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Xiong F, Zhang Y, Jiao J, Zhu Y, Mo T, Li Y. Towards new bioactive fluorine-containing 1,3,4-oxadiazole-amide derivatives: synthesis, antibacterial activity, molecular docking and molecular dynamics simulation study. Mol Divers 2024:10.1007/s11030-024-10893-x. [PMID: 38900333 DOI: 10.1007/s11030-024-10893-x] [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: 03/22/2024] [Accepted: 05/09/2024] [Indexed: 06/21/2024]
Abstract
Through the approach of molecular hybridization, this study rationally designed and synthesized new trifluoromethyl-1,3,4-oxadiazole amide derivatives, denoted as 1a-1n. The findings reveal that these novel molecules exhibit potent inhibitory effects against various bacterial strains. Thereinto, compounds 1c, 1d, 1i, 1j and 1n, demonstrate relatively superior antimicrobial performance against B. cereus FM314, with a minimum inhibitory concentration (MIC) of 0.03907 μg/mL. Molecular docking analysis suggests the potential importance of the Ser57 and Thr125 amino acid residues (PDB ID: 4EI9) in contributing to the inhibitory activity against B. cereus. The consistency of these results was further corroborated through subsequent molecular dynamics simulations and MMPBSA validations. The insights gained from this study serve to facilitate the rational design and efficient development of novel eco-friendly antimicrobial inhibitors based on the trifluoromethyl-1,3,4-oxadiazole amide scaffold.
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Affiliation(s)
- Fei Xiong
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, 200093, People's Republic of China.
| | - Yanjun Zhang
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, 200093, People's Republic of China
| | - Jinlong Jiao
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, People's Republic of China
| | - Yiren Zhu
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, 200093, People's Republic of China
| | - Tianlu Mo
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, People's Republic of China.
| | - Yeji Li
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, 200093, People's Republic of China
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2
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Kuang Y, Ma X, Shen W, Rao Q, Yang S. Discovery of 3CLpro inhibitor of SARS-CoV-2 main protease. Future Sci OA 2023; 9:FSO853. [PMID: 37090493 PMCID: PMC10116374 DOI: 10.2144/fsoa-2023-0020] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 03/20/2023] [Indexed: 04/08/2023] Open
Abstract
Coronavirus main protease (3CLpro), a special cysteine protease in coronavirus family, is highly desirable in the life cycle of coronavirus. Here, molecular docking, ADMET pharmacokinetic profiles and molecular dynamics (MD) simulation were performed to develop specific 3CLpro inhibitor. The results showed that the 137 compounds originated from Chinese herbal have good binding affinity to 3CLpro. Among these, Cleomiscosin C, (+)-Norchelidonine, Protopine, Turkiyenine, Isochelidonine and Mallotucin A possessed prominent drug-likeness properties. Cleomiscosin C and Turkiyenine exhibited excellent pharmacokinetic profiles. Furthermore, the complex of Cleomiscosin C with SARS-CoV-2 main protease presented high stability. The findings in this work indicated that Cleomiscosin C is highly promising as a potential 3CLpro inhibitor, thus facilitating the development of effective drugs for COVID-19.
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Affiliation(s)
- Yi Kuang
- College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, Zhejiang, 311300, PR China
| | - Xiaodong Ma
- College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, Zhejiang, 311300, PR China
| | - Wenjing Shen
- College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, Zhejiang, 311300, PR China
| | - Qingqing Rao
- College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, Zhejiang, 311300, PR China
| | - Shengxiang Yang
- College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, Zhejiang, 311300, PR China
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3
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Moharana M, Pattanayak SK, Khan F. Molecular recognition of bio-active triterpenoids from Swertia chirayita towards hepatitis Delta antigen: a mechanism through docking, dynamics simulation, Gibbs free energy landscape. J Biomol Struct Dyn 2023; 41:14651-14664. [PMID: 36856037 DOI: 10.1080/07391102.2023.2184173] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 02/18/2023] [Indexed: 03/02/2023]
Abstract
Medicinal plants the underpinning of indigenous herbal serve, are the possible source of key compounds for the development of new drugs. Hepatitis D, one of the most widespread infectious diseases associated with global public health issues. Therefore, we aim to screen natural compounds to find out potent inhibitor towards hepatitis delta antigen. Through ADMET investigation, we have screened twenty phytochemicals for this study. Additionally, using molecular docking, these phytochemicals were docked with the HDV protease which signifies the phytochemicals beta-amyrin, chiratenol, episwertenol and swertanone have a significant capability to bind with hepatitis D virus protein. The docking study was further accompanied by analyzes RMSD, RMSF, Rg, SASA, Hbond number, and principal component analysis through 100 ns MD simulations. Based on our principal component analysis, beta-amyrin, chiratenol, episwertenol and swertanone phytochemicals can be a potential drug candidates for inhibition of hepatitis D. The above observation is also supported by our Gibbs free energy landscape study. The potential therapeutic characteristics of the phytochemicals against hepatitis D inhibition offer additional support for the in vitro and in vivo studies in future.
