scholarly journals DESIGN AND SCREENING OF GALLIC ACID DERIVATIVES AS INHIBITORS OF MALARIAL DIHYDROFOLATE REDUCTASE (DHFR) BY IN SILICO DOCKING

2017 ◽  
Vol 10 (2) ◽  
pp. 330 ◽  
Author(s):  
Ade Arsianti Arsianti ◽  
Hendri Astuty ◽  
Fadilah Fadilah ◽  
Anton Bahtiar ◽  
Hiroki Tanimoto ◽  
...  
Keyword(s):  
Gallic Acid ◽  
Dihydrofolate Reductase ◽  
In Silico ◽  
3D Structure ◽  
Geometry Optimization ◽  
Docking Study ◽  
Open Chain ◽  
In Silico Docking ◽  
High Prevalence ◽  
Infection Disease

Objective: Malaria is an infection disease caused by plasmodium parasite with high prevalence in tropic and subtropic countries. The aim of this work was to design and screening of  gallic acid derivatives as inhibitors of malarial dihydrofolate reductase (DHFR) by in silico docking.Methods: The derivatives were designed by expanding the carboxyl group of gallic acid with open-chain moiety of L-threonine-allyl esters, as well as to modify the hydroxy groups on the aromatic ring of gallic acid with methoxyl group in the derivatives.  In silico approach has been utilized in finding the potential antimalaria of gallic acid derivatives. Fourteen Gallic acid derivatives (compound 2-15) were modeled into 3D structures by  ACD Labs software. Geometry optimization and minimization of energy 3D structure of gallic acid derivatives as ligands using the MOE software.  Docking process and amino acid analysis were executed by using MOE software. Results: In silico docking study resulted in the three top-ranked compounds, namely compound 5, 8 and 12. Among those three top-ranked compounds, compound 12 (octyl gallate), exhibited the strongest interaction and greatest inhibitory activity against the receptor of malarial DHFR.Conclusion Our results clearly demonstrated that compound 12 (octyl gallate) could be developed as a promising candidate for  the new anti-malarial agent.   

scholarly journals MOLECULAR DOCKING OF ANTIMYCIN A3 ANALOGS AND ITS AROMATIC SEGMENTS AS INHIBITORS OF APOPTOSIS PROTEIN MARKER BCL-XL AND MCL-1

2017 ◽  
Vol 10 (8) ◽  
pp. 317
Author(s):  
Ade Arsianti ◽  
Fadilah Fadilah ◽  
Linda Erlina ◽  
Rafika Indah Paramita
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Residue Analysis ◽  
3D Structure ◽  
Geometry Optimization ◽  
B Cell Lymphoma ◽  
Protein Marker ◽  
In Silico Docking ◽  
Apoptosis Protein ◽  
In Silico Molecular Docking

  Objective: Apoptosis is an important cellular process that causes the death of damaged cells. Its malfunction can lead to cancer development and poor response to conventional chemotherapy. Cellular proteins from the B-cell lymphoma 2 (BCL-2) family are crucial for apoptosis. Breast cancer is the most commonly diagnosed cancer among women worldwide. The aim of this work was to design using in silico docking antimycin A3, antimycin analogs, and its aromatic segments as inhibitors of Bcl-xl and Mcl-1.Methods: In silico molecular docking approach has been utilized to find the potential anticancer from antimycin A3 analogs and its aromatic segments. Antimycin A3 analogs and its aromatic segments were modeled into three-dimensional (3D) structures using Marvin Sketch. Based on Protein Data Bank, 3ZLN for Bcl-xl, and 5IEZ for Mcl-1 were selected as apoptosis protein marker from BCL-2 family. Geometry optimization and minimization of energy 3D structure of antimycin A3 analogs and segments (ligands) using the AutoDock software. Docking process and amino acid residue analysis were executed using AutoDock software. The best docking score was shown by the lowest binding energy and also checked with Lipinski rule of five.Results: In silico molecular docking showed antimycin A3 analogs, amide 5 and aromatic segment 14 have the best interaction and activity for Bcl-xl receptor inhibition. Moreover, amide 5 and segment 15 showed the best interaction and activity for Mcl-1 receptor inhibition.Conclusion: Our results clearly demonstrate that amide 5, segment 14, and segment 15 of antimycin A3 analog have a strong inhibitory activity against Bcl-xl and Mcl-1, and should be further developed as a promising candidate for the new anti-apoptosis agents. 

