scholarly journals Studies on Computational Molecular Interaction Between SARS-CoV-2 Main Protease and Natural Products

2020 ◽  
Author(s):  
Manish Manish
Keyword(s):  
Natural Products ◽  
Molecular Interaction ◽  
Scientific Literature ◽  
Dynamics Simulation ◽  
Major Constituent ◽  
Literature Mining ◽  
Hydroxyl Groups ◽  
Scoring Functions ◽  
Protease Inhibition ◽  
Main Protease

A combination of docking approaches, scoring functions, molecular dynamic simulation, and literature mining have been employed to screen readily available natural products (unique 27256 chemical entities, 598435 unique compounds), which can inhibit the SARS-CoV-2 main protease. Theaflavin digallate, a major constituent of black tea, has been observed to be as three top hits after the virtual screening of 598435 unique compounds. The main protease-theaflavin digallate complex appeared to be in the metastable stage and interact with critical active site residues of the main protease during molecular dynamics simulation for 200 ns. <i>Invitro</i> evidence on main protease inhibition of 2003 SARS-CoV by theaflavin digallate is available in the scientific literature. As evident by the dynamics of intermolecular interactions, theaflavin digallate, forms approximately three hydrogen bonds with Glu166 of main protease, mostly through hydroxyl groups in the benzene ring of benzo(7) annulen-6-one. Glu166 is the most critical amino acid for main protease dimerization, which in turn, is necessary for catalytic activity.<i> </i>We have employed chloroquine and epigallocatechin gallate (green tea component) as a control set. Based on computational molecular interaction and data available in scientific literature, theaflavin digallate can inhibit the main protease of SARS-CoV-2.

scholarly journals Studies on Computational Molecular Interaction Between SARS-CoV-2 Main Protease and Natural Products

2020 ◽  
Author(s):  
Manish Manish
Keyword(s):  
Natural Products ◽  
Molecular Interaction ◽  
Scientific Literature ◽  
Dynamics Simulation ◽  
Major Constituent ◽  
Literature Mining ◽  
Hydroxyl Groups ◽  
Scoring Functions ◽  
Protease Inhibition ◽  
Main Protease

A combination of docking approaches, scoring functions, molecular dynamic simulation, and literature mining have been employed to screen readily available natural products (unique 27256 chemical entities, 598435 unique compounds), which can inhibit the SARS-CoV-2 main protease. Theaflavin digallate, a major constituent of black tea, has been observed to be as three top hits after the virtual screening of 598435 unique compounds. The main protease-theaflavin digallate complex appeared to be in the metastable stage and interact with critical active site residues of the main protease during molecular dynamics simulation for 200 ns. <i>Invitro</i> evidence on main protease inhibition of 2003 SARS-CoV by theaflavin digallate is available in the scientific literature. As evident by the dynamics of intermolecular interactions, theaflavin digallate, forms approximately three hydrogen bonds with Glu166 of main protease, mostly through hydroxyl groups in the benzene ring of benzo(7) annulen-6-one. Glu166 is the most critical amino acid for main protease dimerization, which in turn, is necessary for catalytic activity.<i> </i>We have employed chloroquine and epigallocatechin gallate (green tea component) as a control set. Based on computational molecular interaction and data available in scientific literature, theaflavin digallate can inhibit the main protease of SARS-CoV-2.

scholarly journals Studies on Computational Molecular Interaction Between SARS-CoV-2 Main Protease and Natural Products

2020 ◽  
Author(s):  
Manish Manish
Keyword(s):  
Natural Products ◽  
Molecular Interaction ◽  
Scientific Literature ◽  
Dynamics Simulation ◽  
Major Constituent ◽  
Literature Mining ◽  
Hydroxyl Groups ◽  
Scoring Functions ◽  
Protease Inhibition ◽  
Main Protease

