scholarly journals IN SILICO BINDING INTERACTION STUDY OF MEFENAMIC ACID AND PIROXICAM ON HUMAN ALBUMIN

2017 ◽  
Vol 9 ◽  
pp. 102
Author(s):  
Joshita Djajadisastra ◽  
Hamka Decky Purnama ◽  
Arry Yanuar

Objective: A drug can replace other drugs in the same binding position in protein plasma, increasing pharmacological response due to the increasedfree drug concentration. Drug shifting is critical when a compound is tightly bound to a protein. For example, a binding fraction change, from 98% to94%, may increase the free fraction 3 times, from 2% to 6%. Knowing that there is an interaction between mefenamic acid and piroxicam on plasmaprotein, more specifically on human albumin, this study aimed to visualize the interaction between both drugs and human albumin in silico.Methods: This study used AutoDock4 as a molecular docking technique, obtaining binding visualizations, binding energies (ΔG), and inhibitionconstants (Ki) of both mefenamic acid-albumin and piroxicam-albumin bindings.Results: It is shown that the ΔG and Ki of both mefenamic acid and piroxicam are −5.47 kcal/mol (98.59 μM) and −7.46 kcal/mol (3.42 μM), respectively.Conclusions: The process of binding mefenamic acid to albumin can be substituted with piroxicam due to its higher ΔG and Ki values. It can bepredicted that this interaction will increase the free mefenamic acid concentration in blood plasma which, in turn, enhances the therapeutic effect.

2021 ◽  
pp. 1-6
Author(s):  
Vikil Ramesh ◽  
◽  
Megha Mathur ◽  
Kiran S ◽  
Rajeswari N ◽  
...  

Background and Objectives: (Eleusine coracana) is a rich source of proteins, phytochemicals, and fibers with several health benefits. Cancer accounts for 12c/o of death worldwide, which requires superior therapeutic strategies. Polyphenols are a class of phytochemicals in plant derived compounds, that has been reported to exhibit anticancer, antioxidant, anti-inflammatory and antimicrobial properties. The objective was to investigate the binding potential of selected polyphenols against probable drug targets of various types of cancer and provide an insight on the anti-inflammatory, antioxidant, and antimicrobial properties by using molecular docking method. Materials and Methods: Ten receptors were analyzed for anticancer, two receptors for anti- inflammatory, three receptors for antioxidant, and five receptors for antimicrobial studies. The binding competences of polyphenol towards selected targets were studied by molecular docking. Results: Affinity of polyphenols as an anticancer agent with respect specific targets viz CDKN1A, FOXO1, FGFR2, CTNNB1, and GST-PI was evident. The binding energies of docked complexes were found to be -116.56, -114.5, -110.38, -106.9, and -105.07 kcal/mol, respectively. In case of anti-inflammatory the best binding was seen in between COX-2 receptor with and COX-1 receptors. Antioxidant studies it was observed that SOD2 showed the best binding energy followed by SOD3. Followed by antimicrobial studies the best binding interaction some how were shown by IARS and PBP1a receptors. Conclusion: Present studies revealed that polyphenols has superior interacting properties towards these cancer targets than their normal ligands and shows a strong approach to anti-inflammatory, antioxidant, and antimicrobial activity


2021 ◽  
pp. 1-2
Author(s):  
Derqaoui Sabrine ◽  
◽  
EL Majoudi Salma ◽  
Rouas Lamia ◽  
Lamalmi Najat ◽  
...  

Background and Objectives: (Eleusine coracana) is a rich source of proteins, phytochemicals, and fibers with several health benefits. Cancer accounts for 12c/o of death worldwide, which requires superior therapeutic strategies. Polyphenols are a class of phytochemicals in plant derived compounds, that has been reported to exhibit anticancer, antioxidant, anti-inflammatory and antimicrobial properties. The objective was to investigate the binding potential of selected polyphenols against probable drug targets of various types of cancer and provide an insight on the anti-inflammatory, antioxidant, and antimicrobial properties by using molecular docking method. Materials and Methods: Ten receptors were analyzed for anticancer, two receptors for anti- inflammatory, three receptors for antioxidant, and five receptors for antimicrobial studies. The binding competences of polyphenol towards selected targets were studied by molecular docking. Results: Affinity of polyphenols as an anticancer agent with respect specific targets viz CDKN1A, FOXO1, FGFR2, CTNNB1, and GST-PI was evident. The binding energies of docked complexes were found to be -116.56, -114.5, -110.38, -106.9, and -105.07 kcal/mol, respectively. In case of anti-inflammatory the best binding was seen in between COX-2 receptor with and COX-1 receptors. Antioxidant studies it was observed that SOD2 showed the best binding energy followed by SOD3. Followed by antimicrobial studies the best binding interaction some how were shown by IARS and PBP1a receptors. Conclusion: Present studies revealed that polyphenols has superior interacting properties towards these cancer targets than their normal ligands and shows a strong approach to anti-inflammatory, antioxidant, and antimicrobial activity


