Plant-Based Phytochemical Screening by Targeting Main Protease of SARS-CoV-2 to Design Effective Potent Inhibitors
Shafi Mahmud,Suvro Biswas,Gobindo Kumar Paul,Mohasana Akter Mita,Maria Meha Promi,Shamima Afrose,Md. Robiul Hasan,Shahriar Zaman,Md. Salah Uddin,Kuldeep Dhama,Talha Bin Emran,Md. Abu Saleh,Jesus Simal-Gandara +12 more
Reads0
Chats0
TLDR
A molecular docking program was used to screen the top three candidate compounds: epicatechin-3-O-gallate, psi-taraxasterol, and catechin gallate as mentioned in this paper.Abstract:
Currently, a worldwide pandemic has been declared in response to the spread of coronavirus disease 2019 (COVID-19), a fatal and fast-spreading viral infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The low availability of efficient vaccines and treatment options has resulted in a high mortality rate, bringing the world economy to its knees. Thus, mechanistic investigations of drugs capable of counteracting this disease are in high demand. The main protease (Mpro) expressed by SARS-CoV-2 has been targeted for the development of potential drug candidates due to the crucial role played by Mpro in viral replication and transcription. We generated a phytochemical library containing 1672 phytochemicals derived from 56 plants, which have been reported as having antiviral, antibacterial, and antifungal activity. A molecular docking program was used to screen the top three candidate compounds: epicatechin-3-O-gallate, psi-taraxasterol, and catechin gallate, which had respective binding affinities of −8.4, −8.5, and −8.8 kcal/mol. Several active sites in the targeted protein, including Cys145, His41, Met49, Glu66, and Met165, were found to interact with the top three candidate compounds. The multiple simulation profile, root-mean-square deviation, root-mean-square fluctuation, radius of gyration, and solvent-accessible surface area values supported the inflexible nature of the docked protein–compound complexes. The toxicity and carcinogenicity profiles were assessed, which showed that epicatechin-3-O-gallate, psi-taraxasterol, and catechin gallate had favorable pharmacological properties with no adverse effects. These findings suggest that these compounds could be developed as part of an effective drug development pathway to treat COVID-19.read more
Citations
More filters
Journal ArticleDOI
Phytochemicals from Leucas zeylanica Targeting Main Protease of SARS-CoV-2: Chemical Profiles, Molecular Docking, and Molecular Dynamics Simulations
Mycal Dutta,Abu Montakim Tareq,Ahmed Rakib,Shafi Mahmud,Saad Ahmed Sami,Jewel Mallick,Mohammad Nazmul Islam,Mohuya Majumder,Md. Zia Uddin,Abdullah Alsubaie,Abdulraheem S. A. Almalki,Mayeen Uddin Khandaker,D.A. Bradley,Md. Sohel Rana,Talha Bin Emran +14 more
TL;DR: In this article, the authors used prime molecular mechanics-generalized Born surface area (MM-GBSA) to screen 34 compounds identified from Leucas zeylanica for potential inhibitory activity against the SARS-CoV-2 Mpro.
Journal ArticleDOI
In Silico Evaluation of Iranian Medicinal Plant Phytoconstituents as Inhibitors against Main Protease and the Receptor-Binding Domain of SARS-CoV-2.
Seyyed Sasan Mousavi,Akbar Karami,Tahereh Movahhed Haghighi,Sefren Geiner Tumilaar,Fatimawali,Rinaldi Idroes,Shafi Mahmud,Ismail Celik,Duygu Ağagündüz,Trina Ekawati Tallei,Talha Bin Emran,Raffaele Capasso +11 more
TL;DR: In this paper, the authors determined whether components of natural origin from Iranian medicinal plants have an antiviral effect that can prevent humans from this coronavirus infection using the most reliable molecular docking method; in their case, they focused on the main protease and a receptor-binding domain (RBD).
Journal ArticleDOI
Inhibition of the main protease of SARS-CoV-2 (Mpro) by repurposing/designing drug-like substances and utilizing nature’s toolbox of bioactive compounds
TL;DR: The main protease (Mpro) of the virus is an appealing target for the development of inhibitors, due to its importance in the viral life cycle and its high conservation among different coronaviruses as mentioned in this paper .
