scholarly journals Molecular docking of lutein as anti-photoaging agent in silico

2021 ◽  
Vol 1 (1) ◽  
pp. 15
Author(s):  
I Gede Bayu Krisnayana ◽  
Putu Dewi Febyani ◽  
Ida Ayu Yadnyaningtias Permata Sari ◽  
Ni Putu Linda Laksmiani
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Uv Exposure ◽  
Type I ◽  
Fibrillar Collagen ◽  
Matrix Metalloproteinase 1 ◽  
High Antioxidant Activity ◽  
In Silico Molecular Docking ◽  
Native Ligand ◽  
Autodock 4.2

The accumulation of UV exposure resulted in the loss of skin elasticity, and the appearance of wrinkles on the skin is commonly known as photoaging. Matrix metalloproteinase-1 (MMP-1) is an enzyme that degrades type I and III fibrillar collagen. This study aims to determine the mechanism of MMP-1 inhibition by lutein, a carotenoid compound with high antioxidant activity, using in silico molecular docking. This study was conducted by optimization of lutein structure using HyperChem 8, preparation of MMP-1 (PDB ID: 966C) using Chimera 1.10.1, validation of the method, and docking lutein against MMP-1 using Autodock 4.2. The results showed lutein had binding energy of -12.28 kcal/mol, lower than RS2 native ligand (-10.83 kcal/mol). The hydrogen bond formed between lutein and MMP-1 through HIS228 residue. To conclude, lutein may be developed as an anti-photoaging agent by inhibiting the MMP-1.

scholarly journals In silico molecular docking of quercetin as anti-colorectal cancer agents by inhibiting LT4AH

2021 ◽  
Vol 1 (2) ◽  
pp. 16
Author(s):  
Made Agus Widiana Saputra ◽  
Anak Agung Istri Rani Mahaswari ◽  
Ni Ketut Sri Anggreni ◽  
Wahyu Nadi Eka Putri ◽  
Ni Putu Linda Laksmiani
Keyword(s):  
Colorectal Cancer ◽  
Molecular Docking ◽  
Binding Energy ◽  
In Silico ◽  
Malignant Neoplasm ◽  
Docking Method ◽  
Leukotriene A4 Hydrolase ◽  
Leukotriene A4 ◽  
In Silico Molecular Docking ◽  
Native Ligand

Colorectal cancer is a malignant neoplasm originating from the colon or rectum. Overexpression of leukotriene A4 hydrolase (LTA4H) increases the growth of HCT116 colon cancer cells, therefore, this enzyme becomes an attractive target for commercial drug bestatin. Meanwhile, quercetin is a member of flavonoids possessing a wide variety of anticancer. This study aimed to determine the potential of quercetin as anti-colorectal cancer by inhibiting LTA4H through in silico molecular docking. The docking process involved optimizing quercetin structure, preparing LTA4H protein (PDB ID: 3U9W), validating the molecular docking method, and docking quercetin and bestatin on LTA4H. The binding energy of quercetin to LTA4H was -9.57 kcal/mol, while 28P native ligand and bestatin yielded -10.22 kcal/mol and -9.10 kcal/mol, respectively. Based on the binding energy value, quercetin has a potential inhibitory against the LTA4H.

scholarly journals Molecular docking of gallic acid as anti-photoaging in silico

2021 ◽  
Vol 1 (2) ◽  
pp. 18
Author(s):  
Ni Kadek Diah Parwati Dewi ◽  
Kadek Dinda Suryadewi ◽  
Diah Mawarni Fitriari ◽  
Kadek Lia Andini ◽  
Ni Putu Linda Laksmiani
Keyword(s):  
Molecular Docking ◽  
Gallic Acid ◽  
In Silico ◽  
Potential Effect ◽  
Skin Aging ◽  
Amino Acid Residues ◽  
Docking Protocol ◽  
Skin Photoaging ◽  
In Silico Molecular Docking ◽  
Native Ligand

