041 DOI: 10.1016/j.csbj.2022.05.053] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 05/27/2022] [Accepted: 05/27/2022] [Indexed: 11/27/2022] Open
Abstract
Andrographolide analogues were found to inhibit SARS-CoV-2 main protease. The compounds 3k, 3l, 3m and 3t showed promising in vitro inhibitory activity. Most of the candidates could bind well to the SARS-CoV-2 main protease active site.
A global crisis of coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has impacted millions of people’s lives throughout the world. In parallel to vaccine development, identifying potential antiviral agents against SARS-CoV-2 has become an urgent need to combat COVID-19. One of the most attractive drug targets for discovering anti-SARS-CoV-2 agents is the main protease (Mpro), which plays a pivotal role in the viral life cycle. This study aimed to elucidate a series of twenty-one 12-dithiocarbamate-14-deoxyandrographolide analogues as SARS-CoV-2 Mpro inhibitors using in vitro and in silico studies. These compounds were initially screened for the inhibitory activity toward SARS-CoV-2 Mpro by in vitro enzyme-based assay. We found that compounds 3k, 3l, 3m and 3t showed promising inhibitory activity against SARS-CoV-2 Mpro with >50% inhibition at 10 μM. Afterward, the binding mode of each compound in the active site of SARS-CoV-2 Mpro was explored by molecular docking. The optimum docked complexes were then chosen and subjected to molecular dynamic (MD) simulations. The MD results suggested that all studied complexes were stable along the simulation time, and most of the compounds could fit well with the SARS-CoV-2 Mpro active site, particularly at S1, S2 and S4 subsites. The per-residue decomposition free energy calculations indicated that the hot-spot residues essential for ligand binding were T25, H41, C44, S46, M49, C145, H163, M165, E166, L167, D187, R188, Q189 and T190. Therefore, the obtained information from the combined experimental and computational techniques could lead to further optimization of more specific and potent andrographolide analogues toward SARS-CoV-2 Mpro.
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Boonma T, Nutho B, Darai N, Rungrotmongkol T, Nunthaboot N. Exploring of paritaprevir and glecaprevir resistance due to A156T mutation of HCV NS3/4A protease: molecular dynamics simulation study. J Biomol Struct Dyn 2021; 40:5283-5294. [PMID: 33430709 DOI: 10.1080/07391102.2020.1869587] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Hepatitis C virus (HCV) NS3/4A serine protease is a promising drug target for the discovery of anti-HCV drugs. However, its amino acid mutations, particularly A156T, commonly lead to rapid emergence of drug resistance. Paritaprevir and glecaprevir, the newly FDA-approved HCV drugs, exhibit distinct resistance profiles against the A156T mutation of HCV NS3/4A serine protease. To illustrate their different molecular resistance mechanisms, molecular dynamics simulations and binding free energy calculations were carried out on the two compounds complexed with both wild-type (WT) and A156T variants of HCV NS3/4A protease. QM/MM-GBSA-based binding free energy calculations revealed that the binding affinities of paritaprevir and glecaprevir towards A156T NS3/4A were significantly reduced by ∼4 kcal/mol with respect to their WT complexes, which were in line with the experimental resistance folds. Moreover, the relatively weak intermolecular interactions with amino acids such as H57, R155, and T156 of NS3 protein, the steric effect and the destabilized protein binding surface, which is caused by the loss of salt bridge between R123 and D168, are the main contributions for the higher fold-loss in potency of glecaprevir due to A156T mutation. An insight into the difference of molecular mechanism of drug resistance against the A156T substitution among the two classes of serine protease inhibitors could be useful for further optimization of new generation HCV NS3/4A inhibitors with enhanced inhibitory potency.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Thitiya Boonma
- Supramolecular Chemistry Research Unit and Department of Chemistry, Faculty of Science, Mahasarakham University, Maha Sarakham, Thailand.,Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH‒CIC), Faculty of Science, Mahasarakham University, Maha Sarakham, Thailand
| | - Bodee Nutho
- Center of Excellence in Computational Chemistry (CECC), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Nitchakan Darai
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Thanyada Rungrotmongkol
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand.,Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Nadtanet Nunthaboot
- Supramolecular Chemistry Research Unit and Department of Chemistry, Faculty of Science, Mahasarakham University, Maha Sarakham, Thailand.,Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH‒CIC), Faculty of Science, Mahasarakham University, Maha Sarakham, Thailand