Hetero-Tricyclic Lead Scaffold as Novel PDE5A Inhibitor for Antihypertensive Activity: In Silico Docking Studies

2019 ◽  
Vol 15 (4) ◽  
pp. 318-333
Author(s):  
Dipak P. Mali ◽  
Neela M. Bhatia
Keyword(s):  
In Silico ◽  
Docking Study ◽  
Docking Studies ◽  
Antihypertensive Activity ◽  
In Silico Docking ◽  
Π Stacking ◽  
Π Stacking Interaction ◽  
Nitrogen Heteroatom ◽  
Inhibitory Potential ◽  
Vlife Mds

Objective:To screen the phytochemicals for phosphodiesterase 5A (PDE5A) inhibitory potential and identify lead scaffolds of antihypertensive phytochemicals using in silico docking studies.Methods:In this perspective, reported 269 antihypertensive phytochemicals were selected. Sildenafil, a PDE5A inhibitor was used as the standard. In silico docking study was carried out to screen and identify the inhibiting potential of the selected phytochemicals against PDE5A enzyme using vLife MDS 4.4 software.Results:Based on docking score, π-stacking, H-bond and ionic interactions, 237 out of 269 molecules were selected which have shown one or more interactions. Protein residue Gln817A was involved in H-boding whereas Val782A, Phe820A and Leu804A were involved in π-stacking interaction with ligand. The selected 237 phytochemicals were structurally diverse, therefore 82 out of 237 molecules with one or more tricycles were filtered out for further analysis. Amongst tricyclic molecules, 14 molecules containing nitrogen heteroatom were selected for lead scaffold identification which finally resulted in three different basic chemical backbones like pyridoindole, tetrahydro-pyridonaphthyridine and dihydro-pyridoquinazoline as lead scaffolds.Conclusion:In silico docking studies revealed that nitrogen-containing tetrahydro-pyridonaphthyridine and dihydro-pyridoquinazoline tricyclic lead scaffolds have emerged as novel PDE5A inhibitors for antihypertensive activity. The identified lead scaffolds may provide antihypertensive lead molecules after its optimization.

scholarly journals ANTI-PARKINSON POTENTIAL OF PERSEA AMERICANA SEED EXTRACTS THROUGH IN-SILICO DOCKING STUDY

2020 ◽  
pp. 152-155
Author(s):  
RACHAEL EVANGELINE ◽  
NIHAL AHMED
Keyword(s):  
Binding Energy ◽  
Hydrogen Bonds ◽  
In Silico ◽  
Water Extract ◽  
Docking Study ◽  
Persea Americana ◽  
Ligand Docking ◽  
Docking Analysis ◽  
In Silico Docking ◽  
Free Binding Energy

Objective: The aim of this study is to investigate the potential of Persea americana extracts for their Anti-Parkinson application through an in-silico docking study. Methods: PubChem and protein data bank databases were used to retrieve 3D structures. AutoDock4 was used to perform protein-ligand docking analysis. PyMOL was used to visualize the docking results. Results: Among the 30 ligand, the highest affinity was demonstrated by Hesperidin with a free binding energy of −6.8 kcal/mol and formation of five hydrogen bonds. The second highest significance was demonstrated by Biphenyl 4-(4-diethylaminobenzylidenamino) with a free binding energy of −5.9 kcal/mol with the formation of 2 hydrogen bonds. Among the three sets of phytochemicals from different solvent extracts, water extract demonstrated the highest potential as Anti-Parkinson active. Conclusion: P. americana extracts were analyzed for their Anti-Parkinson potential, and among the three extracts, the aqueous extract was predicted to have significant Anti-Parkinson potential, based on in silico docking analysis, due to the presence of active phytochemicals such as Hesperidin and others.

scholarly journals In silico docking analysis of selective bioactive compounds of Phyllanthus acidusaqueousfruit extractagainst MAPK1

Biomedicine ◽  
2021 ◽  
Vol 41 (2) ◽  
pp. 349-357
Author(s):  
E. Padmini ◽  
M. Kavitha
Keyword(s):  
Binding Energy ◽  
Cell Survival ◽  
Bioactive Compounds ◽  
In Silico ◽  
Docking Study ◽  
Mitogen Activated Protein Kinase ◽  
Molecular Docking Study ◽  
Ligand Complex ◽  
In Silico Docking ◽  
Methyl Prednisolone

Introduction and Aim: Phyllanthus acidus L.Skeels (Family: Phyllanthaceae) or Star Gooseberry which bears small, edible, juicy, sour, yellow berries fruit is known as a “liver tonic” in ayurvedic medicine. However, the behavior of the plant fruit or its constituents in cell apoptosis/cell survival is unknown. Hence, the purpose of thepresent study was to perform an in silico docking of selective bioactive compounds of aqueous extract of fruit of P.acidus (PAFAE) against MAPK1. Mitogen activated protein kinase is a family of serine threonine specific protein kinases- MAPK1/ERK1/2, JNK1-3, p38MAPK and ERK5.Activation ofMAPK1 promotes cell survival in certain tissues by inhibiting proapoptotic proteins and by stimulating anti apoptotic factors.   Methodology: In silico docking studies was carried out using bioinformatics tools.The active compounds (Trihomovitamin D3; 2Z,6Z,8Z,12E Hexadecatetraenoic acid, Methyl prednisolone, Hydroxysalmeterol and Tridesacetoxykhivorin) ofP.acidus aqueous fruit extract were docked against MAPK1 resulting in receptor-ligand complex.   Results: The binding energy is correlated with the probability of affinity and stable bound between ligand and its receptor.   Conclusion: The molecular docking study of selective bioactive compounds of PAFAE with MAPK1 protein revealed that Tridesacetoxykhivorinand Methyl Prednisolone, is having good interaction in favorable pose with MAPK1 as shownfrom theireffective binding energy(-7.79kcal/mol and -7.19 kcal/mol), strong bond length and interactions with active site of MAPK1.