Skin aging caused by excessive exposure to ultraviolet is known as photoaging. The mechanism underlying skin photoaging relates to collagen degradation in the extracellular matrix (ECM) by overexpression of matrix metalloproteinases-1 (MMP-1). Gallic acid is a phenolic antioxidant found in many types of plants and can be used as an anti-photoaging agent due to its antioxidant activity. This study aims to determine the potential effect of gallic acid as an anti-photoaging against MMP-1 using in silico molecular docking. The stages included gallic acid structure optimization using the HyperChem 8, preparation of protein target MMP-1 (PDB ID: 966C) using the Chimera1.10.1, validation the molecular docking protocol, and docking gallic acid on MMP-1 with the Autodock 1.5.6. The results showed that gallic acid had an affinity for MMP-1 with a binding energy of -6.0 kcal/mol. There are similar amino acid residues in hydrogen bonds between the native ligand RS2 with MMP-1 and gallic acid with MMP-1, namely ALA 182, LEU 181, and HIS 218. The results suggest that gallic acid has the potential as the anti-photoaging agent through the inhibition of the MMP-1 enzyme.

scholarly journals MOLECULAR DOCKING AKTIVITAS ANTIKANKER DARI KUERSETIN TERHADAP KANKER PAYUDARA SECARA IN SILICO

Jurnal Kimia ◽  
2019 ◽  
pp. 180
Author(s):  
M. B. O. Rastini ◽  
N. K. M. Giantari ◽  
K. D. Adnyani ◽  
N. P. L. Laksmiani
Keyword(s):  
Breast Cancer ◽  
Molecular Docking ◽  
Bond Energy ◽  
In Silico ◽  
Flavonoid Compound ◽  
Molecular Formula ◽  
Mechanism Of Inhibition ◽  
Her 2 ◽  
In Silico Molecular Docking ◽  
Native Ligand

Breast cancer can be initiated by either overexpression of HER-2 protein which can induce dimerization and autophosphorylation so that it triggers the activation of Focal Adhesion Kinase (FAK) resulting in migration and metastasis in breast cancer cells. Quercetin which has another name 3,5,7,3 ', 4'-pentahydroxyflavon with the molecular formula of (C15H10O7) is a flavonoid compound which is very widely found in nature. The purpose of this study was to determine the mechanism of inhibition of overexpression of HER-2 proteins by quercetin compounds by in silico molecular docking. In silico molecular docking was carried out in several stages namely method validation, optimization of 3D quercetin compound structure, docking between quercetin compounds optimized with HER-2 protein based on bond energy parameters the lower the bond energy the stronger and the more stable the bond is. The results of docking expressed by the binding energy of quercetin compounds with HER-2 protein are -8.24 kcal / mol, while the energy of the native ligand bond with HER-2 protein is -10.45 kcal / mol. The bonding energy shows that quercetin compounds have the potential as breast anticancer because they can modulate the overexpression of HER-2 proteins.   Keywords: quercetin, breast cancer, HER-2, in silico

The Antiviral and Antimalarial Drug Repurposing in Quest of Chemotherapeutics to Combat COVID-19 Utilizing Structure-Based Molecular Docking

2020 ◽  
Vol 23 ◽  
Author(s):  
Sisir Nandi ◽  
Mohit Kumar ◽  
Mridula Saxena ◽  
Anil Kumar Saxena
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Drug Repurposing ◽  
Clinical Settings ◽  
The Novel ◽  
In Silico Docking ◽  
Biochemical Mechanisms ◽  
Novel Coronavirus ◽  
In Silico Molecular Docking

