scholarly journals Molecular Docking studies on the Anti-fungal activity of Allium sativum (Garlic) against Mucormycosis (black fungus) by BIOVIA discovery studio visualizer 21.1.0.0

2021 ◽  
pp. 028-032
Author(s):  
Sharma Shaweta ◽  
Sharma Akhil ◽  
Gupta Utsav
Keyword(s):  
Binding Energy ◽  
Hydrogen Bonds ◽  
Docking Studies ◽  
Binding Energies ◽  
Inhibition Constant ◽  
Beta Glucan ◽  
Glucan Synthase ◽  
Fungal Protein ◽  
Discovery Studio ◽  
Black Fungi

Background: The COVID-19 pandemic is a major concern. However, its association and rising cases of mucormycosis, also known as black fungus make the scenario even more troublesome. In addition, no specific medication against mucormycosis/black fungus makes things even worse. Objective: Garlic phytoconstituents have shown remarkable antifungal properties against various fungal species in various studies. Thus, the objective of the study was to check the potency of garlic phytoconstituents against the 1,3-beta-glucan synthase fungal protein using in-silico methods. Method: Auto Dock was used to evaluate selected garlic phytochemical molecules against 1,3-beta-glucan synthase fungal protein, and Discovery studio visualizer was used to create 3D and 2D interaction photos. Results: Five out of 9 phytoconstituents were found to form conventional hydrogen bonds, and only alliin formed the highest number of hydrogen bonds. However, the binding energy and inhibition constant of all nine phytoconstituents were determined. Interestingly, Z-ajoene showed the lowest binding energy of -5.07 kcal/mol and inhibition constant of 192.57µM. Conclusion: The results of our investigation suggested that garlic phytochemicals can have a good impact against black fungi, pertaining to the significant binding energies of phytoconstituents during blind docking. Specifically, Z-ajoene could be a good alternate against black fungi. However, detailed research is required to explore the antifungal activity of garlic against mucormycosis.

Molecular Docking Studies on the Anti-Fungal Activity of Allium Sativum (Garlic) Against Mucormycosis (Black Fungus) by BIOVIA Discovery Studio Visualizer 21.1.0.0

2021 ◽  
Author(s):  
Shaweta Sharma ◽  
Akhil Sharma ◽  
Utsav Gupta
Keyword(s):  
Binding Energy ◽  
Hydrogen Bonds ◽  
Docking Studies ◽  
Binding Energies ◽  
Inhibition Constant ◽  
Beta Glucan ◽  
Glucan Synthase ◽  
Fungal Protein ◽  
Discovery Studio ◽  
Black Fungi

Abstract Background: The COVID-19 pandemic is a major concern. However, its association and rising cases of mucormycosis, also known as black fungus make the scenario even more troublesome. In addition, no specific medication against mucormycosis/black fungus makes things even worse.Objective: Garlic phytoconstituents have shown remarkable antifungal properties against various fungal species in various studies. Thus, the objective of the study was to check the potency of garlic phytoconstituents against the 1,3-beta-glucan synthase fungal protein using in-silico methods.Method: Auto Dock was used to evaluate selected garlic phytochemical molecules against 1,3-beta-glucan synthase fungal protein, and Discovery studio visualizer was used to create 3D and 2D interaction photos.Results: Five out of 9 phytoconstituents were found to form conventional hydrogen bonds, and only alliin formed the highest number of hydrogen bonds. However, the binding energy and inhibition constant of all nine phytoconstituents were determined. Interestingly, Z-ajoene showed the lowest binding energy of -5.07 kcal/mol and inhibition constant of 192.57µM.Conclusion: The results of our investigation suggested that garlic phytochemicals can have a good impact against black fungi, pertaining to the significant binding energies of phytoconstituents during blind docking. Specifically, Z-ajoene could be a good alternate against black fungi. However, detailed research is required to explore the antifungal activity of garlic against mucormycosis.

scholarly journals MOLECULAR DOCKING STUDIES ON SCREENING AND ASSESSMENT OF SELECTED BIOFLAVONOIDS AS POTENTIAL INHIBITORS OF COVID-19 MAIN PROTEASE

2020 ◽  
pp. 174-178
Author(s):  
SHAILENDRA SANJAY SURYAWANSHI ◽  
POOJA BHAVAKANA JAYANNACHE ◽  
RAJKUMAR SANJAY PATIL ◽  
PALLED MS ◽  
ALEGAON SG
Keyword(s):  
Molecular Docking ◽  
Treatment Options ◽  
Docking Studies ◽  
Binding Energies ◽  
Molecular Docking Studies ◽  
Discovery Studio ◽  
Main Protease ◽  
Potential Inhibitors ◽  
Binding Energy Calculations ◽  
Native Ligand

