Implications of Molecular Docking Assay for Bioremediation

2017 ◽  
pp. 24-45 ◽  
Author(s):  
Zarrin Basharat ◽  
Monazza Bibi ◽  
Azra Yasmin
Keyword(s):  
Molecular Docking ◽  
Environmental Pollution ◽  
Active Site ◽  
Low Cost ◽  
Vantage Point ◽  
Environmental Research ◽  
Computational Techniques ◽  
Active Site Residues ◽  
Pollution Remediation ◽  
Binding Characteristics

Bioremediation utilizes microbes to control environmental pollution, primarily through diverse enzymatic processes. With the incorporation of computation in biological experimentation, bioremediation has also been influenced by computational techniques. Molecular docking assay is one such pedestal of computational assisted bioremediation, which has been elaborated in this chapter. It helps in inferring whether the active site accommodate the pollutant molecules or not, depending on the stearic hindrance of the residues and nature of the active site pocket. The spotting of consequential active site residues and binding characteristics of compounds under study can conceivably be employed for site-directed mutagenic testing. From a vantage point, no one had expected such a remarkable usefulness of molecular docking assay for environmental research. Positive shades of low cost and efficiency, combined with eco-friendliness have made it a valuable method for analyzing biodegradative properties of enzymes responsible for pollution remediation.

Implications of Molecular Docking Assay for Bioremediation

2020 ◽  
pp. 1556-1577 ◽  
Author(s):  
Zarrin Basharat ◽  
Monazza Bibi ◽  
Azra Yasmin
Keyword(s):  
Molecular Docking ◽  
Environmental Pollution ◽  
Active Site ◽  
Low Cost ◽  
Vantage Point ◽  
Environmental Research ◽  
Computational Techniques ◽  
Active Site Residues ◽  
Pollution Remediation ◽  
Binding Characteristics

Bioremediation utilizes microbes to control environmental pollution, primarily through diverse enzymatic processes. With the incorporation of computation in biological experimentation, bioremediation has also been influenced by computational techniques. Molecular docking assay is one such pedestal of computational assisted bioremediation, which has been elaborated in this chapter. It helps in inferring whether the active site accommodate the pollutant molecules or not, depending on the stearic hindrance of the residues and nature of the active site pocket. The spotting of consequential active site residues and binding characteristics of compounds under study can conceivably be employed for site-directed mutagenic testing. From a vantage point, no one had expected such a remarkable usefulness of molecular docking assay for environmental research. Positive shades of low cost and efficiency, combined with eco-friendliness have made it a valuable method for analyzing biodegradative properties of enzymes responsible for pollution remediation.

Synthesis, characterization and molecular docking studies on some new N-substituted 2-phenylpyrido[2,3-d]pyrimidine derivatives

2021 ◽  
pp. 3846-3854
Author(s):  
Vivek B. Panchabhai ◽  
Santosh R. Butle ◽  
Parag G. Ingole
Keyword(s):  
Crystal Structure ◽  
Antibacterial Activity ◽  
Molecular Docking ◽  
Active Site ◽  
Docking Studies ◽  
Biotin Carboxylase ◽  
Active Site Residues ◽  
Pyrimidine Derivatives ◽  
Molecular Docking Studies ◽  
Novel Scaffold

We report a novel scaffold of N-substituted 2-phenylpyrido(2,3-d)pyrimidine derivatives with potent antibacterial activity by targeting this biotin carboxylase enzyme. The series of eighteen N-substituted 2-phenylpyrido(2,3-d)pyrimidine derivatives were synthesized, characterized and further molecular docking studied to determine the mode of binding and energy changes with the crystal structure of biotin carboxylase (PDB ID: 2V58) was employed as the receptor with compounds 6a-r as ligands. The results obtained from the simulation were obtained in the form of dock score; these values represent the minimum energies. Compounds 6d, 6l, 6n, 6o, 6r and 6i showed formation of hydrogen bonds with the active site residues and van Der Walls interactions with the biotin carboxylase enzyme in their molecular docking studies. This compound can be studied further and developed into a potential antibacterial lead molecule.

scholarly journals Molecular docking and pharmacokinetic screening of eucalyptol (1,8 cineole) from eucalyptus essential oil against SARS-CoV-2

2020 ◽  
Vol 12 (3) ◽  
pp. 536-545
Author(s):  
Arun D. SHARMA ◽  
Inderjeet KAUR
Keyword(s):  
Molecular Docking ◽  
Essential Oil ◽  
Active Site ◽  
In Silico ◽  
Hydrophobic Interactions ◽  
Rna Virus ◽  
In Silico Analysis ◽  
Active Site Residues ◽  
Virus Family

