scholarly journals The impact of curcumin derived polyphenols on the structure and flexibility COVID-19 main protease binding pocket: a molecular dynamics simulation study

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11590
Author(s):  
Aweke Mulu ◽  
Mulugeta Gajaa ◽  
Haregewoin Bezu Woldekidan ◽  
Jerusalem Fekadu W/mariam
Keyword(s):  
Molecular Dynamics ◽  
Binding Affinity ◽  
Binding Pocket ◽  
Dynamics Simulation ◽  
World Health ◽  
Main Protease ◽  
Health Organization ◽  
Dynamics Simulations ◽  
Simulation Parameters ◽  
The Impact

The newly occurred SARS-CoV-2 caused a leading pandemic of coronavirus disease (COVID-19). Up to now it has infected more than one hundred sixty million and killed more than three million people according to 14 May 2021 World Health Organization report. So far, different types of studies have been conducted to develop an anti-viral drug for COVID-19 with no success yet. As part of this, silico were studied to discover and introduce COVID-19 antiviral drugs and results showed that protease inhibitors could be very effective in controlling. This study aims to investigate the binding affinity of three curcumin derived polyphenols against COVID-19 the main protease (Mpro), binding pocket, and identification of important residues for interaction. In this study, molecular modeling, auto-dock coupled with molecular dynamics simulations were performed to analyze the conformational, and stability of COVID-19 binding pocket with diferuloylmethane, demethoxycurcumin, and bisdemethoxycurcumin. All three compounds have shown binding affinity −39, −89 and −169.7, respectively. Demethoxycurcumin and bisdemethoxycurcumin showed an optimum binding affinity with target molecule and these could be one of potential ligands for COVID-19 therapy. And also, COVID-19 main protease binding pocket binds with the interface region by one hydrogen bond. Moreover, the MD simulation parameters indicated that demethoxycurcumin and bisdemethoxycurcumin were stable during the simulation run. These findings can be used as a baseline to develop therapeutics with curcumin derived polyphenols against COVID-19.

scholarly journals Structure-Based Virtual Screening and Molecular Dynamics of Quercetin and Its Natural Derivatives as Potent Oxidative Stress Modulators in ROS-induced Cancer

2021 ◽  
Vol 3 (2) ◽  
pp. 60
Author(s):  
Abd. Kakhar Umar ◽  
James H. Zothantluanga
Keyword(s):  
Oxidative Stress ◽  
Molecular Dynamics ◽  
Binding Affinity ◽  
3D Structure ◽  
Binding Pocket ◽  
Structure Type ◽  
Dynamics Simulation ◽  
Quercetin Derivatives ◽  
A Value ◽  
The Impact

Quercetin derivatives are known to have significant anticancer activity. The activity is strongly influenced by the type and position of the substituent group. By studying the structural pattern of quercetin and its impact on their binding affinity, the development of quercetin-based drugs can be optimized. The study aimed to determine the impact of 3D structure, type, and position of quercetin moiety on its activity against ROS-modulating enzymes that play a role in the induction and growth of ROS-induced cancer. The 23 natural quercetin derivatives were docked to 7 ROS-modulating enzymes using Autodock Vina to determine their binding affinity and interaction. The interaction stability was further studied through molecular dynamics simulation using the CABS Flex 2.0 server. Determination of crucial amino acid targets of the quercetin group was determined using DockFlin. Finally, the toxicity of each test ligand was determined using the pkCSM server. The highest binding affinity for SOD and NOX was produced by quercetin 3'-glucoside with the binding energy of -10.2 and -12.8 kcal/mol. Quercetin 3,4'-diglucoside had the highest binding affinity for CAT and GR at -11.5 and -10.5 kcal/mol, respectively. Routine produced the highest binding affinity at LOX (-10.9). Quercetin 3-O-xyloside and quercetin 3-O-rhamnoside-7-O-glucoside had the highest binding affinity in XO with a value of -10.4 kcal/mol. The glucose and prenyl groups are beneficial for quercetin in interacting with all ROS-modulating enzymes except XO. In contrast, the methoxy group negatively affects all interactions of quercetin with receptors. The perfect fit between the binding pocket and the 3D structure of the ligand greatly benefits the ligand in accessing more amino acids in the binding pocket. Their interaction stability and toxicity show that quercetin 3'-glucoside, quercetin 3,4'-diglucoside, and rutin are potent oxidative stress modulators in treating ROS-induced cancer.