Objectives: The objective of the study was to screen and assess the selected bioactive bioflavonoids in medicinal plants as potential coronaviruses (CoV) main protease (Mpro) inhibitors using molecular docking studies. Methods: We have investigated several bioflavonoids which include apigenin, galangin, glycitein, luteolin, morin, naringin, resveratrol, and rutin. Nelfinavir and lopinavir were used as standard antiviral drugs for comparison. Mpro was docked with selected compounds using PyRx 0.8 and docking was analyzed by PyRx 0.8 and Biovia Discovery Studio 2019. Results: The binding energies obtained from the docking of 6LU7 with native ligand, nelfinavir, lopinavir, apigenin, galangin, glycitein, luteolin, morin, naringin, resveratrol, and rutin were found to be −7.4, −8.3, −8.0, −7.8, −7.3, −7, −7.4, −7.6, −7.8, −6.9, and −9 kcal/mol, respectively. Conclusion: From the binding energy calculations, we can conclude that nelfinavir and lopinavir may represent potential treatment options and apigenin, galangin, glycitein, luteolin, morin, naringin, resveratrol, and rutin found to possess the best inhibitors of CoV disease-19 main protease.

scholarly journals Molecular docking studies of N-substituted 4-methoxy-6-oxo-1-aryl-pyridazine-3-carboxamide derivatives as potential modulators of glutamate receptors

2020 ◽  
Vol 6 (1) ◽  
pp. 69-82 ◽  
Author(s):  
Hanna I. Severina ◽  
Victoriya A. Georgiyants ◽  
Sergiy M. Kovalenko ◽  
Natalia V. Avdeeva ◽  
Artem I. Yarcev ◽  
...  
Keyword(s):  
Binding Energy ◽  
Glutamate Receptors ◽  
Active Sites ◽  
Docking Studies ◽  
Reference Drug ◽  
Discovery Studio ◽  
Group Iii ◽  
Modern Drug ◽  
Nmda Glutamate Receptors ◽  
Pyridazine Derivatives

Introduction: The virtual target-oriented screening is a necessary stage of modern drug-design. In the present study, the affinity of pyridazine derivatives for the most promising antiparkinsonian biotargets – I–III groups of metabotropic and ionotropic NMDA-glutamate receptors – was evaluated. Materials and methods: Docking of the studied ligands to the active sites of biotargets – mGluR5, mGluR3, mGluR8, NMDA GluN2B – was performed using AutoDockVina. Base of the preparation of ligands and proteins – AutoDockTools-1.5.6. A Discovery Studio Visualizer 2017/R2 was used to visualize the interpretation of the results. Results and discussion: A high degree of the affinity is predicted for group III of the metabotropic mGlu8 receptors – binding energy from -5.0 to -8.7 kcal/mol, compared to -6.1 kcal/mol of that of the reference drug (L-AP4), as well as for the ionotropic NMDA GluN2B receptors –binding energy from -8.7 to -11.6 kcal/mol, compared to -11.3 kcal/mol of that of ifenprodil. Conclusion: The prospects of the searching for glutamate receptor modulators in a number of n-substituted 4-methoxy-6-oxo-1-aryl-pyridazine-3-carboxamide derivatives are proved. Some aspects of the structure-affinity relationship are discussed.

scholarly journals Virtual Screening of Curcumin and Its Analogs Against the Spike Surface Glycoprotein of SARS-CoV-2 and SARS-CoV

2020 ◽  
Author(s):  
Ashish Patel ◽  
Malathi Rajendran ◽  
Suresh B Pakala ◽  
Ashish Shah ◽  
Harnisha Patel ◽  
...  
Keyword(s):  
Binding Energy ◽  
Viral Entry ◽  
Curcuma Longa ◽  
Docking Studies ◽  
Binding Energies ◽  
Surface Glycoprotein ◽  
Spike Protein ◽  
Pharmacokinetic Parameters ◽  
Angiotensin Converting Enzyme 2 ◽  
Potential Inhibitors

