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Jia ZJ, Lan XW, Lu K, Meng X, Jing WJ, Jia SR, Zhao K, Dai YJ. Synthesis, molecular docking, and binding Gibbs free energy calculation of β-nitrostyrene derivatives: Potential inhibitors of SARS-CoV-2 3CL protease. J Mol Struct 2023; 1284:135409. [PMID: 36993878 PMCID: PMC10033154 DOI: 10.1016/j.molstruc.2023.135409] [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: 12/29/2022] [Revised: 03/10/2023] [Accepted: 03/21/2023] [Indexed: 03/24/2023]
Abstract
The outbreak of novel coronavirus disease 2019 (COVID-19), caused by the novel coronavirus (SARS-CoV-2), has had a significant impact on human health and the economic development. SARS-CoV-2 3CL protease (3CLpro) is highly conserved and plays a key role in mediating the transcription of virus replication. It is an ideal target for the design and screening of anti-coronavirus drugs. In this work, seven β-nitrostyrene derivatives were synthesized by Henry reaction and β-dehydration reaction, and their inhibitory effects on SARS-CoV-2 3CL protease were identified by enzyme activity inhibition assay in vitro. Among them, 4-nitro-β-nitrostyrene (compound a) showed the lowest IC50 values of 0.7297 μM. To investigate the key groups that determine the activity of β-nitrostyrene derivatives and their interaction mode with the receptor, the molecular docking using the CDOCKER protocol in Discovery Studio 2016 was performed. The results showed that the hydrogen bonds between β-NO2 and receptor GLY-143 and the π-π stacking between the aryl ring of the ligand and the imidazole ring of receptor HIS-41 significantly contributed to the ligand activity. Furthermore, the ligand-receptor absolute binding Gibbs free energies were calculated using the Binding Affinity Tool (BAT.py) to verify its correlation with the activity of β-nitrostyrene 3CLpro inhibitors as a scoring function. The higher correlation(r2=0.6) indicates that the absolute binding Gibbs free energy based on molecular dynamics can be used to predict the activity of new β-nitrostyrene 3CLpro inhibitors. These results provide valuable insights for the functional group-based design, structure optimization and the discovery of high accuracy activity prediction means of anti-COVID-19 lead compounds.
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Affiliation(s)
- Ze-Jun Jia
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Xiao-Wei Lan
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Kui Lu
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Xuan Meng
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Wen-Jie Jing
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Shi-Ru Jia
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Kai Zhao
- Hebei Kaisheng Medical Technology Co. LTD, No.319 of Xiangjiang Road, High-tech Zone, Shijiazhuang 050000, PR China
- Jiangxi Oushi Pharmaceutical Co. LTD, 1115 Saiwei Dadao, Yushui District, Xinyu 338004, PR China
| | - Yu-Jie Dai
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, PR China
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Nicoletti G, White K. The Anti-Fungal Activity of Nitropropenyl Benzodioxole (NPBD), a Redox-Thiol Oxidant and Tyrosine Phosphatase Inhibitor. Antibiotics (Basel) 2022; 11:antibiotics11091188. [PMID: 36139967 PMCID: PMC9495065 DOI: 10.3390/antibiotics11091188] [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: 08/05/2022] [Revised: 08/28/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
Phylogenetically diverse fungal species are an increasing cause of severe disease and mortality. Identification of new targets and development of new fungicidal drugs are required to augment the effectiveness of current chemotherapy and counter increasing resistance in pathogens. Nitroalkenyl benzene derivatives are thiol oxidants and inhibitors of cysteine-based molecules, which show broad biological activity against microorganisms. Nitropropenyl benzodioxole (NPBD), one of the most active antimicrobial derivatives, shows high activity in MIC assays for phylogenetically diverse saprophytic, commensal and parasitic fungi. NPBD was fungicidal to all species except the dermatophytic fungi, with an activity profile comparable to that of Amphotericin B and Miconazole. NPBD showed differing patterns of dynamic kill rates under different growth conditions for Candida albicans and Aspergillus fumigatus and was rapidly fungicidal for non-replicating vegetative forms and microconidia. It did not induce resistant or drug tolerant strains in major pathogens on long term exposure. A literature review highlights the complexity and interactivity of fungal tyrosine phosphate and redox signaling pathways, their differing metabolic effects in fungal species and identifies some targets for inhibition. A comparison of the metabolic activities of Amphotericin B, Miconazole and NPBD highlights the multiple cellular functions of these agents and the complementarity of many mechanisms. The activity profile of NPBD illustrates the functional diversity of fungal tyrosine phosphatases and thiol-based redox active molecules and contributes to the validation of tyrosine phosphatases and redox thiol molecules as related and complementary selective targets for antimicrobial drug development. NPBD is a selective antifungal agent with low oral toxicity which would be suitable for local treatment of skin and mucosal infections.