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Affiliation(s)
- Maheswata Moharana
- Department of Chemistry, National Institute of Technology, Raipur, India
| | | | - Fahmida Khan
- Department of Chemistry, National Institute of Technology, Raipur, India
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4
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Sahu SN, Satpathy SS, Pattnaik S, Mohanty C, Pattanayak SK. Boerhavia diffusa plant extract can be a new potent therapeutics against mutant nephrin protein responsible for type1 nephrotic syndrome: Insight into hydrate-ligand docking interactions and molecular dynamics simulation study. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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5
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Moharana M, Pattanayak SK, Khan F. Identification of phytochemicals from Eclipta alba and assess their potentiality against Hepatitis C virus envelope glycoprotein: virtual screening, docking, and molecular dynamics simulation study. J Biomol Struct Dyn 2022:1-17. [PMID: 35694813 DOI: 10.1080/07391102.2022.2085804] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Hepatitis C virus has a major role in spreading chronic liver disease and hepatocellular carcinoma. Factors such as high costs, pharmacological side effects, and the development of drug resistance strains require the development of new and potentially effective antiviral to treat the various stages of Hepatitis C. Bioactive chemicals have been extracted from medicinal plants and are utilized by humans for the goal of maintaining a healthy lifestyle. The goal of this work is to recognize phytochemicals from Eclipta alba and assess their potentiality activity against the hepatitis C virus envelope glycoprotein using in silico approaches. Phytochemicals from Eclipta alba were virtually screened by Auto dock raccoon and 12 compounds were selected for molecular docking to probe the active binding site. The top two compounds based on the binding score like ecliptalbine and oleanolic acid with HCV E2 glycoprotein exhibit binding energy -8.88 and -8.02 kcal/mol, respectively. The chemicals' usefulness was reinforced by positive pharmacokinetic data. The phytocompounds were identified as potent HCV inhibitors based on the drug likeness and ADMET properties. Both ecliptalbine and oleanolic acid underwent molecular dynamics simulations to determine features such as RMSD, RMSF, SASA, hydrogen-bond number, and MM-PBSA-based binding free energy. From the molecular docking and molecular dynamics simulation study revealed that oleanolic acid obtained from Eclipta alba can be used as inhibitors against Hepatitis C. The identified inhibitor from our study will be study in vitro and in vivo studies to check their efficacy against Hepatitis C.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Maheswata Moharana
- Department of Chemistry, National Institute of Technology, Raipur, India
| | | | - Fahmida Khan
- Department of Chemistry, National Institute of Technology, Raipur, India
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Kawsar SMA, Hosen MA, El Bakri Y, Ahmad S, Affi ST, Goumri-Said S. In silico approach for potential antimicrobial agents through antiviral, molecular docking, molecular dynamics, pharmacokinetic and bioactivity predictions of galactopyranoside derivatives. ARAB JOURNAL OF BASIC AND APPLIED SCIENCES 2022. [DOI: 10.1080/25765299.2022.2068275] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Affiliation(s)
- Sarkar M. A. Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, Bangladesh
| | - Mohammed A. Hosen
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, Bangladesh
| | - Youness El Bakri
- Department of Theoretical and Applied Chemistry, South Ural State University, Chelyabinsk, Russian Federation
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Sopi T. Affi
- Laboratory of Thermodynamics and Medium Physico-Chemistry (LTPCM), Faculty of Basic and Applied Sciences (UFR-SFA), University of Nangui Abrogoua (UNA), Abidjan, Côte-d'Ivoire
| | - Souraya Goumri-Said
- College of Science, Physics Department, Alfaisal University, Riyadh, Saudi Arabia
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Han Z, Xue J, Li Y. Phthalate's multiple hormonal effects and their supplementary dietary regulation scheme of health risks for children. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:29016-29032. [PMID: 34993781 DOI: 10.1007/s11356-021-17798-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/23/2021] [Indexed: 06/14/2023]
Abstract
Four common phthalic acid esters (PAEs), namely, butylbenzyl phthalate (BBzP), dibutyl phthalate (DBP), di(2-ethylhexyl) phthalate (DEHP), and di-n-octyl phthalate (DNOP) that are known to affect children upon exposure, were selected, and the hormone effects were explored during different supplementary food intakes by using methods such as factorial design experiment, molecular docking, and dynamics simulation techniques. A supplementary diet regulation scheme to prevent health risks of PAEs was constructed to avoid or mitigate the hormonal effects in children exposed to PAEs. Firstly, the MM/PBSA binding energy of PAEs with single hormone receptors and multiple hormone receptor complexes was calculated. In addition, 10 foods were selected as external interference conditions to carry out dynamic simulation, which showed that kiwi fruit and broccoli can effectively alleviate the PAEs' hormone effects. Furthermore, inference of the metabolic process of DEHP found that the supplementary diets could effectively promote the metabolism of PAEs. Finally, based on the mechanism analysis, it was confirmed that the selected supplementary diets could inhibit the binding process. This study aims to explore the role of supplementary diets in regulating various PAEs' hormone effects and thereby provide theoretical support for slowing down hormonal effects in children.