COVID-19, a new pandemic caused by SARS-CoV-2, was first identified in 2019 in Wuhan, China. The novel corona virus SARS-CoV-2 and the 2002 SARS-CoV have 74 % identity and use similar mechanisms to gain entry into the cell. Both the viruses enter the host cell by binding of the viral spike glycoprotein to the host receptor, angiotensin converting enzyme 2 (ACE2). Targeting entry of the virus has a better advantage than inhibiting the later stages of the viral life cycle. Potential inhibitors of SARS-CoV and SARS-CoV-2 Spike proteins was determined using molecular docking studies. Curcumin, a naturally occurring phytochemical in Curcuma longa, is known to have broad pharmacological properties. In the present study, curcumin and its derivatives were docked, using Autodock 4.2, onto the 6CRV and 6M0J to study their capability to act as inhibitors of the spike protein and thereby, viral entry. The curcumin and its derivatives displayed binding energies, ΔG, ranging from -14.18 to -4.04 kcal/mol (6CRV) and -10.01 to -5.33 kcal/mol (6M0J). The least binding energy was seen in bis-desmethoxycurcumin with: ΔG = -14.18 kcal/mol (6CRV) and -10.01 kcal/mol (6M0J). A good binding energy, drug likeness and efficient pharmacokinetic parameters suggest the potential of curcumin and few of its derivatives as SARS-CoV-2 spike protein inhibitors.<br>

Molecular modeling and docking calculations of 4-acyloxy-biphenyl-4′-N-butylcarbamates as potential inhibitors of human butyrylcholinesterase

2016 ◽  
Vol 94 (1) ◽  
pp. 72-77 ◽  
Author(s):  
Yu-Fang Shen ◽  
Gan-Hong Chen ◽  
Shu-Hsien Lin ◽  
Gialih Lin
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Binding Energy ◽  
Linear Correlation ◽  
Kinetic Studies ◽  
Docking Studies ◽  
Binding Energies ◽  
Binding Modes ◽  
Docking Calculations ◽  
Potential Inhibitors

The kinetic studies and drug designs of butyrylcholinesterase play an important role in the development of Alzheimer’s disease therapeutics. In this research, automated docking studies were performed to provide useful insights into butyrylcholinesterase inhibition binding modes with designed 4-acyloxy-biphenyl-4′-N-butylcarbamates (compounds 1–8). Moreover, several significant linear correlations between experimental and calculated docking results are observed. Among compounds 1–7, compound 3, which exhibits the strongest hydrophobicity and has four carbonyl hydrogen bindings, shows the highest binding affinity (Ki = 1.4 μmol/L) with a binding energy of −7.99 kcal/mol. The observed linear correlation of experimental and calculated inhibition constants (Ki) indicates that the molecular docking results are reliable. Moreover, a good linear correlation is observed between calculated binding energies and experimental pKi. The experimental Hansch hydrophobicity constants (π values) are also correlated with the docked binding energy. This study reveals important correlations between butyrylcholinesterase experimental and docking results that contribute to the kinetic based identification of antagonists for the treatment of Alzheimer’s disease. Furthermore, these docked models provide important insights into a potential series of 4,4′-biphenol-based inhibitors of butyrylcholinesterase.

scholarly journals Elucidation of the interactions between SARS-CoV-2 Spike protein and wild and mutant types of IFITM proteins by in silico methods

2021 ◽  
Author(s):  
Nazli Irmak Giritlioglu ◽  
Gizem Koprululu Kucuk
Keyword(s):  
Molecular Docking ◽  
Amino Acid ◽  
Binding Energy ◽  
Hydrogen Bonds ◽  
In Silico ◽  
Protein Complexes ◽  
Protein Product ◽  
Binding Energies ◽  
Spike Protein ◽  
Web Based

COVID-19 is a viral disease that has been a threat to the whole world since 2019. Although effective vaccines against the disease have been developed, there are still points to be clarified about the mechanism of SARS-CoV-2, which is the causative agent of COVID-19. In this study, we determined the binding energies and the bond types of complexes formed by open (6VYB) and closed (6VXX) forms of the Spike protein of SARS-CoV-2 and wild and mutant forms of IFITM1, IFITM2, and IFITM3 proteins using the molecular docking approach. First, all missense SNPs were found in the NCBI Single Nucleotide Polymorphism database (dbSNP) for IFITM1, IFITM2, and IFITM3 and analyzed with SIFT, PROVEAN, PolyPhen-2, SNAP2, Mutation Assessor, and PANTHER cSNP web-based tools to determine their pathogenicity. When at least four of these analysis tools showed that the SNP had a pathogenic effect on the protein product, this SNP was saved for further analysis. Delta delta G (DDG) and protein stability analysis for amino acid changes were performed in the web-based tools I-Mutant, MUpro, and SAAFEC-SEQ. The structural effect of amino acid change on the protein product was made using the HOPE web-based tool. HawkDock server was used for molecular docking and Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) analysis and binding energies of all complexes were calculated. BIOVIA Discovery Studio program was utilized to visualize the complexes. Hydrogen bonds, salt bridges, and non-bonded contacts between Spike and IFITM protein chains in the complexes were detected with the PDBsum web-based tool. The best binding energy among the 6VYB-IFITM wild protein complexes belong to 6VYB-IFITM1 (-46.16 kcal/mol). Likewise, among the 6VXX-IFITM wild protein complexes, the most negative binding energy belongs to 6VXX-IFITM1 (-52.42 kcal/mol). An interesting result found in the study is the presence of hydrogen bonds between the cytoplasmic domain of the IFITM1 wild protein and the S2 domain of 6VYB. Among the Spike-IFITM mutant protein complexes, the best binding energy belongs to the 6VXX-IFITM2 N63S complex (-50.77 kcal/mol) and the worst binding energy belongs to the 6VXX-IFITM3 S50T complex (4.86 kcal/mol). The study suggests that IFITM1 protein may act as a receptor for SARS-CoV-2 Spike protein. Assays must be advanced from in silico to in vitro for the determination of the receptor-ligand interactions between IFITM proteins and SARS-CoV-2.