Author(s):  
Kanishka Uthansingh ◽  
Ratna Kumari ◽  
Girish Kumar Pati ◽  
Manas Kumar Behera ◽  
Mahesh Chandra Sahu ◽  
...  

Helicobacter pylorus (H. pylori) is a deadly bacterium responsible for significant worldwide Gastric Cancer (GC) related mortality. The present study aimed to screen all the anti-microbial drugs used to eradicate H .pylori infection and to identify the most efficient drug by using computational methods through molecular docking analysis. The 3-D structure of protein chorismate synthase of H. pylori was downloaded from the Protein data bank (PDB) online browser. The x-ray crystallography structures of 13 common drugs used against H.pylori infection were also downloaded from the drug bank. We screened all 13 common drugs through molecular docking to know the most efficient binding interaction between the diverse ligand-protein complexes. The results were further compared with clinical survey data from the patients with diverse gastrointestinal H. pylori infected cases. Among the screened compounds, by in-silico approach we found that fluoroquinolone (FLRQ) and tetracycline (TET) manifested more significant interactions with chorismate synthase (CS) protein along with binding energies of -9.2 and -8.1 kcal/mole respectively. Further, the drugs were also corroborated with the survey data from patients with varied gastrointestinal disorders in our study. With this computational study, we could find FLRQ and TET may be the most efficient drug for H. pylori treatment, which can be tried in case of anti H. Pylori treatment failure due to resistance. Hence, effective inter-analysis between the experimental and computational approaches is crucial to build up a strong inhibitor.


2020 ◽  
Author(s):  
Sahar Qazi ◽  
Mustafa Alhaji Isa ◽  
Adam Mustapha ◽  
Khalid Raza ◽  
Ibrahim Alkali Allamin ◽  
...  

<p>The Severe Acute Respiratory Syndrome 2 (SARS-CoV-2) is an infectious virus that causes mild to severe life-threatening upper respiratory tract infection. The virus emerged in Wuhan, China in 2019, and later spread across the globe. Its genome has been completely sequenced and based on the genomic information, the virus possessed 3C-Like Main Protease (3CLpro), an essential multifunctional enzyme that plays a vital role in the replication and transcription of the virus by cleaving polyprotein at eleven various sites to produce different non-structural proteins. This makes the protein an important target for drug design and discovery. Herein, we analyzed the interaction between the 3CLpro and potential inhibitory compounds identified from the extracts of <i>Zingiber offinale</i> and <i>Anacardium occidentale</i> using in silico docking and Molecular Dynamics (MD) Simulation. The crystal structure of SARS-CoV-2 main protease in complex with 02J (5-Methylisoxazole-3-carboxylic acid) and PEJ (composite ligand) (PDB Code: 6LU7,2.16Å) retrieved from Protein Data Bank (PDB) and subject to structure optimization and energy minimization. A total of twenty-nine compounds were obtained from the extracts of <i>Zingiber offinale </i>and the leaves of <i>Anacardium occidentale. </i>These compounds were screened for physicochemical (Lipinski rule of five, Veber rule, and Egan filter), <i>Pan</i>-Assay Interference Structure (PAINS), and pharmacokinetic properties to determine the Pharmaceutical Active Ingredients (PAIs). Of the 29 compounds, only nineteen (19) possessed drug-likeness properties with efficient oral bioavailability and less toxicity. These compounds subjected to molecular docking analysis to determine their binding energies with the 3CLpro. The result of the analysis indicated that the free binding energies of the compounds ranged between ˗5.08 and -10.24kcal/mol, better than the binding energies of 02j (-4.10kcal/mol) and PJE (-5.07kcal.mol). Six compounds (CID_99615 = -10.24kcal/mol, CID_3981360 = 9.75kcal/mol, CID_9910474 = -9.14kcal/mol, CID_11697907 = -9.10kcal/mol, CID_10503282 = -9.09kcal/mol and CID_620012 = -8.53kcal/mol) with good binding energies further selected and subjected to MD Simulation to determine the stability of the protein-ligand complex. The results of the analysis indicated that all the ligands form stable complexes with the protein, although, CID_9910474 and CID_10503282 had a better stability when compared to other selected phytochemicals (CID_99615, CID_3981360, CID_620012, and CID_11697907). </p>


