IN VITRO AND IN SILICO ALPHA-AMYLASE INHIBITION POTENTIAL (ANTI-DIABETIC ACTIVITY) OF PSEUDERANTHEMUM BICOLOR (SIMS) RADIK

2020 ◽  
pp. 157-161
Author(s):  
RAMESH BS ◽  
LOKESH RAVI
Keyword(s):  
Binding Energy ◽  
Hydrogen Bonds ◽  
Ethyl Acetate ◽  
Bioactive Compounds ◽  
Methyl Ether ◽  
Docking Study ◽  
Alpha Amylase ◽  
Ligand Docking ◽  
Standard Drug ◽  
Reference Drug

Objective: Aim of this study is to evaluate theanti-diabetic activity of Pseuderanthemum bicolor commonly called limang-sugat by inhibiting alpha-amylase protein. Methods: Leaves of P. bicolor were extracted with methanol, chloroform, and ethyl acetate. The extracts were subjected for alpha-amylase inhibition assay and gas chromatography–mass spectrometry (GC–MS) analysis. Phytochemical compounds identified by GC-MS were subjected for protein-ligand docking study against alpha-amylase protein. Acarbose was used as a positive standard drug. Results: The major bioactive compounds obtained from methanol, chloroform, and ethyl acetate extracts were 1,6;2,3-Dianhydro-4-Deoxy-Beta-D-Ribo-Hexopyranose, Pseduosarsasapogenin-5,20-Dien, methyl ether/Hexatriacontane, Di-N-decylsulfone/Octadecanal, and squalene, respectively. A total of 19 secondary metabolites were subjected for protein–ligand docking study against the alpha-amylase protein. The reference drug acarbose demonstrated binding energy of −7.8 Kcal/mol and formed 20 hydrogen bonds with the enzyme. Acarbose signified high polar interaction with the amylase enzyme. Among the 19 test ligands, “2,2-Dibromocholestanone” from ethyl acetate extract exemplified the highest binding energy of −9.3 Kcal/mol. The next highest remarkable inhibition was showed by “Pseduosarsasapogenin-5,20-Dien Methyl Ether” present in the methanol extract, with a binding energy of -9.3 Kcal/mol with the formation of 2 hydrogen bonds. Conclusion: From the result, it could be concluded that the P. bicolor leaves contain various bioactive compounds which are considered as a good anti-diabetic drug.

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 ANTI-METHICILLIN RESISTANT STAPHYLOCOCCUS AUREUS POTENTIAL OF PHYTOCHEMICALS IN TERMINALIA CATAPPA AND THEIR PROPOSED IN SILICO MECHANISM OF ACTION

2019 ◽  
pp. 133-137
Author(s):  
LOKESH RAVI ◽  
DIVYA JINDAM ◽  
SUGANYA KUMARESAN ◽  
VENKATESH SELVARAJ ◽  
JAYARAMA REDDY
Keyword(s):  
Staphylococcus Aureus ◽  
Binding Energy ◽  
Hydrogen Bonds ◽  
Mechanism Of Action ◽  
In Silico ◽  
Ethanol Extract ◽  
Docking Study ◽  
Ligand Docking ◽  
Methicillin Resistant ◽  
Antibacterial Potential

Objective: The objective of this study was to investigate the antibacterial potential of leaves of this Terminalia catappa and identify the mechanism of action for those phytochemicals present in this leaves. Methods: Phytochemicals were extracted using maceration and the extracts were analyzed using gas chromatography–mass spectrometry (GC-MS) to identify the chemical structure. Antibacterial potential was evaluated using agar well diffusion. The phytochemicals were subjected to in silico protein–ligand docking study to identify the mechanism of action. Results: In vitro antibacterial study demonstrated that the ethanol extract of the leaves has significant antibacterial activity against Staphylococcus aureus (SA) and methicillin-resistant SA (MRSA) with a zone of inhibition of 16 mm and 18 mm, respectively, at a concentration of 2 mg/ml. The chloroform and hexane extracts of the leaves did not demonstrate any significant activity. Based on GC-MS analysis and literature review, 12 phytochemicals were identified to be present in the ethanol extract of the T. catappa leaves. These molecules were subjected to in silico protein–ligand docking study against common drug target proteins of SA and MRSA. Among the studied ligands, granatin A demonstrated the highest significance to inhibit topoisomerase IV with a binding energy of −11.3 kcal/mol and produced 7 hydrogen bonds, followed by punicalin with −10.7 kcal/mol binding energy toward penicillin-binding protein 2a with 6 hydrogen bonds. Conclusion: Phytochemicals of T. catappa demonstrates significant drug ability potential against drug-resistant MRSA pathogen and demands further investigation on their individual activity and mechanism.