Molecular Docking Studies for Protein-Targeted Drug Development in SARS-CoV-2

2021 ◽  
Vol 18 ◽  
Author(s):  
Ahmad Dzulfikri Nurhan ◽  
Maria Apriliani Gani ◽  
Saipul Maulana ◽  
Siswandono Siswandono ◽  
Chrismawan Ardianto ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Docking Studies ◽  
Binding Energies ◽  
Spike Glycoprotein ◽  
Protein Targets ◽  
Lipinski’S Rule ◽  
Global Pandemic ◽  
Potential Inhibitors ◽  
3Cl Protease

Background: The SARS-CoV-2/COVID-19 infection has resulted in a global pandemic and emergency. Currently, there is no therapeutic agent that has been proven to be effective and selective to deal with this pandemic. Objective: In this study, we explored and screened 401 compounds-related viruses that may inhibit one or more of the three protein targets in SARS-CoV-2 (3CL protease, RdRp, and spike glycoprotein) using in-silico approach. Methods: Lipinski's rule of five was used as an initial screening for these compounds. Ligand preparation was carried out using JChem software and Schrödinger's LigPrep module, while protein elucidation used AutoDockTools-1.5.6. Molecular docking was analyzed using AutoDockVina. Results: A total of five compounds-related viruses were obtained from each SARS-CoV-2 protein with ideal and potential binding energy as a candidate for target protein inhibitor on SARS-CoV-2. At the protein 3CL protease imatinib, TAK-981, lopinavir, mefloquine, and sitagliptin were found to be potential inhibitors of this protein. In the protein RdRp tetrandrine, relacatib, AZD7986, imatinib, and TAK-981 revealed potential as an inhibitor of this protein. At the protein spike, glycoprotein AZD7986, selinexor, imatinib, lopinavir, and ciclesonide, were found to have potential as inhibitors of these proteins. All these compounds have better binding energy than the three comparator drugs (remdesivir, chloroquine, and hydroxychloroquine). Conclusion: We have obtained several compounds-related viruses with reliable binding energies to the SARS-CoV-2 proteins and potentially better than the three comparator drugs. Furthermore, this research will pave the way for accelerating the development of Covid-19 drugs.

Marine Streptomyces-derived Antibacterial Compound [2, 4-Dichloro-5-sulfamoyl benzoic acid] for MRSA and VRE Strains

2016 ◽  
Vol 9 (5) ◽  
pp. 3458-3461
Author(s):  
Kannabiran K. ◽  
Benita Mercy Rajan
Keyword(s):  
Folic Acid ◽  
Binding Energy ◽  
Hydrogen Bonds ◽  
Benzoic Acid ◽  
Inhibition Constant ◽  
Ligand Docking ◽  
Drug Candidate ◽  
Synthesis Inhibitor ◽  
Carcinogenic Effect ◽  
Dps Protein