A combination of docking approaches, scoring functions, molecular dynamic simulation, and literature mining have been employed to screen readily available natural products (unique 27256 chemical entities, 598435 unique compounds), which can inhibit the SARS-CoV-2 main protease. Theaflavin digallate, a major constituent of black tea, has been observed to be as three top hits after the virtual screening of 598435 unique compounds. The main protease-theaflavin digallate complex appeared to be in the metastable stage and interact with critical active site residues of the main protease during molecular dynamics simulation for 200 ns. <i>Invitro</i> evidence on main protease inhibition of 2003 SARS-CoV by theaflavin digallate is available in the scientific literature. As evident by the dynamics of intermolecular interactions, theaflavin digallate, forms approximately three hydrogen bonds with Glu166 of main protease, mostly through hydroxyl groups in the benzene ring of benzo(7) annulen-6-one. Glu166 is the most critical amino acid for main protease dimerization, which in turn, is necessary for catalytic activity.<i> </i>We have employed chloroquine and epigallocatechin gallate (green tea component) as a control set. Based on computational molecular interaction and data available in scientific literature, theaflavin digallate can inhibit the main protease of SARS-CoV-2.

scholarly journals Screening of Potent Phytochemical Inhibitors Against SARS-CoV-2 Main Protease: An Integrative Computational Approach

2021 ◽  
Vol 1 ◽  
Author(s):  
Shafi Mahmud ◽  
Md. Robiul Hasan ◽  
Suvro Biswas ◽  
Gobindo Kumar Paul ◽  
Shamima Afrose ◽  
...  
Keyword(s):  
Root Mean Square ◽  
Global Economy ◽  
Transmission Rate ◽  
Accessible Surface Area ◽  
Dynamics Simulation ◽  
Solvent Accessible Surface Area ◽  
Radius Of Gyration ◽  
Mean Square ◽  
Protease Inhibition ◽  
Main Protease

Coronavirus disease 2019 (COVID-19) is a potentially lethal and devastating disease that has quickly become a public health threat worldwide. Due to its high transmission rate, many countries were forced to implement lockdown protocols, wreaking havoc on the global economy and the medical crisis. The main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative virus for COVID-19, represent an effective target for the development of a new drug/vaccine because it is well-conserved and plays a vital role in viral replication. Mpro inhibition can stop the replication, transcription as well as recombination of SARS-CoV-2 after the infection and thus can halt the formation of virus particles, making Mpro a viable therapeutic target. Here, we constructed a phytochemical dataset based on a rigorous literature review and explored the probability that various phytochemicals will bind with the main protease using a molecular docking approach. The top three hit compounds, medicagol, faradiol, and flavanthrin, had binding scores of −8.3, −8.6, and −8.8 kcal/mol, respectively, in the docking analysis. These three compounds bind to the active groove, consisting of His41, Cys45, Met165, Met49, Gln189, Thr24, and Thr190, resulting in main protease inhibition. Moreover, the multiple descriptors from the molecular dynamics simulation, including the root-mean-square deviation, root-mean-square fluctuation, solvent-accessible surface area, radius of gyration, and hydrogen bond analysis, confirmed the stable nature of the docked complexes. In addition, absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis confirmed a lack of toxicity or carcinogenicity for the screened compounds. Our computational analysis may contribute toward the design of an effective drug against the main protease of SARS-CoV-2.

scholarly journals Natural Products-Based Drug Design against SARS-CoV-2 Mpro 3CLpro

2021 ◽  
Vol 22 (21) ◽  
pp. 11739
Author(s):  
Rai C. Silva ◽  
Humberto F. Freitas ◽  
Joaquín M. Campos ◽  
Njogu M. Kimani ◽  
Carlos H. T. P. Silva ◽  
...  
Keyword(s):  
Public Health ◽  
Molecular Dynamics ◽  
Natural Products ◽  
Structural Data ◽  
Dynamics Simulation ◽  
Semiarid Region ◽  
Main Protease ◽  
Global Spread ◽  
Catalytic Cysteine