2020 ◽  
Author(s):  
Sahar Qazi ◽  
Mustafa Alhaji Isa ◽  
Adam Mustapha ◽  
Khalid Raza ◽  
Ibrahim Alkali Allamin ◽  
...  

<p>The Severe Acute Respiratory Syndrome 2 (SARS-CoV-2) is an infectious virus that causes mild to severe life-threatening upper respiratory tract infection. The virus emerged in Wuhan, China in 2019, and later spread across the globe. Its genome has been completely sequenced and based on the genomic information, the virus possessed 3C-Like Main Protease (3CLpro), an essential multifunctional enzyme that plays a vital role in the replication and transcription of the virus by cleaving polyprotein at eleven various sites to produce different non-structural proteins. This makes the protein an important target for drug design and discovery. Herein, we analyzed the interaction between the 3CLpro and potential inhibitory compounds identified from the extracts of <i>Zingiber offinale</i> and <i>Anacardium occidentale</i> using in silico docking and Molecular Dynamics (MD) Simulation. The crystal structure of SARS-CoV-2 main protease in complex with 02J (5-Methylisoxazole-3-carboxylic acid) and PEJ (composite ligand) (PDB Code: 6LU7,2.16Å) retrieved from Protein Data Bank (PDB) and subject to structure optimization and energy minimization. A total of twenty-nine compounds were obtained from the extracts of <i>Zingiber offinale </i>and the leaves of <i>Anacardium occidentale. </i>These compounds were screened for physicochemical (Lipinski rule of five, Veber rule, and Egan filter), <i>Pan</i>-Assay Interference Structure (PAINS), and pharmacokinetic properties to determine the Pharmaceutical Active Ingredients (PAIs). Of the 29 compounds, only nineteen (19) possessed drug-likeness properties with efficient oral bioavailability and less toxicity. These compounds subjected to molecular docking analysis to determine their binding energies with the 3CLpro. The result of the analysis indicated that the free binding energies of the compounds ranged between ˗5.08 and -10.24kcal/mol, better than the binding energies of 02j (-4.10kcal/mol) and PJE (-5.07kcal.mol). Six compounds (CID_99615 = -10.24kcal/mol, CID_3981360 = 9.75kcal/mol, CID_9910474 = -9.14kcal/mol, CID_11697907 = -9.10kcal/mol, CID_10503282 = -9.09kcal/mol and CID_620012 = -8.53kcal/mol) with good binding energies further selected and subjected to MD Simulation to determine the stability of the protein-ligand complex. The results of the analysis indicated that all the ligands form stable complexes with the protein, although, CID_9910474 and CID_10503282 had a better stability when compared to other selected phytochemicals (CID_99615, CID_3981360, CID_620012, and CID_11697907). </p>


Author(s):  
Tahmeena Khan ◽  
Rumana Ahmad ◽  
Iqbal Azad ◽  
Saman Raza ◽  
Seema Joshi ◽  
...  