scholarly journals PHYTOCHEMICAL SCREENING AND BIOLOGICAL EVALUATION OF DYPSIS LEPTOCHEILOS LEAVES EXTRACT AND MOLECULAR DOCKING STUDY OF THE ISOLATED COMPOUNDS

2020 ◽  
pp. 106-113
Author(s):  
HAITHAM ALI IBRAHIM ◽  
FATEHIA SAYED ELSHARAWY ◽  
MAHMMOUD ELHASSAB ◽  
SAMAH SHABANA ◽  
EMAN GABER HAGGAG
Keyword(s):  
Antioxidant Activity ◽  
Phenolic Compounds ◽  
Ethyl Acetate ◽  
Chromatographic Separation ◽  
Ethyl Acetate Fraction ◽  
Docking Study ◽  
Separation Techniques ◽  
Reference Drug ◽  
First Time ◽  
Mcf 7

Objective: phytochemical investigation of the ethyl acetate fraction (EAF) of 80% aqueous methanol extract (AME) of Dypsis leptocheilos leaves, in addition to evaluation of the antioxidant, cytotoxic and antimicrobial activities of the AME and EAF. Docking was used to predict and understand cytotoxicity of the isolated compounds. Methods: The ethyl acetate fraction (EAF) of Dypsis leptocheilos leaves was subjected to different chromatographic separation techniques. Structures of the isolated compounds were established by different spectroscopic techniques (1H/13C NMR). Antioxidant activity was evaluated by DPPH assay, while cytotoxicity was evaluated by MTT cell viability assay. Antimicrobial activity was evaluated by agar diffusion method. The docking study was conducted using Auto Dock Vina; the estrogen receptor (PDB 5t92) was used as a receptor for the docking. Results: Chromatographic separation techniques were led to the isolation of five phenolic compounds; these compounds were identified to be apigenin 8-C-β-D-glucopyranoside (Vitexin) (1), apigenin 6-C-β-D-glucopyranoside (Isovitexin) (2), luteolin 7-O-β-D-glucopyranoside (3), luteolin 8-C-β-D-glucopyranoside (Orientin) (4), luteolin 6-C-β-D-glucopyranoside (Isoorientin) (5). They were isolated and identified for the first time from this plant species. The AME and EAF showed moderate activity against Gram positive and Gram negatvie bacteria, while both of them showed similar and powerful antioxidant activity with SC50 = 12.8±0.56 µg/ml and SC50 = 17±0.77 µg/ml respectively, compared to ascorbic (reference drug) SC50 = 14.2±0.35 µg/ml. The EAF showed higher cytotoxic activity on the MCF-7 cells (human breast cancer cell line), with IC50 = 12.3 ± 1.82 µg/ml, compared to Vinblastine Sulfate (reference drug). All isolated compounds showed good binding affinity to the estrogen receptors existed in the MCF-7 cell. Conclusion: Five phenolic compounds were isolated for the first time from the EAF of Dypsis leptocheilos leaves. The AME and EAF extracts showed variable antioxidant, antimicrobial and cytotoxic activities.

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.

scholarly journals An In-silico and In-vitro Comparative Study of Compounds from Phoenix sylvestris Roxb. For Alpha-Amylase Enzyme Inhibition Involved in Diabetes Mellitus

2021 ◽  
Vol 11 (5) ◽  
pp. 13347-13358
Keyword(s):  
Ethyl Acetate ◽  
Enzyme Inhibition ◽  
Ethyl Acetate Extract ◽  
Binding Free Energy ◽  
Docking Study ◽  
Alpha Amylase ◽  
Amino Acid Residues ◽  
Docking Method ◽  
Treatment Of Diabetes