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has received global attention due to the serious threat it poses to public health. Since the outbreak in December 2019, millions of people have been affected and its rapid global spread has led to an upsurge in the search for treatment. To discover hit compounds that can be used alone or in combination with repositioned drugs, we first analyzed the pharmacokinetic and toxicological properties of natural products from Brazil’s semiarid region. After, we analyzed the site prediction and druggability of the SARS-CoV-2 main protease (Mpro), followed by docking and molecular dynamics simulation. The best SARS-CoV-2 Mpro complexes revealed that other sites were accessed, confirming that our approach could be employed as a suitable starting protocol for ligand prioritization, reinforcing the importance of catalytic cysteine-histidine residues and providing new structural data that could increase the antiviral development mainly against SARS-CoV-2. Here, we selected 10 molecules that could be in vitro assayed in response to COVID-19. Two compounds (b01 and b02) suggest a better potential for interaction with SARS-CoV-2 Mpro and could be further studied.

scholarly journals Structure-Based Virtual Screening of a Natural Product Database to Identify Several Possible SARS-CoV-2 Main Protease Inhibitors

2020 ◽  
Author(s):  
Azhagiya Singam Ettayapuram Ramaprasad ◽  
Michele La merrill ◽  
Kathleen A. Durkin ◽  
Martyn T. Smith
Keyword(s):  
Natural Products ◽  
Natural Product ◽  
Respiratory Illness ◽  
Dynamics Simulation ◽  
Effective Vaccine ◽  
Main Protease ◽  
Novel Coronavirus ◽  
Seriously Ill Patients ◽  
Enormous Number ◽  
Seriously Ill

<p>A novel coronavirus (SARS-CoV-2) has been the cause of a recent pandemic of respiratory illness known as COVID-19. The lack of anti-viral drugs or vaccines to control the infection has resulted in an enormous number of seriously ill patients requiring hospitalization. In the absence of an effective vaccine, there is an urgent need for therapies which can fight COVID-19 infection. Readily available compounds in foods and plants may be one source of anti-viral compounds. Here, natural product chemicals from the Nuclei of Bioassays, Ecophysiology and Biosynthesis of Natural Products Database (NuBBE<sub>DB</sub>) were screened against the main protease (Mpro) of SARS-CoV-2. This protease was chosen as a target due to its importance in the replication of SARS-CoV-2. Molecular docking was used to screen the natural products against Mpro to identify potential candidates. The identified candidates were further filtered using molecular dynamics simulation investigation. Nine natural compounds were identified for experimental validation, with carlinoside and quercetin 3-o-sophoroside being the top candidates. </p>

scholarly journals Structure-Based Virtual Screening of a Natural Product Database to Identify Several Possible SARS-CoV-2 Main Protease Inhibitors

2020 ◽  
Author(s):  
Azhagiya Singam Ettayapuram Ramaprasad ◽  
Michele La merrill ◽  
Kathleen A. Durkin ◽  
Martyn T. Smith
Keyword(s):  
Natural Products ◽  
Natural Product ◽  
Respiratory Illness ◽  
Dynamics Simulation ◽  
Effective Vaccine ◽  
Main Protease ◽  
Novel Coronavirus ◽  
Seriously Ill Patients ◽  
Enormous Number ◽  
Seriously Ill

<p>A novel coronavirus (SARS-CoV-2) has been the cause of a recent pandemic of respiratory illness known as COVID-19. The lack of anti-viral drugs or vaccines to control the infection has resulted in an enormous number of seriously ill patients requiring hospitalization. In the absence of an effective vaccine, there is an urgent need for therapies which can fight COVID-19 infection. Readily available compounds in foods and plants may be one source of anti-viral compounds. Here, natural product chemicals from the Nuclei of Bioassays, Ecophysiology and Biosynthesis of Natural Products Database (NuBBE<sub>DB</sub>) were screened against the main protease (Mpro) of SARS-CoV-2. This protease was chosen as a target due to its importance in the replication of SARS-CoV-2. Molecular docking was used to screen the natural products against Mpro to identify potential candidates. The identified candidates were further filtered using molecular dynamics simulation investigation. Nine natural compounds were identified for experimental validation, with carlinoside and quercetin 3-o-sophoroside being the top candidates. </p>