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Affiliation(s)
- Zhenzhen Han
- Key Laboratory of Resource and Environmental System Optimization, Ministry of Education, North China Electric Power University, Beijing, 102206, China
- College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, China
| | - Jiaqi Xue
- Key Laboratory of Resource and Environmental System Optimization, Ministry of Education, North China Electric Power University, Beijing, 102206, China
- College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, China
| | - Yu Li
- Key Laboratory of Resource and Environmental System Optimization, Ministry of Education, North China Electric Power University, Beijing, 102206, China.
- College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, China.
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A molecular docking and dynamics study to screen phytochemicals that target mutant thymidine phosphorylase for colon cancer therapy. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100476] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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9
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Evaluation of binding performance of bioactive compounds against main protease and mutant model spike receptor binding domain of SARS-CoV-2: Docking, ADMET properties and molecular dynamics simulation study. J INDIAN CHEM SOC 2022. [PMCID: PMC8900880 DOI: 10.1016/j.jics.2022.100417] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Phytochemicals present in medicinal plants have a variety of biological activities that help to combat against diseases. As part of efforts to study the binding performance of different phytochemicals derived from different plants like Zingiber officinale, Citrus limon, Syzygiumaromaticum, Ocimum tenuiflorum and Curcumin. We have screened 424 molecules. The binding affinity as well as physicochemical properties of the thebaine, acacetin, indomethacin, crinamineacetate, (S)-1-Piperideine-6-carboxylate, levamisole, melatonin, nicotinicacid, curcumin, methotrimeprazine, omeprazole, and methaqualone phytocompounds were analyzed through computational study. From the molecular docking study we found that, LEU50, ASN72, PRO96, TYR154, GLY170, ALA193, ARG222, and MET274 residues of main protease play a crucial role in binding with ligands. The present study revealed a noticeable interaction of GLY446, SER477, GLY482, THR500 and LEU518 residues with mutant of spike receptor binding domain SARS-CoV-2 protein were observed. Finally, 100 ns molecular dynamics simulation were used to study their dynamic properties as well as conformational flexibility. Free energy landscape analysis was performed of the 6LU7- acacetin and 6Y2E-acacetin systems and spike RBD-acacetin system. From molecular docking study and molecular dynamics study revealed that, the compound acacetin shows promising inhibitor towards both main protease as well as mutant spike RBD of SARS-CoV-2 protein.