Molecular Dynamics Simulations of Structures of Amorphous Carbon Films via Deposition

2011 ◽  
Vol 194-196 ◽  
pp. 2220-2224
Author(s):  
Hui Qing Lan ◽  
Zheng Ling Kang
Keyword(s):  
Molecular Dynamics ◽  
Amorphous Carbon ◽  
Growth Dynamics ◽  
Carbon Films ◽  
Film Structure ◽  
Dynamics Simulation ◽  
Carbon Ions ◽  
Amorphous Carbon Films ◽  
Dynamics Simulations ◽  
The Impact

The growth of amorphous carbon films via deposition is investigated using molecular dynamics simulation with a modified Tersoff potential. The impact energy of carbon atoms ranges from 1 to 50 eV and the temperature of the diamond substrate is 300 K. The effects of the incident energy on the growth dynamics and film structure are studied in a detail. Simulation results show that the mobility of surface atoms in the cascade region is enhanced by impacting energetic carbon ions, especially at moderate energy, which favors the growth of denser and smoother films with better adhesion to the substrate. Our results agree qualitatively with the experimental observation.

Computational Design of Thiourea-based Cyclophane Sensors for Small Anions

2012 ◽  
Vol 65 (3) ◽  
pp. 303 ◽  
Author(s):  
Huifang Xie ◽  
Ming Wah Wong
Keyword(s):  
Molecular Dynamics ◽  
Binding Affinity ◽  
Density Functional ◽  
Computational Design ◽  
Binding Pocket ◽  
Solvent Medium ◽  
Guest Binding ◽  
Molecular Dynamics Calculations ◽  
Anion Complexes ◽  
Dynamics Simulations

The host–guest binding properties of a tri-thiourea cyclophane receptor (1) with several common anions have been investigated using density functional theory (DFT) and molecular dynamics calculations. Receptor 1 is predicted to be an effective receptor for binding small halogen and Y-shaped (NO3– and AcO–) anions in the gas phase, cyclohexane and chloroform. The calculated order of anion binding affinity for the receptor 1 in chloroform is F– > Cl– > AcO– > NO3– >Br– > H2PO4– > HSO4–. The binding free energies are strongly influenced by a dielectric solvent medium. The structures of the receptor–anion complexes are characterized by multiple (typically 6) hydrogen bonds in all cases. The overall binding affinity of various anions is determined by the basicity of anion, size and shape of the binding site, and solvent medium. Explicit chloroform solvent molecular dynamics simulations of selected receptor–anion complexes reveal that the anions are strongly bound within the binding pocket via hydrogen-bonding interactions to all the receptor protons throughout the simulation. A sulfur analogue of receptor 1 (2), with a larger central cavity, is shown to be a more effective sensor than 1 for small anions. Two different approaches to develop the thiourea-based cyclophane receptor into a chromogenic sensor were examined.

scholarly journals Molecular Dynamics Simulations on Influence of Defect on Thermal Conductivity of Silicon Nanowires

2021 ◽  
Vol 9 ◽  
Author(s):  
Hao Li ◽  
Qiancheng Rui ◽  
Xiwen Wang ◽  
Wei Yu
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Silicon Nanowires ◽  
Surface Defects ◽  
Low Frequency ◽  
Simulation Method ◽  
Dynamics Simulation ◽  
Non Equilibrium Molecular Dynamics ◽  
Dynamics Simulations ◽  
The Impact

A non-equilibrium molecular dynamics simulation method is conducted to study the thermal conductivity (TC) of silicon nanowires (SiNWs) with different types of defects. The impacts of defect position, porosity, temperature, and length on the TC of SiNWs are analyzed. The numerical results indicate that SiNWs with surface defects have higher TC than SiNWs with inner defects, the TC of SiNWs gradually decreases with the increase of porosity and temperature, and the impact of temperature on the TC of SiNWs with defects is weaker than the impact on the TC of SiNWs with no defects. The TC of SiNWs increases as their length increases. SiNWs with no defects have the highest corresponding frequency of low-frequency peaks of phonon density of states; however, when SiNWs have inner defects, the lowest frequency is observed. Under the same porosity, the average phonon participation of SiNWs with surface defects is higher than that of SiNWs with inner defects.

scholarly journals A computational biology approach for the identification of potential SARS-CoV-2 main protease inhibitors from natural essential oil compounds.

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 1313
Author(s):  
Rizone Al Hasib ◽  
Md. Chayan Ali ◽  
Md. Shahedur Rahman ◽  
Md. Mafizur Rahman ◽  
Fee Faysal Ahmed ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Essential Oil ◽  
New Drugs ◽  
Dynamics Simulation ◽  
World Health ◽  
Drug Candidates ◽  
Main Protease ◽  
Essential Oil Compounds