Background: The novel coronavirus disease (COVID-19) is caused by a new strain (SARS-CoV-2) erupted in 2019. Nowadays, it is a great threat that claims uncountable lives worldwide. There is no specific chemotherapeutics developed yet to combat COVID-19. Therefore, scientists have been devoted in the quest of the medicine that can cure COVID- 19. Objective: Existing antivirals such as ASC09/ritonavir, lopinavir/ritonavir with or without umifenovir in combination with antimalarial chloroquine or hydroxychloroquine have been repurposed to fight the current coronavirus epidemic. But exact biochemical mechanisms of these drugs towards COVID-19 have not been discovered to date. Method: In-silico molecular docking can predict the mode of binding to sort out the existing chemotherapeutics having a potential affinity towards inhibition of the COVID-19 target. An attempt has been made in the present work to carry out docking analyses of 34 drugs including antivirals and antimalarials to explain explicitly the mode of interactions of these ligands towards the COVID-19protease target. Results: 13 compounds having good binding affinity have been predicted towards protease binding inhibition of COVID-19. Conclusion: Our in silico docking results have been confirmed by current reports from clinical settings through the citation of suitable experimental in vitro data available in the published literature.

Promising Anti-stroke Signature of Voglibose: Investigation through In- Silico Molecular Docking and Virtual Screening in In-Vivo Animal Studies

2020 ◽  
Vol 20 (3) ◽  
pp. 223-235
Author(s):  
Pooja Shah ◽  
Vishal Chavda ◽  
Snehal Patel ◽  
Shraddha Bhadada ◽  
Ghulam Md. Ashraf
Keyword(s):  
Molecular Docking ◽  
Virtual Screening ◽  
In Silico ◽  
Reductase Activity ◽  
Infarct Volume ◽  
Docking Studies ◽  
Serum Glucose ◽  
In Vivo Studies ◽  
In Silico Molecular Docking

Background: Postprandial hyperglycemia considered to be a major risk factor for cerebrovascular complications. Objective: The current study was designed to elucidate the beneficial role of voglibose via in-silico in vitro to in-vivo studies in improving the postprandial glycaemic state by protection against strokeprone type 2 diabetes. Material and Methods: In-Silico molecular docking and virtual screening were carried out with the help of iGEMDOCK+ Pymol+docking software and Protein Drug Bank database (PDB). Based on the results of docking studies, in-vivo investigation was carried out for possible neuroprotective action. T2DM was induced by a single injection of streptozotocin (90mg/kg, i.v.) to neonates. Six weeks after induction, voglibose was administered at the dose of 10mg/kg p.o. for two weeks. After eight weeks, diabetic rats were subjected to middle cerebral artery occlusion, and after 72 hours of surgery, neurological deficits were determined. The blood was collected for the determination of serum glucose, CK-MB, LDH and lipid levels. Brains were excised for determination of brain infarct volume, brain hemisphere weight difference, Na+-K+ ATPase activity, ROS parameters, NO levels, and aldose reductase activity. Results: In-silico docking studies showed good docking binding score for stroke associated proteins, which possibly hypotheses neuroprotective action of voglibose in stroke. In the present in-vivo study, pre-treatment with voglibose showed a significant decrease (p<0.05) in serum glucose and lipid levels. Voglibose has shown significant (p<0.05) reduction in neurological score, brain infarct volume, the difference in brain hemisphere weight. On biochemical evaluation, treatment with voglibose produced significant (p<0.05) decrease in CK-MB, LDH, and NO levels in blood and reduction in Na+-K+ ATPase, oxidative stress, and aldose reductase activity in brain homogenate. Conclusion: In-silico molecular docking and virtual screening studies and in-vivo studies in MCAo induced stroke, animal model outcomes support the strong anti-stroke signature for possible neuroprotective therapeutics.

scholarly journals In Silico Molecular Docking and Interaction Analysis of Traditional Chinese Medicines Against SARS-CoV-2 Receptor

2021 ◽  
Vol 16 (5) ◽  
pp. 1934578X2110150
Author(s):  
Gang Li ◽  
Wei Zhou ◽  
Xiurong Zhao ◽  
Ying Xie
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Interaction Analysis ◽  
Herbal Remedies ◽  
Receptor Protein ◽  
Stable Complex ◽  
Traditional Chinese Medicines ◽  
Ligand Interaction ◽  
Chinese Medicines ◽  
In Silico Molecular Docking