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Khalid H, Landry KB, Ijaz B, Ashfaq UA, Ahmed M, Kanwal A, Froeyen M, Mirza MU. Discovery of novel Hepatitis C virus inhibitor targeting multiple allosteric sites of NS5B polymerase. INFECTION GENETICS AND EVOLUTION 2020; 84:104371. [PMID: 32485331 DOI: 10.1016/j.meegid.2020.104371] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 05/13/2020] [Accepted: 05/18/2020] [Indexed: 02/07/2023]
Abstract
HCV is a viral infection posing a severe global threat when left untreated progress to end-stage liver disease, including cirrhosis and HCC. The NS5B polymerase of HCV is the most potent target that harbors four allosteric binding sites that could interfere with the HCV infection. We present the discovery of a novel synthetic compound that harbors the potential of NS5B polymerase inhibition. All eight compounds belonging to the benzothiazine family of heterocycles displayed no cellular cytotoxicity in HepG2 cells at nontoxic dose concentration (200 μM). Subsequently, among eight compounds of the series, merely compound 5b exhibited significant inhibition of the expression of the HCV NS5B gene as compared to DMSO control in semi-quantitative PCR. Based on our western blot result, 5b at the range of 50, 100 and 200 μM induced 20, 40, and 70% inhibition of NS5B protein respectively. To estimate the binding potential, 5b was docked at respective allosteric sites followed by molecular dynamics (MD) simulations for a period of 20 ns. In addition, binding free energy calculation by MM-GB/PBSA method revealed a conserved interaction profile of residues lining the allosteric sites in agreement with the reported NS5B co-crystallized inhibitors. The presented results provide important information about a novel compound 5b which may facilitate the the discovery of novel inhibitors that tends to target multiple sites on NS5B polymerase.
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Affiliation(s)
- Hina Khalid
- Department of Bioinformatics and Biotechnology, Government College University, 38000 Faisalabad, Pakistan
| | - Koloko Brice Landry
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Bushra Ijaz
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University, 38000 Faisalabad, Pakistan.
| | - Matloob Ahmed
- Department of Chemistry, Government College University, 38000 Faisalabad, Pakistan
| | - Afshan Kanwal
- Department of Chemistry, Government College University, 38000 Faisalabad, Pakistan
| | - Matheus Froeyen
- Department of Pharmaceutical Sciences, REGA Institute for Medical Research, Medicinal Chemistry, University of Leuven, 3000 Leuven, Belgium
| | - Muhammad Usman Mirza
- Department of Pharmaceutical Sciences, REGA Institute for Medical Research, Medicinal Chemistry, University of Leuven, 3000 Leuven, Belgium
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Shakibzadeh A, Sarvari J, Sabahi F, Ravanshad M. Antiviral activity and possible site of action of zinc against Hepatitis C virus in vitro. GAZZETTA MEDICA ITALIANA ARCHIVIO PER LE SCIENZE MEDICHE 2019. [DOI: 10.23736/s0393-3660.18.03964-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Binding pattern and susceptibility of epigallocatechin gallate against envelope protein homodimer of Zika virus: A molecular dynamics study. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2018.10.111] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Panman W, Nutho B, Chamni S, Dokmaisrijan S, Kungwan N, Rungrotmongkol T. Computational screening of fatty acid synthase inhibitors against thioesterase domain. J Biomol Struct Dyn 2018; 36:4114-4125. [PMID: 29161996 DOI: 10.1080/07391102.2017.1408496] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/10/2017] [Indexed: 12/17/2022]
Abstract
Thioesterase (TE) domain of fatty acid synthase (FAS) is an attractive therapeutic target for design and development of anticancer drugs. In this present work, we search for the potential FAS inhibitors of TE domain from the ZINC database based on similarity search using three natural compounds as templates, including flavonoids, terpenoids, and phenylpropanoids. Molecular docking was used to predict the interaction energy of each screened ligand compared to the reference compound, which is methyl γ-linolenylfluorophosphonate (MGLFP). Based on this computational technique, rosmarinic acid and its eight analogs were observed as a new series of potential FAS inhibitors, which showed a stronger binding affinity than MGLFP. Afterward, nine docked complexes were studied by molecular dynamics simulations for investigating protein-ligand interactions and binding free energies using MM-PB(GB)SA, MM-3DRISM-KH, and QM/MM-GBSA methods. The binding free energy calculation indicated that the ZINC85948835 (R34) displayed the strongest binding efficiency against the TE domain of FAS. There are eight residues (S2308, I2250, E2251, Y2347, Y2351, F2370, L2427, and E2431) mainly contributed for the R34 binding. Moreover, R34 could directly form hydrogen bonds with S2308, which is one of the catalytic triad of TE domain. Therefore, our finding suggested that R34 could be a potential candidate as a novel FAS-TE inhibitor for further drug design.