SARS-CoV-2 (COVID-19), member of corona virus family, is a positive single stranded RNA virus. Due to lack of drugs it is spreading its tentacles across the world. Being associated with cough, fever, and respiratory distress, this disease caused more than 15% mortality worldwide. Mpro/3CLpro has recently been regarded as a suitable target for drug design due to its vital role in virus replication. The current study focused on the inhibitory activity of eucalyptol (1,8 cineole), an essential oil component from eucalyptus oil, against Mpro/3CLprofrom SARS-CoV-2. Till date there is no work is undertaken on in-silico analysis of this compound against Mpro/3CLproof SARS-CoV-2. Molecular docking studies were conducted by using 1-click dock tool and Patchdock analysis. In-silico absorption, distribution, metabolism, excretion and toxicity (ADMET) profile were also studied. The calculated parameters such as docking score indicated effective binding of eucalyptol to COVID-19 Mpro protein. Active site prediction revealed the involvement of active site residues in ligand binding. Interactions results indicated that, Mpro/3CLpro/eucalyptol complexes forms hydrophobic interactions. ADMET studies provided guidelines and mechanistic scope for identification of potent anti-COVID 19 drug. Therefore, eucalyptol may represent potential herbal treatment to act as COVID-19 Mpro/3CLproinhibitor, a finding which must be validated in vivo.

scholarly journals Synthesis and Molecular Docking Studies of some Pyrano[2,3-c] Pyrazole as an Inhibitor of SARS-Coronavirus 3CL Protease

2021 ◽  
Vol 11 (3) ◽  
pp. 3780-3801
Keyword(s):  
Molecular Docking ◽  
Active Site ◽  
Antiviral Treatment ◽  
Specific Treatment ◽  
Docking Studies ◽  
Strong Hydrogen Bond ◽  
Active Site Residues ◽  
Hydrogen Bond Interaction ◽  
Main Protease ◽  
3Cl Protease

The widespread global COVID-19 pandemic due to the lack of specific treatment and the urgent situation requires the use of all resources to remedy this scourge. The current study aimed to use molecular docking tools to find potential drug candidates for treatment. The pyrano[2,3-c] pyrazole 5(a-e) was targeted against the Main protease (Mpro), which plays a vital role in the replication and transcription of the Corona viral genome. The 3CL Protease (PDB ID 6LU7) was modeled, and the compounds were docked using Autodock Vina software, and ADMET data have been studied. All synthesized compounds were well engaged into the active site of the main protease with strong hydrogen bond interaction and a good score of energy. The 5b have been classed as the best inhibitor with an energy score of -6.2 kcal/mol, similar to the one given by chloroquine (-6.2Kcal/mol). Moreover, the molecular interaction studies showed that protease structure had multiple active site residues for all studied compounds. Our finding confirms the potential of these derivatives as lead compounds against the selected target protein of coronavirus, which needs further analysis and dynamic simulation studies to propose then develop a new antiviral treatment.

Enzyme Inhibition, Kinetic, and Molecular Docking Studies of α-glucosidase

2020 ◽  
Vol 16 (2) ◽  
pp. 155-161
Author(s):  
Ebrahim S. Moghadam ◽  
Mohammad A. Faramarzi ◽  
Somayeh Imanparast ◽  
Mohsen Amini
Keyword(s):  
Molecular Docking ◽  
Active Site ◽  
Competitive Inhibition ◽  
Kinetic Studies ◽  
Developed Countries ◽  
Docking Studies ◽  
Antidiabetic Activity ◽  
Active Site Residues ◽  
Efficient Treatment ◽  
Enzyme Active Site

Background: Diabetes mellitus (DM) is an important global health problem especially in developed countries and insufficient lifestyle induces this phenomenon. Finding efficient treatment for DM is an interesting goal for researchers. Objective: Herein we tried to design and synthesize a series of quinazoline derivatives and investigate their bioactivity as possible α-Glucosidase inhibitor agents. Method: Compounds 1-14 were synthesized using a multicomponent reaction. 1HNMR, 13C NMR, MS, and IR spectroscopy were used for the characterization of synthesized compounds. α- Glucosidase inhibitory activity of compounds 1-14 was evaluated using p-nitrophenyl‐α‐Dglucopyranoside (pNPG) as a substrate of the α-glucosidase enzyme (EC3.2.1.20, Saccharomyces cerevisiae). The mechanism of inhibition of the α-glucosidase enzyme was investigated using kinetic studies. Molecular docking was also done using autodock software to find the possible mode of interaction of compound 8 and the enzyme active site. Results: Most of the tested compounds showed higher activity in inhibition of the enzyme in comparison to the standard, acarbose. Compound 8 exerted the best activity with the IC50 value of 291.5 μM. A kinetic study indicated a competitive inhibition of the α-glucosidase enzyme by compound 8. Finally, docking studies showed the interactions between compound 8 and enzyme active site residues. Conclusion: 2,4-Diarylquinazoline scaffold has good antidiabetic activity, so it is interesting to synthesize more 2,4-diarylquinazoline derivatives and evaluate their antidiabetic activities.