Background: Mixed ligand-metal complexes are efficient chelating agents because of flexible donor ability. Mixed ligand complexes containing hetero atoms sulphur, nitrogen and oxygen have been probed for their biological significance. Objective: Nine mixed ligand-metal complexes of 2-(butan-2-ylidene) hydrazinecarbothioamide (2-butanone thiosemicarbazone) and pyridine, bipyridine or 2-picoline as co-ligands were synthesized with Cu, Fe and Zn. The complexes were tested against MDA-MB231 (MDA) and A549 cell lines. Antibacterial activity was tested against S. aureus and E. coli. The drug character of the complexes was evaluated on several parameters viz. physicochemical properties, bioactivity scores, toxicity assessment and absorption, distribution, metabolism, excretion and toxicity (ADMET) profile assessment using various automated softwares. Molecular docking of the complexes was also performed with two target proteins. Method and Results: The mixed ligand-metal complexes were synthesized by condensation reaction for 4-5 h. The characterization was done by elemental analysis, 1H-NMR, FT-IR, molar conductance and UV spectroscopies. Molecular docking was performed against ribonucleotide reductase (RR) and topoisomerase II (topo II). [Cu(C5H11N3S)(py)2(CH3COO)2], [Zn(C5H11N3S)(bpy)(SO4)] and [Zn(C5H11N3S)(2-pic)2(SO4)] displayed the lowest binding energies with respect to RR. Against topo II [Cu(C5H11N3S)(py)2(CH3COO)2], [Cu(C5H11N3S)(bpy)(CH3COO)2] and [Zn(C5H11N3S)(2-pic)2(SO4)] had the lowest energies. The druglikness assessment was done using Leadlikeness and Lipinski’s rules. Against topo II [Cu(C5H11N3S)(py)2(CH3COO)2], [Cu(C5H11N3S)(bpy)(CH3COO)2] and [Zn(C5H11N3S)(2-pic)2(SO4)] had the lowest energies. Not more than two violations were obtained in case of each filtering rule showing drug like character of the mixed ligand complexes. Several of the complexes exhibited positive bioactivity scores and almost all the complexes were predicted to be safe with no hazardous effects. All the complexes were predicted to have no mutagenic character as shown by the Ames test [Zn(C5H11N3S)(py)2(SO4)] showed potential activity against MDA. [Co(C5H11N3S(bpy)(Cl)2] was also active against MDA. [Cu(C5H11N3S)(2-pic)2(CH3COO)2] also showed 27.6% cell viability at 100 µM against MDA. Against A549 [Co(C5H11N3S)(py)2(Cl)2], [Cu(C5H11N3S)(py)2(CH3COO)2] and [Co(C5H11N3S(bpy)(Cl)2] were active. [Co(C5H11N3S)(bpy)(Cl)2] and [Cu(C5H11N3S)(2-pic)2(CH3COO)2] were active against S. aureus. [Co(C5H11N3S)(2-pic)2(Cl)2] and [Zn(C5H11N3S)(2-pic)2(SO4)] were active at lower concentrations against S.aureus. Against E. coli, [Zn(C5H11N3S)(2-pic)2(SO4)] showed activity at 18-20mg dose range.


Author(s):  
Anuradha Thakur ◽  
Kamalpreet Kaur ◽  
Praveen Sharma ◽  
Ramit Singla ◽  
Sandeep Singh ◽  
...  

Background: Breast cancer (BC) is a leading cause of cancer-related deaths in women next to skin cancer. Estrogen receptors (ERs) play an important role in the progression of BC. Current anticancer agents have several drawbacks such as serious side effects and the emergence of resistance to chemotherapeutic drugs. As coumarins possess minimum side effect along with multi-drug reversal activity, it has a tremendous ability to regulate a diverse range of cellular pathways that can be explored for selective anticancer activity. Objectives: Synthesis and evaluation of new coumarin analogues for anti-proliferative activity on human breast cancer cell line MCF-7 along with exploration of binding interaction of the compounds for ER-α target protein by molecular docking. Method: In this study, the anti-proliferative activity of C-3 substituted coumarins analogues (1-17) has been evaluated against estrogen receptor-positive MCF-7 breast cancer cell lines. Molecular interactions and ADME study of the compounds were analyzed by using Schrodinger software. Results: Among the synthesized analogues 12 and 13 show good antiproliferative activity with IC50 values 1and 1.3 µM respectively. Molecular docking suggests a remarkable binding pose of all the seventeen compounds. Compounds 12 and 13 were found to exhibit dock score of -4.10 kcal/mol and -4.38 kcal/mol respectively. Conclusion: Compounds 12 and 13 showed the highest activity followed by 1 and 5. ADME properties of all compounds were in the acceptable range. The active compounds can be taken for lead optimization and mechanistic interventions for their in vivo study in the future.