The novel coronavirus, 2019-nCoV, has led to a major pandemic in 2020 and is responsible for more than 2.9 million officially recorded deaths worldwide. As well as synthetic anti-viral drugs, there is also a need to explore natural herbal remedies. The Traditional Chinese Medicines (TCMs) system has been used for thousands of years for the prevention, diagnosis, and treatment of several chronic diseases. In this paper, we performed an in silico molecular docking and interaction analysis of TCMs against SARS-CoV-2 receptor RNA-dependent RNA polymerase (RdRp). We obtained the 5 most effective plant compounds which had a better binding affinity towards the target receptor protein. These compounds areforsythoside A, rutin, ginkgolide C, icariside II, and nolinospiroside E. The top-ranked compound, based on docking score, was nolinospiroside, a glycoside found in Ophiopogon japonicas that has antioxidant properties. Protein-ligand interaction analysis discerned that nolinospiroside formed a strong bond between ARG 349 of the protein receptor and the carboxylate group of the ligand, forming a stable complex. Hence, nolinospiroside could be deployed as a lead compound against SARS-CoV-2 infection that can be further investigated for its potential benefits in curbing the viral infection.

scholarly journals In silico molecular docking and in vitro antimicrobial efficacy of phytochemicals against multi-drug-resistant enteroaggregative Escherichia coli and non-typhoidal Salmonella spp.

Gut Pathogens ◽  
2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Padikkamannil Abishad ◽  
Pollumahanti Niveditha ◽  
Varsha Unni ◽  
Jess Vergis ◽  
Nitin Vasantrao Kurkure ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Molecular Docking ◽  
In Silico ◽  
Docking Studies ◽  
Antimicrobial Efficacy ◽  
Drug Resistant ◽  
Protein Motifs ◽  
Phytochemical Compounds ◽  
In Silico Molecular Docking

Abstract Background In the wake of emergence of antimicrobial resistance, bioactive phytochemical compounds are proving to be important therapeutic agents. The present study envisaged in silico molecular docking as well as in vitro antimicrobial efficacy screening of identified phytochemical ligands to the dispersin (aap) and outer membrane osmoporin (OmpC) domains of enteroaggregative Escherichia coli (EAEC) and non-typhoidal Salmonella spp. (NTS), respectively. Materials and methods The evaluation of drug-likeness, molecular properties, and bioactivity of the identified phytocompounds (thymol, carvacrol, and cinnamaldehyde) was carried out using Swiss ADME, while Protox-II and StopTox servers were used to identify its toxicity. The in silico molecular docking of the phytochemical ligands with the protein motifs of dispersin (PDB ID: 2jvu) and outer membrane osmoporin (PDB ID: 3uu2) were carried out using AutoDock v.4.20. Further, the antimicrobial efficacy of these compounds against multi-drug resistant EAEC and NTS strains was determined by estimating the minimum inhibitory concentrations and minimum bactericidal concentrations. Subsequently, these phytochemicals were subjected to their safety (sheep and human erythrocytic haemolysis) as well as stability (cationic salts, and pH) assays. Results All the three identified phytochemicals ligands were found to be zero violators of Lipinski’s rule of five and exhibited drug-likeness. The compounds tested were categorized as toxicity class-4 by Protox-II and were found to be non- cardiotoxic by StopTox. The docking studies employing 3D model of dispersin and ompC motifs with the identified phytochemical ligands exhibited good binding affinity. The identified phytochemical compounds were observed to be comparatively stable at different conditions (cationic salts, and pH); however, a concentration-dependent increase in the haemolytic assay was observed against sheep as well as human erythrocytes. Conclusions In silico molecular docking studies provided useful insights to understand the interaction of phytochemical ligands with protein motifs of pathogen and should be used routinely before the wet screening of any phytochemicals for their antibacterial, stability, and safety aspects.

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