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Affiliation(s)
- Wanwisa Panman
- a Multidisciplinary Program of Petrochemistry and Polymer Science, Faculty of Science , Chulalongkorn University , Bangkok 10330 , Thailand
| | - Bodee Nutho
- b Program in Biotechnology, Faculty of Science , Chulalongkorn University , Bangkok 10330 , Thailand
| | - Supakarn Chamni
- c Faculty of Pharmaceutical Sciences, Department of Pharmacognosy and Pharmaceutical Botany , Chulalongkorn University , Bangkok 10330 , Thailand
| | - Supaporn Dokmaisrijan
- d Division of Chemistry, School of Science , Walailak University , Nakon Si Thammarat 80161 , Thailand
| | - Nawee Kungwan
- e Faculty of Science, Department of Chemistry , Chiang Mai University , 239 Huay Kaew Road, Muang District, Chiang Mai 50200 , Thailand
- f Research Center on Chemistry for Development of Health Promoting Products from Northern Resources , Chiang Mai University , Chiang Mai , 50200 , Thailand
| | - Thanyada Rungrotmongkol
- g Faculty of Science, Structural and Computational Biology Research Group, Department of Biochemistry , Chulalongkorn University , Bangkok 10330 , Thailand
- h Faculty of Science, Program in Bioinformatics and Computational Biology , Chulalongkorn University , Bangkok 10330 , Thailand
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Do PC, Lee EH, Le L. Steered Molecular Dynamics Simulation in Rational Drug Design. J Chem Inf Model 2018; 58:1473-1482. [DOI: 10.1021/acs.jcim.8b00261] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Phuc-Chau Do
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City 700000, Vietnam
| | - Eric H. Lee
- Department of Medicine and Division of Hematology and Oncology, Loma Linda University Medical Center, Loma Linda, California 92350, United States
| | - Ly Le
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City 700000, Vietnam
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Theoretical and Experimental Studies on Inclusion Complexes of Pinostrobin and β-Cyclodextrins. Sci Pharm 2018; 86:scipharm86010005. [PMID: 29385698 PMCID: PMC5874535 DOI: 10.3390/scipharm86010005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 01/20/2018] [Accepted: 01/22/2018] [Indexed: 12/23/2022] Open
Abstract
Pinostrobin (PNS) belongs to the flavanone subclass of flavonoids which shows several biological activities such as anti-inflammatory, anti-cancerogenic, anti-viral and anti-oxidative effects. Similar to other flavonoids, PNS has a quite low water solubility. The purpose of this work is to improve the solubility and the biological activities of PNS by forming inclusion complexes with β-cyclodextrin (βCD) and its derivatives, heptakis-(2,6-di-O-methyl)-β-cyclodextrin (2,6-DMβCD) and (2-hydroxypropyl)-β-cyclodextrin (HPβCD). The AL-type diagram of the phase solubility studies of PNS exhibited the formed inclusion complexes with the 1:1 molar ratio. Inclusion complexes were prepared by the freeze-drying method and were characterized by differential scanning calorimetry (DSC). Two-dimensional nuclear magnetic resonance (2D-NMR) and steered molecular dynamics (SMD) simulation revealed two different binding modes of PNS, i.e., its phenyl- (P-PNS) and chromone- (C-PNS) rings preferably inserted into the cavity of βCD derivatives whilst only one orientation of PNS, where the C-PNS ring is inside the cavity, was detected in the case of the parental βCD. All PNS/βCDs complexes had a higher dissolution rate than free PNS. Both PNS and its complexes significantly exerted a lowering effect on the IL-6 secretion in LPS-stimulated macrophages and showed a moderate cytotoxic effect against MCF-7 and HeLa cancer cell lines in vitro.
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El-Hasab MAEM, El-Bastawissy EE, El-Moselhy TF. Identification of potential inhibitors for HCV NS3 genotype 4a by combining protein–ligand interaction fingerprint, 3D pharmacophore, docking, and dynamic simulation. J Biomol Struct Dyn 2017; 36:1713-1727. [DOI: 10.1080/07391102.2017.1332689] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
| | | | - Tarek Faathy El-Moselhy
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Tanta University , Tanta, Egypt
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