2019 ◽  
Vol 16 (6) ◽  
pp. 696-710
Author(s):  
Mahmoud Balbaa ◽  
Doaa Awad ◽  
Ahmad Abd Elaal ◽  
Shimaa Mahsoub ◽  
Mayssaa Moharram ◽  
...  

Background: ,2,3-Triazoles and imidazoles are important five-membered heterocyclic scaffolds due to their extensive biological activities. These products have been an area of growing interest to many researchers around the world because of their enormous pharmaceutical scope. Methods: The in vivo and in vitro enzyme inhibition of some thioglycosides encompassing 1,2,4- triazole N1, N2, and N3 and/or imidazole moieties N4, N5, and N6. The effect on the antioxidant enzymes (superoxide dismutase, glutathione S-transferase, glutathione peroxidase and catalase) was investigated as well as their effect on α-glucosidase and β-glucuronidase. Molecular docking studies were carried out to investigate the mode of the binding interaction of the compounds with α- glucosidase and β -glucuronidase. In addition, quantitative structure-activity relationship (QSAR) investigation was applied to find out the correlation between toxicity and physicochemical properties. Results: The decrease of the antioxidant status was revealed by the in vivo effect of the tested compounds. Furthermore, the in vivo and in vitro inhibitory effects of the tested compounds were clearly pronounced on α-glucosidase, but not β-glucuronidase. The IC50 and Ki values revealed that the thioglycoside - based 1,2,4-triazole N3 possesses a high inhibitory action. In addition, the in vitro studies demonstrated that the whole tested 1,2,4-triazole are potent inhibitors with a Ki magnitude of 10-6 and exhibited a competitive type inhibition. On the other hand, the thioglycosides - based imidazole ring showed an antioxidant activity and exerted a slight in vivo stimulation of α-glucosidase and β- glucuronidase. Molecular docking proved that the compounds exhibited binding affinity with the active sites of α -glucosidase and β-glucuronidase (docking score ranged from -2.320 to -4.370 kcal/mol). Furthermore, QSAR study revealed that the HBD and RB were found to have an overall significant correlation with the toxicity. Conclusion: These data suggest that the inhibition of α-glucosidase is accompanied by an oxidative stress action.


Biomolecules ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 653
Author(s):  
Seth O. Asiedu ◽  
Samuel K. Kwofie ◽  
Emmanuel Broni ◽  
Michael D. Wilson

Severely ill coronavirus disease 2019 (COVID-19) patients show elevated concentrations of pro-inflammatory cytokines, a situation commonly known as a cytokine storm. The p38 MAPK receptor is considered a plausible therapeutic target because of its involvement in the platelet activation processes leading to inflammation. This study aimed to identify potential natural product-derived inhibitory molecules against the p38α MAPK receptor to mitigate the eliciting of pro-inflammatory cytokines using computational techniques. The 3D X-ray structure of the receptor with PDB ID 3ZS5 was energy minimized using GROMACS and used for molecular docking via AutoDock Vina. The molecular docking was validated with an acceptable area under the curve (AUC) of 0.704, which was computed from the receiver operating characteristic (ROC) curve. A compendium of 38,271 natural products originating from Africa and China together with eleven known p38 MAPK inhibitors were screened against the receptor. Four potential lead compounds ZINC1691180, ZINC5519433, ZINC4520996 and ZINC5733756 were identified. The compounds formed strong intermolecular bonds with critical residues Val38, Ala51, Lys53, Thr106, Leu108, Met109 and Phe169. Additionally, they exhibited appreciably low binding energies which were corroborated via molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) calculations. The compounds were also predicted to have plausible pharmacological profiles with insignificant toxicity. The molecules were also predicted to be anti-inflammatory, kinase inhibitors, antiviral, platelet aggregation inhibitors, and immunosuppressive, with probable activity (Pa) greater than probable inactivity (Pi). ZINC5733756 is structurally similar to estradiol with a Tanimoto coefficient value of 0.73, which exhibits anti-inflammatory activity by targeting the activation of Nrf2. Similarly, ZINC1691180 has been reported to elicit anti-inflammatory activity in vitro. The compounds may serve as scaffolds for the design of potential biotherapeutic molecules against the cytokine storm associated with COVID-19.


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