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has fomented a climate of fear worldwide due to its rapidly spreading nature, and high mortality rate. The World Health Organization (WHO) declared it as a global pandemic on 11th March, 2020. Many endeavors have been made to find appropriate medications to restrain the SARS CoV-2 infection from spreading but there is no specific antiviral therapy to date. However, a computer-aided drug design approach can be an alternative to identify probable drug candidates within a short time. SARS-CoV-2 main protease is a proven drug target, and it plays a pivotal role in viral replication and transcription. Methods: In this study, we identified a total of 114 essential oil compounds as a feasible anti-SARS-CoV-2 agent from several online reservoirs. These compounds were screened by incorporating ADMET profiling, molecular docking, and 50 ns of molecular dynamics simulation to identify potential drug candidates against the SARS-CoV-2 main protease. The crystallized SARS-CoV-2 main protease structure was collected from the RCSB PDB database (PDB ID 6LU7). Results: According to the results of the ADMET study, none of the compounds have any side effects that could reduce their druglikeness or pharmacokinetic properties. Out of 114 compounds, we selected bisabololoxide B, eremanthin, and leptospermone as our top drug candidates based on their higher binding affinity scores, and strong interaction with the Cys 145-His 41 catalytic dyad. Finally, the molecular dynamics simulation was implemented to evaluate the structural stability of the ligand-receptor complex. MD simulations disclosed that all the hits showed conformational stability compared to the positive control α-ketoamide. Conclusions: Our study showed that the top three hits might work as potential anti-SARS-CoV-2 agents, which can pave the way for discovering new drugs, but for experimental validation, they will require more in vivo trials.

scholarly journals Identification of CDK7 Inhibitors from Natural Sources Using Pharmacoinformatics and Molecular Dynamics Simulations

Biomedicines ◽  
2021 ◽  
Vol 9 (9) ◽  
pp. 1197
Author(s):  
Vikas Kumar ◽  
Shraddha Parate ◽  
Gunjan Thakur ◽  
Gihwan Lee ◽  
Hyeon-Su Ro ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Binding Affinity ◽  
Cost Effective ◽  
Binding Mode ◽  
Kinase Domain ◽  
Dynamics Simulation ◽  
Mode Analysis ◽  
Atp Binding Site ◽  
Dynamics Simulations

The cyclin-dependent kinase 7 (CDK7) plays a crucial role in regulating the cell cycle and RNA polymerase-based transcription. Overexpression of this kinase is linked with various cancers in humans due to its dual involvement in cell development. Furthermore, emerging evidence has revealed that inhibiting CDK7 has anti-cancer effects, driving the development of novel and more cost-effective inhibitors with enhanced selectivity for CDK7 over other CDKs. In the present investigation, a pharmacophore-based approach was utilized to identify potential hit compounds against CDK7. The generated pharmacophore models were validated and used as 3D queries to screen 55,578 natural drug-like compounds. The obtained compounds were then subjected to molecular docking and molecular dynamics simulations to predict their binding mode with CDK7. The molecular dynamics simulation trajectories were subsequently used to calculate binding affinity, revealing four hits—ZINC20392430, SN00112175, SN00004718, and SN00262261—having a better binding affinity towards CDK7 than the reference inhibitors (CT7001 and THZ1). The binding mode analysis displayed hydrogen bond interactions with the hinge region residues Met94 and Glu95, DFG motif residue Asp155, ATP-binding site residues Thr96, Asp97, and Gln141, and quintessential residue outside the kinase domain, Cys312 of CDK7. The in silico selectivity of the hits was further checked by docking with CDK2, the close homolog structure of CDK7. Additionally, the detailed pharmacokinetic properties were predicted, revealing that our hits have better properties than established CDK7 inhibitors CT7001 and THZ1. Hence, we argue that proposed hits may be crucial against CDK7-related malignancies.

scholarly journals Design of a New α-1-C-Alkyl-DAB Derivative Acting as a Pharmacological Chaperone for β-Glucocerebrosidase Using Ligand Docking and Molecular Dynamics Simulation

Molecules ◽  
2018 ◽  
Vol 23 (10) ◽  
pp. 2683 ◽  
Author(s):  
Izumi Nakagome ◽  
Atsushi Kato ◽  
Noriyuki Yamaotsu ◽  
Tomoki Yoshida ◽  
Shin-ichiro Ozawa ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Binding Site ◽  
Binding Affinity ◽  
Gaucher Disease ◽  
Point Mutations ◽  
Dynamics Simulation ◽  
Ligand Docking ◽  
Pharmacological Chaperone ◽  
Pharmacological Chaperones ◽  
Dynamics Simulations

Some point mutations in β-glucocerebrosidase cause either improper folding or instability of this protein, resulting in Gaucher disease. Pharmacological chaperones bind to the mutant enzyme and stabilize this enzyme; thus, pharmacological chaperone therapy was proposed as a potential treatment for Gaucher disease. The binding affinities of α-1-C-alkyl 1,4-dideoxy-1,4-imino-d-arabinitol (DAB) derivatives, which act as pharmacological chaperones for β-glucocerebrosidase, abruptly increased upon elongation of their alkyl chain. In this study, the primary causes of such an increase in binding affinity were analyzed using protein–ligand docking and molecular dynamics simulations. We found that the activity cliff between α-1-C-heptyl-DAB and α-1-C-octyl-DAB was due to the shape and size of the hydrophobic binding site accommodating the alkyl chains, and that the interaction with this hydrophobic site controlled the binding affinity of the ligands well. Furthermore, based on the aromatic/hydrophobic properties of the binding site, a 7-(tetralin-2-yl)-heptyl-DAB compound was designed and synthesized. This compound had significantly enhanced activity. The design strategy in consideration of aromatic interactions in the hydrophobic pocket was useful for generating effective pharmacological chaperones for the treatment of Gaucher disease.