Journal ArticleDOI
Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2
TL;DR: There is a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics as discussed by the authors .
Journal ArticleDOI
Amentoflavone derivatives significantly act towards the main protease (3CLPRO/MPRO) of SARS-CoV-2: in silico admet profiling, molecular docking, molecular dynamics simulation, network pharmacology
Dipta Dey,Rajib Hossain,Partha Biswas,Priya Paul,Md. Aminul Islam,T. Ema,Bibhuti Kumar Gain,Mohammad Mehedi Hasan,Shabana Bibi,Muhammad Torequl Islam,Md. Ataur Rahman,Bonglee Kim +11 more
TL;DR: In this article , amentoflavone derivatives were evaluated against the 3-chymotrypsin-like protease (MPRO) of SARS-CoV-2.
References
More filters
Journal ArticleDOI
Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China
Chaolin Huang,Yeming Wang,Xingwang Li,Lili Ren,Jianping Zhao,Yi Hu,Li Zhang,Guohui Fan,Jiuyang Xu,Xiaoying Gu,Zhenshun Cheng,Ting Yu,Jia'an Xia,Yuan Wei,Wenjuan Wu,Xuelei Xie,Wen Yin,Li Hui,Min Liu,Yan Xiao,Hong Gao,Li Guo,Jungang Xie,Guang-Fa Wang,Rongmeng Jiang,Zhancheng Gao,Qi Jin,Jianwei Wang,Bin Cao +28 more
TL;DR: The epidemiological, clinical, laboratory, and radiological characteristics and treatment and clinical outcomes of patients with laboratory-confirmed 2019-nCoV infection in Wuhan, China, were reported.
Journal ArticleDOI
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
Oleg Trott,Arthur J. Olson +1 more
TL;DR: AutoDock Vina achieves an approximately two orders of magnitude speed‐up compared with the molecular docking software previously developed in the lab, while also significantly improving the accuracy of the binding mode predictions, judging by tests on the training set used in AutoDock 4 development.
Journal ArticleDOI
A pneumonia outbreak associated with a new coronavirus of probable bat origin
Peng Zhou,Xing-Lou Yang,Xian Guang Wang,Ben Hu,Lei Zhang,Wei Zhang,Hao Rui Si,Yan Zhu,Bei Li,Chao Lin Huang,Hui-Dong Chen,Jing Chen,Yun Luo,Hua Guo,Ren Di Jiang,Meiqin Liu,Ying Chen,Xu Rui Shen,Xi Wang,Xiao Shuang Zheng,Kai Zhao,Quanjiao Chen,Fei Deng,Lin Lin Liu,Bing Yan,Fa Xian Zhan,Yan-Yi Wang,Gengfu Xiao,Zhengli Shi +28 more
TL;DR: Identification and characterization of a new coronavirus (2019-nCoV), which caused an epidemic of acute respiratory syndrome in humans in Wuhan, China, and it is shown that this virus belongs to the species of SARSr-CoV, indicates that the virus is related to a bat coronav virus.
Journal ArticleDOI
SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules
TL;DR: The new SwissADME web tool is presented that gives free access to a pool of fast yet robust predictive models for physicochemical properties, pharmacokinetics, drug-likeness and medicinal chemistry friendliness, among which in-house proficient methods such as the BOILED-Egg, iLOGP and Bioavailability Radar are presented.
Journal ArticleDOI
Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94
TL;DR: The first published version of the Merck molecular force field (MMFF) is MMFF94 as mentioned in this paper, which is based on the OPLS force field and has been applied to condensed-phase processes.
Related Papers (5)
Screening of Potent Phytochemical Inhibitors Against SARS-CoV-2 Main Protease: An Integrative Computational Approach
Shafi Mahmud,Md. Robiul Hasan,Suvro Biswas,Gobindo Kumar Paul,Shamima Afrose,Mohsana Akter Mita,Mst Sharmin Sultana Shimu,Maria Meha Promi,Umme Hani,Mohamed Rahamathulla,Md. Arif Khan,Shahriar Zaman,Md. Salah Uddin,Mohammed Rahmatullah,Rownak Jahan,Ali Alqahtani,Md. Abu Saleh,Talha Bin Emran +17 more