Identification of potential phytocompound from Phoenix sylvestris RoxB. For anti-diabetic potential and its validation through computational methods. Partially purified fraction evaluated for Alpha-amylase enzyme inhibition and GC-MS identified fraction validated compounds for potential anti-diabetic activity by Auto docking method. The phytocompounds investigation revealed maximum abundance of total phenol (31.55±0.55 μg/mg equivalent to Gallic acid) and flavonoid (52.90±0.08 μg/mg equivalent to quercetin) content in ethyl acetate extract. Ethyl acetate extract interestingly showed maximum alpha-amylase inhibition (71.15 %, IC50- 98.50±0.10 μg/ml), which was a mixed type of inhibition as compared to acarbose (78.64%, IC50- 88.61±0.50 μg/ml), which showed a competitive type of inhibition analyzed by Line weaver-Burk double reciprocal plot versus 1/v and 1/s. The docking study illustrated that Lupenyl acetate compound was the most active compound that showed maximum binding free energy (-7.16 Kcal/mol) and interacted with the Val64, Asn88, Gly90, Asn87, Arg87, Arg10, Gly9, Gln7, Gln5, Thr5, Trp221, Phe222, Asn5, Pro223, Ser3, Ser226, Lys227 and Gly225 amino acid residues which inhibited the alpha-amylase more efficiently than acarbose (binding energy -4.71 Kcal/mol). The present study concluded that the components of ethyl acetate extract had Alpha enzyme inhibition with reducing potential, and it may be due to the synergistic effect. The study suggested ethyl acetate extract as a natural promising therapeutic compound for the treatment of diabetes.

scholarly journals Design, Synthesis and Molecular Modeling Studies of Thiosemicarbazone & Thiazole Derivatives as Potential Anti-Malarial Agents

2021 ◽  
Author(s):  
Kamalpreet Kaur ◽  
Vivek Asati
Keyword(s):  
Antimalarial Activity ◽  
Docking Study ◽  
Docking Studies ◽  
Amino Acid Residues ◽  
Thiazole Derivatives ◽  
Design Synthesis ◽  
Standard Drug ◽  
Reference Drug ◽  
Electron Withdrawing Group ◽  
Drug Compound

Abstract A series of novel thiosemicarbazone & thiazole derivatives (Kp1-10) have been designed, synthesized and evaluated for potential anti-malarial activity. The antimalarial activity of the synthesized thiazole derivatives (Kp1-10) was assessed against human pathogenic malarial strain viz. Plasmodium falciparum while quinine was taken as the standard drug. compound Kp-9 was found to be most promising which exhibited strongest inhibitory activity against P. falciparumwith an IC50 value of 0.29µg/mL which was higher than the reference drug quinine (1.26µg/mL). The SAR studyrevealed that thesubstitution with electron withdrawing group at phenyl increases anti-malarial activity as shown in compound Kp-9. The result of molecular docking studies showed that compounds Kp-9, Kp-1, Kp-3, Kp-4 showed good docking scores with protein (PDB code: 5TBO). The compound Kp-9 showed highest docking score (-9.519). Whereas, compounds Kp-1, Kp-3, Kp-4 and Kp-10 showed good docking scores (-8.764, -8.406, -9.062, -9.435 respectively) with critical interactions with the amino acid residues such as VAL532, ILE237, LEU531, HIE185, TYR528, ASN274, ARG265. The results of biological activity and docking study revealed that the presence of electron withdrawing group at 4th position of phenyl ring attached is crucial for better anti-malarial activity and favorable drug-like profile which can emerge as a potential drug molecule in further development.

scholarly journals Synthesis of Diabetic II Inhibitors Based on 2-mercaptobenzimidazole and their Molecular Docking Study

2019 ◽  
Author(s):  
Muhammad Taha ◽  
Fazal Rahim ◽  
Shawkat Hayat ◽  
Manikandan Selvaraj ◽  
Rai Khalid Farooq ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Docking Study ◽  
Binding Mode ◽  
Alpha Amylase ◽  
Variable Degree ◽  
Molecular Docking Study ◽  
Standard Drug ◽  
Ic50 Value ◽  
Ic50 Values ◽  
Inhibitory Potential