QM/MM Simulations of Organic Phosphorus Adsorption at the Diaspore-Water Interface

2019 ◽  
Author(s):  
Prasanth Babu Ganta ◽  
Oliver Kühn ◽  
Ashour Ahmed
Keyword(s):  
Interaction Energy ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Hydroxyl Groups ◽  
Water Interface ◽  
Mineral Surfaces ◽  
Soil Mineral ◽  
Phosphorus Adsorption ◽  
Covalent Bonds ◽  
Binding Mechanisms

The phosphorus (P) immobilization and thus its availability for plants are mainly affected by the strong interaction of phosphates with soil components especially soil mineral surfaces. Related reactions have been studied extensively via sorption experiments especially by carrying out adsorption of ortho-phosphate onto Fe-oxide surfaces. But a molecular-level understanding for the P-binding mechanisms at the mineral-water interface is still lacking, especially for forest eco-systems. Therefore, the current contribution provides an investigation of the molecular binding mechanisms for two abundant phosphates in forest soils, inositol hexaphosphate (IHP) and glycerolphosphate (GP), at the diaspore mineral surface. Here a hybrid electrostatic embedding quantum mechanics/molecular mechanics (QM/MM) based molecular dynamics simulation has been applied to explore the diaspore-IHP/GP-water interactions. The results provide evidence for the formation of different P-diaspore binding motifs involving monodentate (M) and bidentate (B) for GP and two (2M) as well as three (3M) monodentate for IHP. The interaction energy results indicated the abundance of the GP B motif compared to the M one. The IHP 3M motif has a higher total interaction energy compared to its 2M motif, but exhibits a lower interaction energy per bond. Compared to GP, IHP exhibited stronger interaction with the surface as well as with water. Water was found to play an important role in controlling these diaspore-IHP/GP-water interactions. The interfacial water molecules form moderately strong H-bonds (HBs) with GP and IHP as well as with the diaspore surface. For all the diaspore-IHP/GP-water complexes, the interaction of water with diaspore exceeds that with the studied phosphates. Furthermore, some water molecules form covalent bonds with diaspore Al atoms while others dissociate at the surface to protons and hydroxyl groups leading to proton transfer processes. Finally, the current results confirm previous experimental conclusions indicating the importance of the number of phosphate groups, HBs, and proton transfers in controlling the P-binding at soil mineral surfaces.

scholarly journals Identification of 3-chymotrypsin like protease (3CLPro) inhibitors as potential anti-SARS-CoV-2 agents

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Vicky Mody ◽  
Joanna Ho ◽  
Savannah Wills ◽  
Ahmed Mawri ◽  
Latasha Lawson ◽  
...  
Keyword(s):  
Inhibitory Effect ◽  
Dynamics Simulation ◽  
Simulation Studies ◽  
Inhibitory Effects ◽  
Major Threat ◽  
Main Protease ◽  
Approved Drugs ◽  
Fda Approved Drugs ◽  
Computational Molecular Modeling

AbstractEmerging outbreak of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection is a major threat to public health. The morbidity is increasing due to lack of SARS-CoV-2 specific drugs. Herein, we have identified potential drugs that target the 3-chymotrypsin like protease (3CLpro), the main protease that is pivotal for the replication of SARS-CoV-2. Computational molecular modeling was used to screen 3987 FDA approved drugs, and 47 drugs were selected to study their inhibitory effects on SARS-CoV-2 specific 3CLpro enzyme in vitro. Our results indicate that boceprevir, ombitasvir, paritaprevir, tipranavir, ivermectin, and micafungin exhibited inhibitory effect towards 3CLpro enzymatic activity. The 100 ns molecular dynamics simulation studies showed that ivermectin may require homodimeric form of 3CLpro enzyme for its inhibitory activity. In summary, these molecules could be useful to develop highly specific therapeutically viable drugs to inhibit the SARS-CoV-2 replication either alone or in combination with drugs specific for other SARS-CoV-2 viral targets.

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