scholarly journals Eucalyptol (1,8 cineole) from Eucalyptus Essential Oil a Potential Inhibitor of COVID 19 Corona Virus Infection by Molecular Docking Studies

2020 ◽  
Author(s):  
Arun Dev Sharma ◽  
inderjeet kaur
Keyword(s):  
Molecular Docking ◽  
Essential Oil ◽  
Active Site ◽  
Hydrophobic Interactions ◽  
Rna Virus ◽  
Docking Studies ◽  
Active Site Residues ◽  
Virus Family ◽  
Molecular Docking Studies ◽  
Corona Virus

Background: COVID-19, a member of corona virus family is spreading its tentacles across the world due to lack of drugs at present. Associated with its infection are cough, fever and respiratory problems causes more than 15% mortality worldwide. It is caused by a positive, single stranded RNA virus from the enveloped coronaviruse family. However, the main viral proteinase (Mpro/3CLpro) has recently been regarded as a suitable target for drug design against SARS infection due to its vital role in polyproteins processing necessary for coronavirus reproduction.Objectives: The present in silico study was designed to evaluate the effect of Eucalyptol (1,8 cineole), a essential oil component from eucalyptus oil, on Mpro by docking study.Methods: In the present study, molecular docking studies were conducted by using 1-click dock and swiss dock tools. Protein interaction mode was calculated by Protein Interactions Calculator.Results: The calculated parameters such as RMSD, binding energy, and binding site similarity indicated effective binding of eucalyptol to COVID-19 proteinase. Active site prediction further validated the role of active site residues in ligand binding. PIC results indicated that, Mpro/eucalyptol complexes forms hydrophobic interactions, hydrogen bond interactions and strong ionic interactions.Conclusions: Therefore, eucalyptol may represent potential treatment potential to act as COVID-19 Mpro inhibitor. However, further research is necessary to investigate their potential medicinal use.

scholarly journals 3D Pharmacophore-based Virtual Screening, Docking Approaches toward the Discovery of Novel HPPD Inhibitors

2017 ◽  
Author(s):  
Ying Fu ◽  
Yi-Na Sun ◽  
Ke-Han Yi ◽  
Ming-Qiang Li ◽  
Hai-feng Cao ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Virtual Screening ◽  
Active Site ◽  
Pharmacophore Model ◽  
Computational Techniques ◽  
Type I ◽  
Binding Model ◽  
Discovery Studio ◽  
Life Threatening ◽  
Key Residues

p-Hydroxyphenylpyruvate dioxygenase (HPPD) is not only the useful molecular target in treating life-threatening tyrosinemia type I, but also an important target for chemical herbicides. A combined in silico structure-based pharmacophore and molecular docking based virtual screening were performed to identify novel potential HPPD inhibitors. The complex based pharmacophore model (CBP) with 0.721 of ROC used for screening compound showed remarkable ability to retrieve known active ligands from decoy molecule. The ChemDiv database was screened using CBP-Hypo2 as a 3D query, and the best-fit hits subjected to molecular docking with two methods of LibDock and CDOCKER in Accelrys Discovery Studio 2.5(DS 2.5) to discern interactions with key residues at the active site of HPPD. 4 Compounds with top rank in HipHop model and well-known binding model were finally chosen as identification of lead compounds with potentially inhibitory effects on active site of target. The results provided powerful insight to the development of novel HPPD inhibitors herbicides using computational techniques.

Treatment of wastewater by constructed wetland in small settlements

2000 ◽  
Vol 41 (1) ◽  
pp. 69-72 ◽  
Author(s):  
S.Ç. Ayaz ◽  
I. Akca
Keyword(s):  
Environmental Pollution ◽  
Constructed Wetland ◽  
Pilot Plant ◽  
Low Cost ◽  
Experimental System ◽  
Suspended Solid ◽  
Loading Conditions ◽  
Treatment Performance ◽  
Per Capita ◽  
One Year

The constructed wetland is a low-cost technology to control environmental pollution. The system is especially suitable for small settlements. An innovative constructed wetland technology is described in this paper. A pilot plant was used to assess the performance of the system. The experimental system consists of two serial connected tanks that settled up with fillers and Cyperus as treatment media. Wastewater is recycled periodically upward and downward between the two tanks. The treatment performance was monitored in different loading conditions in a one-year period. The average COD removal efficiency of 90% was observed at 122 g COD/m2.day average loading conditions. Other average removal values in the same conditions are as follows: suspended solid 95%, TKN 77%, total nitrogen 61%, PO4-P 39%. The land requirement for this system will be 0.82 m2 per capita when applying as full-scale system.

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