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Characterization of Promising Cytotoxic Metabolites from Tabebuia guayacan Hemsl.: Computational Prediction and In Vitro Testing. PLANTS 2022; 11:plants11070888. [PMID: 35406868 PMCID: PMC9002841 DOI: 10.3390/plants11070888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/15/2022] [Accepted: 03/21/2022] [Indexed: 11/16/2022]
Abstract
Genus Tabebuia is famous for its traditional uses and valuable phytoconstituents. Our previous investigation of Tabebuia species noted the promising anticancer activity of T. guayacan Hemsl. leaves extract, however, the mechanism underlying the observed anticancer activity is still unexplored. The current research was designed to explore the phytochemical content as well as to address the phytoconstituent(s) responsible for the recorded anticancer activity. Accordingly, sixteen compounds were isolated, and their structures were elucidated using different spectroscopic techniques. The drug-likeness of the isolated compounds, as well as their binding affinity with four anticancer drug target receptors: CDK-2/6, topoisomerase-1, and VEGFR-2, were evaluated. Additionally, the most promising compounds were in vitro evaluated for inhibitory activities against CDK-2/6 and VEGFR-2 enzymes using kinase assays method. Corosolic acid (3) and luteolin-7-O-β-glucoside (16) were the most active inhibitors against CDK-2 (−13.44 kcal/mol) and topoisomerase 1 (−13.83 kcal/mol), respectively. Meanwhile, quercetin 3-O-β-xyloside (10) scored the highest binding free energies against both CDK-6 (−16.23 kcal/mol) as well as against VEGFR-2 protein targets (−10.39 kcal/mol). Molecular dynamic simulation indicated that quercetin 3-O-β-xyloside (10) exhibited the least fluctuations and deviations from the starting binding pose with RMSD (2.6 Å). Interestingly, in vitro testing results confirmed the potent activity of 10 (IC50 = 0.154 µg/mL) compared to IC50 = 0.159 µg/mL of the reference drug ribociclib. These findings suggest the three noted compounds (3, 10, and 16) for further in vivo anticancer studies.
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Sahu SN, Satpathy SS, Mohanty C, Pattanayak SK. Computational study to evaluate the potency of phytochemicals in Boerhavia diffusa and the impact of point mutation on cyclin-dependent kinase 2-associated protein 1. J Biomol Struct Dyn 2021; 40:8587-8601. [PMID: 33876720 DOI: 10.1080/07391102.2021.1914169] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
A protein's function is closely related to its structural properties. Mutations can affect the functionality of a protein. Different cancer tissues have found disordered expression of the cyclin-dependent kinase 2-associated Protein 1 (CDK2AP1) gene. A protein molecule's conformational flexibility affects its interaction with phytochemicals and their biological partners at various levels. Boerhavia diffusa has been investigated most extensively for its medicinal activities like anticancer properties. It contains many bioactive compounds like Boeravinone A, Boeravinone B, Boeravinone C, Boeravinone D, Boeravinone E, Boeravinone F, Boeravinone G, Boeravinone H, Boeravinone I and Boeravinone J. We have studied to analyse the binding efficacy properties as well as essential dynamic behaviour, free energy landscape of both the native and mutant protein CDK2AP1 with bioactive compounds from Boerhavia diffusa plant extracts through computational approaches by homology modelling, docking and molecular dynamics simulation. From the molecular docking study, we found that. Boeravinone J have best binding affinity (-7.9 kcal/mol) towards the native protein of CDKAP1 compared to others phytochemicals. However, we found the binding energy for H23R and C105R (mutation point) -7.8 and -7.6 kcal/mol, respectively. A single minima energy point (from 100 ns molecular dynamics simulation study) was found in the H23R mutant with Boeravinone J complex suggested that minimum structural changes with less conformational mobility compared C105A mutant model.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Satya Narayan Sahu
- School of Applied Sciences, Kalinga Institute of Industrial Technology (KIIT) Deemed to be University, Bhubaneswar, India
| | - Sneha Shriparna Satpathy
- School of Applied Sciences, Kalinga Institute of Industrial Technology (KIIT) Deemed to be University, Bhubaneswar, India
| | - Chandana Mohanty
- School of Applied Sciences, Kalinga Institute of Industrial Technology (KIIT) Deemed to be University, Bhubaneswar, India
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Sahu SN, Mishra B, Sahu R, Pattanayak SK. Molecular dynamics simulation perception study of the binding affinity performance for main protease of SARS-CoV-2. J Biomol Struct Dyn 2020; 40:2444-2459. [PMID: 33228481 PMCID: PMC7754937 DOI: 10.1080/07391102.2020.1850362] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Like common cold and flu, SARC-CoV-2 virus spreads by droplets of sneezes or coughs which virus affects people of various age groups. Today, this virus is almost distributed all over the world. Since binding process plays a crucial role between host and receptor, therefore, we studied the molecules intended toward inhibition process through molecular docking and molecular dynamics simulation process. From the molecular docking study, it is noteworthy that remdesivir shows better binding affinity toward the main protease of SARS-CoV2 compared to other studied drugs. Within studied phytochemicals, carnosic acid shows better binding poses toward main protease of SARS-CoV2 among studied phytochemicals. The amino acid residues GLN110 and PHE294 were almost found in all the studied interactions of drugs and phytochemicals with main protease of SARS-CoV-2. Furthermore, the results show a larger contribution of the Van der Waals energies as compared to others like electrostatic energies suggesting that ligands at the binding pocket are predominantly stabilized by hydrophobic interactions. The conformational change during ligand binding was predicted from Gibbs free energy landscape analysis through molecular dynamics simulation. We observed that, there were two main free energy basins for both docked carnosic acid complex and for docked remdesivir complex, only one main free energy basin was found in the global free energy minimum region. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Satya Narayan Sahu
- School of Applied Sciences, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India
| | - Biswajit Mishra
- School of Applied Sciences, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India
| | - Rojalin Sahu
- School of Applied Sciences, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India
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Nayarisseri A, Khandelwal R, Madhavi M, Selvaraj C, Panwar U, Sharma K, Hussain T, Singh SK. Shape-based Machine Learning Models for the Potential Novel COVID-19 Protease Inhibitors Assisted by Molecular Dynamics Simulation. Curr Top Med Chem 2020; 20:2146-2167. [PMID: 32621718 DOI: 10.2174/1568026620666200704135327] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/20/2020] [Accepted: 04/25/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND The vast geographical expansion of novel coronavirus and an increasing number of COVID-19 affected cases have overwhelmed health and public health services. Artificial Intelligence (AI) and Machine Learning (ML) algorithms have extended their major role in tracking disease patterns, and in identifying possible treatments. OBJECTIVE This study aims to identify potential COVID-19 protease inhibitors through shape-based Machine Learning assisted by Molecular Docking and Molecular Dynamics simulations. METHODS 31 Repurposed compounds have been selected targeting the main coronavirus protease (6LU7) and a machine learning approach was employed to generate shape-based molecules starting from the 3D shape to the pharmacophoric features of their seed compound. Ligand-Receptor Docking was performed with Optimized Potential for Liquid Simulations (OPLS) algorithms to identify highaffinity compounds from the list of selected candidates for 6LU7, which were subjected to Molecular Dynamic Simulations followed by ADMET studies and other analyses. RESULTS Shape-based Machine learning reported remdesivir, valrubicin, aprepitant, and fulvestrant as the best therapeutic agents with the highest affinity for the target protein. Among the best shape-based compounds, a novel compound identified was not indexed in any chemical databases (PubChem, Zinc, or ChEMBL). Hence, the novel compound was named 'nCorv-EMBS'. Further, toxicity analysis showed nCorv-EMBS to be suitable for further consideration as the main protease inhibitor in COVID-19. CONCLUSION Effective ACE-II, GAK, AAK1, and protease 3C blockers can serve as a novel therapeutic approach to block the binding and attachment of the main COVID-19 protease (PDB ID: 6LU7) to the host cell and thus inhibit the infection at AT2 receptors in the lung. The novel compound nCorv- EMBS herein proposed stands as a promising inhibitor to be evaluated further for COVID-19 treatment.
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Affiliation(s)
- Anuraj Nayarisseri
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore-452010, Madhya Pradesh, India,Bioinformatics Research Laboratory, LeGene Biosciences Pvt Ltd., Mahalakshmi Nagar, Indore-452010, Madhya
Pradesh, India,Research Chair for Biomedical Applications of Nanomaterials, Biochemistry Department, College of Science, King
Saud University, Riyadh, Saudi Arabia,Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 003, Tamil Nadu, India
| | - Ravina Khandelwal
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore-452010, Madhya Pradesh, India
| | - Maddala Madhavi
- Department of Zoology, Nizam College, Osmania University, Hyderabad-500001, Telangana State, India
| | - Chandrabose Selvaraj
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 003, Tamil Nadu, India
| | - Umesh Panwar
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 003, Tamil Nadu, India
| | - Khushboo Sharma
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore-452010, Madhya Pradesh, India
| | - Tajamul Hussain
- Center of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia,Research Chair for Biomedical Applications of Nanomaterials, Biochemistry Department, College of Science, King
Saud University, Riyadh, Saudi Arabia
| | - Sanjeev Kumar Singh
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 003, Tamil Nadu, India
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14