scholarly journals Computational Study on Novel Natural Inhibitors Targeting c-MET

2021 ◽  
Author(s):  
Junliang Ge ◽  
Bo Wu ◽  
Wenzhuo Yang ◽  
Sheng Zhong ◽  
Yuanyuan Hou ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Binding Affinity ◽  
Computational Study ◽  
Developmental Toxicity ◽  
Inhibitory Effect ◽  
Dynamics Simulation ◽  
Drug Candidates ◽  
Zinc Database ◽  
The Stability ◽  
Dynamics Simulations

Abstract Object This study was designed to select ideal lead compounds and preclinical drug candidates with inhibitory effect on c-MET from the drug library (ZINC database).Methods A battery of computer-aided virtual techniques were used to identify possible inhibitors of c-MET. LibDock is applied for structure-based screening followed by ADME (absorption, distribution, metabolic, excretion) and toxicity prediction. Molecular docking was conducted to confirm the binding affinity mechanism between the ligand and c-MET Molecular dynamics simulations were used to assess the stability of ligand-c-MET complexes.Results Two new natural compounds ZINC000005879645 and ZINC000002528509 were found to bind to c-MET in ZINC database, showing higher binding affinity. In addition, they were predicted to have lower rodent carcinogenicity, Ames mutagenicity, developmental toxicity potential, and high tolerance to cytochrome P4502D6. Molecular dynamics simulation shows that ZINC000005879645 and ZINC000002528509 have more favorable potential energies with c-MET, which could exist stably in the natural environment.Conclusion This study suggests that ZINC000005879645 and ZINC000002528509 are ideal latent inhibitors of c-MET targeting. As drug candidates, these two compounds have great security and important implications for the design and improvement of c-MET target drugs.

scholarly journals A Combination of Ivermectin and Doxycycline Possibly Blocks the Viral Entry and Modulate the Innate Immune Response in COVID-19 Patients

2020 ◽  
Author(s):  
Dharmendra Kumar Maurya
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Binding Affinity ◽  
Viral Entry ◽  
Virus Disease ◽  
Host Cells ◽  
Dynamics Simulation ◽  
Host Immune System ◽  
Main Protease ◽  
Approved Drugs

<p></p><p>The current outbreak of the corona virus disease 2019 (COVID-19), has affected almost entire world and become pandemic now. Currently, there is neither any FDA approved drugs nor any vaccines available to control it. Very recently in Bangladesh, a group of doctors reported astounding success in treating patients suffering from COVID-19 with two commonly used drugs, Ivermectin and Doxycycline. In the current study we have explored the possible mechanism by which these drugs might have worked for the positive response in the COVID-19 patients. To explore the mechanism we have used molecular docking and molecular dynamics simulation approach. Effectiveness of Ivermectin and doxycycline were evaluated against Main Protease (Mpro), Spike (S) protein, Nucleocapsid (N), RNA-dependent RNA polymerase (RdRp, NSP12), ADP Ribose Phosphatase (NSP3), Endoribonuclease (NSP15) and methyltransferase (NSP10-NSP16 complex) of SARS-CoV-2 as well as human angiotensin converting enzyme 2 (ACE2) receptor. Our study shows that both Ivermectin and doxycycline have significantly bind with SARS-CoV-2 proteins but Ivermectin was better binding than doxycycline. Ivermectin showed a perfect binding site to the Spike-RBD and ACE2 interacting region indicating that it might be interfering in the interaction of spike with ACE2 and preventing the viral entry in to the host cells. Ivermectin also exhibited significant binding affinity with different SARS-CoV-2 structural and non-structural proteins (NSPs) which have diverse functions in virus life cycle. Significant binding of Ivermectin with RdRp indicate its role in the inhibition of the viral replication and ultimately impeding the multiplication of the virus. Ivermectin also possess significant binding affinity with NSP3, NSP10, NSP15 and NSP16 which helps virus in escaping from host immune system. Molecular dynamics simulation study shows that binding of the Ivermectin with Mpro, Spike, NSP3, NSP16 and ACE2 was quiet stable. Thus, our docking and simulation studies reveal that combination of Ivermectin and doxycycline might be executing the effect by inhibition of viral entry and enhance viral load clearance by targeting various viral functional proteins.</p><p></p>

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