The aim of the present study was to predict the interaction of 4-dichloro-5-sulfamoyl benzoic acid (DSBA) derived from Streptomyces sp. VITBRK3 with the drug target enzymes of methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin resistant Enterococci (VRE) strains procured from ATCC. Two proteins dihydropteroate synthetase (DPS) and dihydrofolate reductase (DFR) were chosen as drug targets. The well-known folic acid synthesis inhibitor amino salicylic acid (ASA) was taken as a positive control. AutoDock 4.2.1 was used to perform the protein-ligand docking analysis. DSBA showed least binding energy of –6.99 kcal/mol and inhibition constant of 7.5 µM and formed 8 hydrogen bonds with DFR. DSBA showed least binding energy of -5.6 kcal/mol and inhibition constant of 78.58 µM and formed 7 hydrogen bonds with DPS.  ASA showed the binding energy of –4.97 kcal/mol, and inhibition constant of 225.9 µM and formed 5 hydrogen bonds with DPS protein. It showed the binding energy of          –4.68 kcal/mol, and inhibition constant of 371.32 µM and formed 4 hydrogen bonds with DFR protein. DSBA has qualified CMC rule, lead like rule and Lipinski’s rule of five. The compound DSBA does not possess any carcinogenic effect in rat or mouse model. Osiris Property Explorer analysis suggested that, DSBA does not possess any major side effects and is a suitable drug candidate. Pre ADMET analysis also suggests that, the lead compound, DSBA is a suitable drug candidate. The results of this study suggest that the antimicrobial activity of DSBA against MRSA and VRE strains is due to its inhibition over bacterial cell wall folic acid biosynthesis.

Geometrical and vibrational DFT studies of HOBr·(H2O)n clusters (n = 1–4)

2003 ◽  
Vol 81 (9) ◽  
pp. 961-970 ◽  
Author(s):  
Cristina Maria P Santos ◽  
Roberto B Faria ◽  
Wagner B De Almeida ◽  
Juan O Machuca-Herrera ◽  
Sérgio P Machado
Keyword(s):  
Binding Energy ◽  
Hydrogen Bonds ◽  
Water Molecule ◽  
Vibrational Spectra ◽  
Low Frequency ◽  
Binding Energies ◽  
Basis Sets ◽  
Dft Studies ◽  
Geometrical Structures ◽  
Stable Structures

The geometrical structures and the vibrational spectra of the HOBr·(H2O)n clusters (n = 1–4) have been calculated at the DFT level of theory, using the pBP method and the DN* and DN** numerical basis sets. The results showed that the interaction involving the H of the HOBr and the O of the water molecule represent the preferred arrangements for these hydrated compounds. Both HOBr·H2O and HOBr·(H2O)2 clusters presented stable structures with syn and anti conformations, the syn being the most stable. The HOBr·(H2O)3 and the HOBr·(H2O)4 clusters have presented stable cyclic structures. In the HOBr·H2O and HOBr·(H2O)2 clusters, low-frequency stretching values could be assigned to hydrogen bonds, but the same could not be done so clearly for the HOBr·(H2O)3 and the HOBr·(H2O)4 cyclic clusters. The binding energies were also determinated for these HOBr hydrated clusters, showing that the addition of a water molecule to the HOBr·H2O and HOBr·(H2O)2 clusters increases the binding energy by approximately 4 kcal mol–1, while the addition of a water molecule to the HOBr·(H2O)3 cluster decreases this value by 4 kcal mol–1.Key words: DFT, numerical basis, HOBr·(H2O)n, clusters.

scholarly journals Molecular docking studies of inhibitory activities of Phytochemicals in Calotropis procera against α-glucosidase hydrolase Sus B.

2021 ◽  
Vol 46 (2) ◽  
Author(s):  
O. O. Adeboye ◽  
S. A. Agboluaje ◽  
O. F. Akinyele
Keyword(s):  
Molecular Docking ◽  
Docking Studies ◽  
Screening Tools ◽  
Inhibition Constant ◽  
Calotropis Procera ◽  
Docking Analysis ◽  
Molecular Docking Studies ◽  
Discovery Studio ◽  
Synthetic Drugs ◽  
Inhibitory Activities

The use of synthetic drugs is associated with various side effects and it is important to look for other drugs from medicinal plants. Therefore, this study aimed at assessing the inhibitory activities of Calotropis procera leaf against α-glucosidase hydrolase Sus B and it‟s possible mode of inhibiting this enzyme through molecular docking studies. From the molecular docking analysis, the results shows that out of the thirty six (36) screened phytochemicals, only twenty six (26) fall between the recommended hit value of inhibition constant of (0.1-1.0 µM) where their inhibition constant range from (0.01-0.59 µM) after docking with target receptor α-glucosidase hydrolase SusB (PDB ID: 2ZQ0) using Pyrx-vitual screening tools (Autodock tool, Autodock vina and Open babel).Visualizing was done using Pymol and Biosvia discovery studio(2019). Considering the other analysis done, Drug likeness of Lipinski rule of five, only six(6): Hesperidine (3),Calotroposide (3),Calotropin (3),Ascleposide (4),Proceroside (4) and Voruschairin (3) out of the potent twenty six (26) contravene more than 2 of the Lipinski rules of five, therefore other twenty (20) compounds can be considered for processing into potent drugs.

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