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Yong L, Huang M, Wei Y, Xu J, Yi Z. Investigating the interaction between three perfluorinated carboxylic acids and the G protein-coupled estrogen receptor: spectroscopic analyses and computational simulations. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:3944-3953. [PMID: 32743632 DOI: 10.1039/d0ay01052a] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In this paper, perfluorinated compounds (PFCs), such as perfluorobutyric acid (PFBA), perfluorooctanoic acid (PFOA) and perfluorododecanoic acid (PFDoA), were selected as typical representatives of perfluorinated carboxylic acids (PFCAs) to study the effects of PFCAs on the G protein-coupled estrogen receptor (GPER). The interaction mechanism of the three types of PFCAs with the GPER was investigated using steady-state fluorescence spectroscopy, ultraviolet-visible spectroscopy, three-dimensional fluorescence spectroscopy, and Fourier transform infrared spectroscopy combined with molecular docking and molecular dynamics simulations. Among these techniques, steady-state fluorescence and ultraviolet-visible spectroscopic analyses showed that PFBA, PFOA and PFDoA quenched the endogenous GPER fluorescence by combined dynamic and static quenching and non-radiative energy transfer. The binding constants (Ka) of PFCAs on the GPER were all larger than 105 L mol-1, indicating that their affinity for the GPER was strong. Fourier transform infrared spectroscopy and three-dimensional fluorescence showed that the secondary structure of the GPER changed after binding to PFCAs. Thermodynamic analysis showed ΔG < 0, which indicated that the interaction between the GPER and PFCAs was spontaneous. For the binding of PFBA and PFOA to the GPER, ΔH > 0 and ΔS > 0, indicating that the interaction was mainly driven by hydrophobic forces; for the binding of PFDoA to the GPER, ΔH < 0 and ΔS < 0, suggesting that van der Waals force and hydrogen bonding were the main interaction forces. Molecular dynamics simulations suggested that the stability of the GPER-PFCA complexes was higher than that of the free GPER, and also that the structure and hydrophobicity of the GPER changed after binding to PFCAs. Molecular docking analysis showed that all three PFCAs could form hydrogen bonds with the GPER, which improved the stability of the complex.
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Affiliation(s)
- Li Yong
- Guangxi Colleges and Universities Key Laboratory of Food Safety and Detection, College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China.
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15
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Karnik KS, Sarkate AP, Lokwani DK, Narula IS, Burra PVLS, Wakte PS. Development of triple mutant T790M/C797S allosteric EGFR inhibitors: a computational approach. J Biomol Struct Dyn 2020; 39:5376-5398. [DOI: 10.1080/07391102.2020.1786460] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Kshipra S. Karnik
- Department of Chemical Technology, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, India
| | - Aniket P. Sarkate
- Department of Chemical Technology, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, India
| | - Deepak K. Lokwani
- R. C. Patel College of Pharmacy, R. C. Patel Institute of Pharmaceutical Education & Research, Shirpur, India
| | - Ishudeep S. Narula
- Department of Chemical Technology, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, India
| | | | - Pravin S. Wakte
- Department of Chemical Technology, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, India
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16
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Wang Q, Bian X, Chen X, Han Y, Yan C. Mechanism and structure of the interaction of water-soluble pillar[5]arene and ibrutinib that enhances the anticancer activity of ibrutinib. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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17
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Zhang Q, Sang F, Qian J, Lyu S, Wang W, Wang Y, Li Q, Du L. Identification of novel potential PI3Kα inhibitors for cancer therapy. J Biomol Struct Dyn 2020; 39:3721-3732. [DOI: 10.1080/07391102.2020.1771421] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Qingyan Zhang
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Department of Acquired Immune Deficiency Syndrome Treatment and Research Center, The First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, China
- Henan Key Laboratory of Viral Diseases Prevention and Treatment of Traditional Chinese Medicine, Henan University of Chinese Medicine, Zhengzhou, China
| | - Feng Sang
- Department of Acquired Immune Deficiency Syndrome Treatment and Research Center, The First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, China
- Henan Key Laboratory of Viral Diseases Prevention and Treatment of Traditional Chinese Medicine, Henan University of Chinese Medicine, Zhengzhou, China
| | - Jieyu Qian
- Department of Acquired Immune Deficiency Syndrome Treatment and Research Center, The First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, China
- Henan Key Laboratory of Viral Diseases Prevention and Treatment of Traditional Chinese Medicine, Henan University of Chinese Medicine, Zhengzhou, China
| | - ShaoLi Lyu
- Department of Ecology and Resource Engineering, Hetao College, Bayannur, Inner Mongolia, PR of China
| | - Wang Wang
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Ying Wang
- The Department of Anesthesiology, the First Affiliated of Henan University, Kaifeng, China
| | - Qiang Li
- Department of Acquired Immune Deficiency Syndrome Treatment and Research Center, The First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, China
- Henan Key Laboratory of Viral Diseases Prevention and Treatment of Traditional Chinese Medicine, Henan University of Chinese Medicine, Zhengzhou, China
| | - LinFang Du
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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