In silico Docking Study of Some Coumarin Derivatives as Potential Inhibitors on Different Dengue Viral Proteins

2019 ◽  
Vol 70 (9) ◽  
pp. 3387-3391
Author(s):  
Gabriela Tataringa ◽  
Balasubramanian Sathyamurthy ◽  
Ion Sandu ◽  
Ana Maria Zbancioc
Keyword(s):  
Virtual Screening ◽  
Dengue Virus ◽  
In Silico ◽  
Viral Proteins ◽  
Docking Study ◽  
Binding Activity ◽  
Coumarin Derivatives ◽  
In Silico Docking ◽  
Potential Inhibitors ◽  
Hybrid Derivative

In this study, the binding efficiency of 10 coumarin derivatives with some selected proteins from Dengue virus through in silico method was done. By virtual screening and docking results, we have found that the hybrid derivative between coumarin and isatin has the most convenient binding activity for the seven selected proteins.

Phytobiological Investigation and In Silico Docking Study of Secondary Metabolites from Saussurea lappa Roots

2022 ◽  
Vol 7 (2) ◽  
Author(s):  
Mahmoud Moustafa ◽  
Mona G. Zaghloul ◽  
Mohamed A. Sabry ◽  
Walaa S. Aboelmaaty ◽  
Refaat B. Hamed ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
In Silico ◽  
Docking Study ◽  
In Silico Docking ◽  
Saussurea Lappa

An in silico Approach Towards Crop Improvement by ACC Synthase Inhibition Declining Ethylene Production

2017 ◽  
Vol 13 (1) ◽  
pp. 11-19
Author(s):  
Jasarat Ali ◽  
Rupesh K. Mishra ◽  
Chhedi L. Gupta ◽  
Dinesh C. Sharma ◽  
Preeti Bajpai ◽  
...  
Keyword(s):  
Binding Energy ◽  
Organic Contaminants ◽  
In Silico ◽  
Growth Promotion ◽  
Crop Improvement ◽  
3D Structure ◽  
Acc Synthase ◽  
Docking Study ◽  
Primary Objective ◽  
Hydrogen Bond Interaction

Introduction: The increased level of ethylene inhibits root elongation and causes physiological damage, thereby reduces ethylene level imparts a positive support against various biotic and abiotic stresses viz. phytopathogens, extreme temperatures, hyper salinity, flooding, drought, metal/organic contaminants and insect predation. The metabolic pathways showed the involvement of ACC synthase inhibition for ethylene suppression in plants. Objective: The primary objective of this study focused towards the use of In-silico approach to assess the inhibitory effect of S-adenosyl methionine (SAM) analogue on ACC synthase activity. Methods: The 3D structure of ACC synthase of Pisum sativum was constructed using modeler 9v11 software. The reliability of developed model was evaluated by PROCHECK, ERRAT and ProSA web servers. Furthermore the molecular interactions between substrate SAM and inhibitors were performed. Result: The docking study demonstrated that the binding energy of the substrate SAM is -5.37 Kcal/mol. The SAM analogue (Inhibitors) considered in this study were 3-dzSAHC, SAHC, sinefungin, SIBA, 7-dz-SIBA, 1-dz-SIBA,3-dz-SIBA and S-n-Butyladenosine. Among these analogues, 7-dz-SIBA was found to be most effective on ACC synthase as inhibitor due to lowest binding energy (- 5.51Kcal/mol) and strong Ki value (91.74M). The LYS276 amino acid residue of ACC synthase was observed in the interaction with both substrates SAM and 7-dz-SIBA (S-isobutyl-7-deazaadenosine) demonstrates as most crucial catalytic residue for molecular interaction. Conclusion: This study successfully screened most potent inhibitor for ACC synthase which have indicated the compounds 7-dz- SIBA as effective inhibitor with lowest binding energy, better hydrogen bond interaction and strong inhibition constant compared to others compounds studied. Thus 7-dz-SIBA can be projected to use as a growth enhancer for overall crop improvement. It may help in plant growth promotion, prevents the plants from various environmental stress and phytopathogenic infections etc.

Sign in / Sign up

Export Citation Format

Share Document