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In silico discovery of multi-targeting inhibitors for the COVID-19 treatment by molecular docking, molecular dynamics simulation studies, and ADMET predictions. Struct Chem 2022. [DOI: 10.1007/s11224-022-01996-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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β-Nitrostyrene derivatives as broad range potential antifungal agents targeting fungal cell wall. Eur J Med Chem 2022; 240:114609. [DOI: 10.1016/j.ejmech.2022.114609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 06/26/2022] [Accepted: 07/10/2022] [Indexed: 11/22/2022]
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Wang Y, Wang H, Xu H, Zheng Z, Meng Z, Xu Z, Li J, Xue M. Design and synthesis of five-membered heterocyclic derivatives of istradefylline with comparable pharmacological activity. Chem Biol Drug Des 2022; 100:534-552. [PMID: 35569008 DOI: 10.1111/cbdd.14067] [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: 11/08/2021] [Revised: 04/01/2022] [Accepted: 05/08/2022] [Indexed: 11/29/2022]
Abstract
Parkinson's disease (PD) is a common degenerative disease of the central nervous system among the elderly. Istradefylline, an FDA-approved adenosine A2A receptor antagonist (anti-PD drug), has good efficacy. However, it has been reported that the double bond of istradefylline is easily converted into cis-configuration when exposed to an indoor environment or direct light in a dilute solution. In order to find more stable adenosine A2A receptor antagonists with similar pharmacological efficacy to istradefylline, the compounds series I-1 (12 compounds) was designed by maintaining the xanthine skeleton of istradefylline unchanged and replacing the trans-double bond with thiazole or benzothiazole and other biologically active heterocyclic compounds. These compounds were synthesized via multi-step experiment and successfully confirmed through different characterization techniques for their ability to inhibit cAMP formation in A2A AR overexpressing cells. The thiazole derivative of istradefylline (Compound I-1-11, I-1-12) exhibited significant activity (IC50 = 16.74 ± 4.11 μM, 10.36 ± 3.09 μM), as compared to istradefylline (IC50 = 5.05 ± 1.32 μM). In addition, the molecular docking of benzothiazole derivatives I-1-11 and thiazole derivatives I-1-12 with higher inhibition rate were carried out and compared with istradefylline. The molecular docking results showed that I-1-11 and I-1-12 anchored in the same site as that of XAC (3REY) with predicted affinity binding energy -6.63 kcal/mol and - 6.75 kcal/mol, respectively. Validation through dynamics simulation also showed stable interactions, with fluctuations <3 Å and MM/GBSA energy <-20 kcal/mol. Hence, this study could provide a basis for the rational design of adenosine A2A receptor antagonists with better potency.
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Affiliation(s)
- Yiyun Wang
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China.,Shandong Xinhua Pharmaceutical Co., Ltd, Zibo, China
| | - Hongyi Wang
- Shandong Xinhua Pharmaceutical Co., Ltd, Zibo, China
| | - Haojie Xu
- Shandong Xinhua Pharmaceutical Co., Ltd, Zibo, China
| | | | - Zihui Meng
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Zhibin Xu
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Jiarong Li
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Min Xue
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
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Antibacterial Profile of a Microbicidal Agent Targeting Tyrosine Phosphatases and Redox Thiols, Novel Drug Targets. Antibiotics (Basel) 2021; 10:antibiotics10111310. [PMID: 34827248 PMCID: PMC8615086 DOI: 10.3390/antibiotics10111310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 10/23/2021] [Accepted: 10/24/2021] [Indexed: 11/16/2022] Open
Abstract
The activity profile of a protein tyrosine phosphatase (PTP) inhibitor and redox thiol oxidant, nitropropenyl benzodioxole (NPBD), was investigated across a broad range of bacterial species. In vitro assays assessed inhibitory and lethal activity patterns, the induction of drug variants on long term exposure, the inhibitory interactions of NPBD with antibiotics, and the effect of plasma proteins and redox thiols on activity. A literature review indicates the complexity of PTP and redox signaling and suggests likely metabolic targets. NPBD was broadly bactericidal to pathogens of the skin, respiratory, urogenital and intestinal tracts. It was effective against antibiotic resistant strains and slowly replicating and dormant cells. NPBD did not induce resistant or drug-tolerant phenotypes and showed low cross reactivity with antibiotics in synergy assays. Binding to plasma proteins indicated lowered in-vitro bioavailability and reduction of bactericidal activity in the presence of thiols confirmed the contribution of thiol oxidation and oxidative stress to lethality. This report presents a broad evaluation of the antibacterial effect of PTP inhibition and redox thiol oxidation, illustrates the functional diversity of bacterial PTPs and redox thiols, and supports their consideration as novel targets for antimicrobial drug development. NPBD is a dual mechanism agent with an activity profile which supports consideration of tyrosine phosphatases and bacterial antioxidant systems as promising targets for drug development.
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