In the search of potent α-amylase inhibitors, we have synthesized seventeen derivatives of 2-mercaptobenzimidazole bearing sulfonamide (1-17) and evaluated for their α-amylase inhibitory potential. All compounds display a variable degree of α-amylase activity having IC50 values ranging between 0.90 ± 0.05 to 11.20 ± 0.30 µM when compared with the standard drug acarbose having IC50 value 1.70 ± 0.10 µM. Compound 1, 2, 11, 12 and 14 having IC50 values 1.40 ± 0.10, 1.30 ± 0.05, 0.90 ± 0.05, 1.60 ± 0.05 and 1.60 ± 0.10 µM respectively were found many folds better than the standard drug acarbose. The remaining analogs showed good inhibitory potentials. All the synthesized compounds were characterized by HREI-MS, 1H and 13C-NMR. Structure activity relationship (SAR) has been recognized for all newly synthesized analogs. Through molecular docking study, binding mode of active analogs with α-amylase enzyme was confirmed.

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.

De novo Design and in-silico Studies of Coumarin Derivatives as Inhibitors of Cyclin Dependent Kinase-2

2017 ◽  
Vol 4 (4) ◽  
pp. 46-56
Author(s):  
Ashok Sharma ◽  
Badvel Pallavi ◽  
Riddhidev Banerjee ◽  
Mariasoosai Ramya Chandar Charles ◽  
Mohane Selvaraj Coumar ◽  
...  
Keyword(s):  
Binding Energy ◽  
In Silico ◽  
De Novo ◽  
Docking Study ◽  
Binding Mode ◽  
Coumarin Derivatives ◽  
Standard Drug ◽  
Lipinski’S Rule ◽  
In Silico Studies ◽  
Binding Cavity

In the present study, around sixty-two novel coumarin derivatives were designed as CDK-2 inhibitors based on essential pharmacophoric requirements. All the designed compounds were subjected to docking study using AutoDock 4.2 against CDK-2 protein (PDB ID: 1HCK). Molinspiration and Osiris property explorer were used to predict Lipinski’s rule of five and toxicity profile. The Structure Activity Relationship study revealed that, the substitution at R1 and R4 of coumarin nucleus enhances the binding energy and inhibitory constant values from nanomolar to picomolar range. Among the designed analogues, compound 15, 28, 43 and 59 showed significant binding energy and inhibitory constant values as compared to the standard drug Olomoucine and Deschloroflavopiridol. Most of the designed analogues showed similar binding mode and orientation inside the active site of the protein as that of the standard drug, which strongly indicates that the designed molecules may emerge as potent inhibitors of CDK-2. Next, molecular dynamics study of the significantly active molecule 15 was studied for 10 ns, in order to determine the stability of the coumarin molecules inside the binding cavity of the protein. In-silico investigations suggest that the de novo designed coumarin derivatives were potentially in-silico bioactive and need to be synthesized and tested further.

scholarly journals TEA BIOACTIVE COMPOUNDS AS INHIBITOR OF MRSA PENICILLIN BINDING PROTEIN 2a (PBP2a): A MOLECULAR DOCKING STUDY

2021 ◽  
Vol 3 (2) ◽  
pp. 70
Author(s):  
Marko Jeremia Kalalo ◽  
Fatimawali Fatimawali ◽  
Tekla Kalalo ◽  
Christani I J Rambi
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Bioactive Compounds ◽  
Docking Study ◽  
Antibacterial Activities ◽  
Multidrug Resistant ◽  
Tea Polyphenols ◽  
Resistant Bacteria ◽  
Molecular Docking Study ◽  
Docking Approach

ABSTRACT Methicillin-Resistant Staphylococcus aureus (MRSA) is a hypervirulent multidrug- resistant bacteria. It is spreading around the globe and starting to be a global health problem. It causes bacteremia, infective endocarditis, and bloodstream infection. PBP2a is a protein responsible for MRSA’s resistance to antibiotics, especially beta-lactams. Tea contains bioactive compounds such as polyphenols. It is known to have great antibacterial activities. Therefore, this study aims to find potentials antibacterial compounds from tea polyphenols that can inhibit PBP2a in MRSA with better binding energy than the currently available drugs using the molecular docking approach. We found that theaflavin (-9,7 kcal/mol), as one of the tea polyphenols compound, has a better binding energy with ceftaroline (9,5 kcal/mol) therefore predicted to have better antibacterial activity. (−)- Epigallocatechingallate (-9,1 kcal/mol), (−)-epicatechingallate (-8,8 kcal/mol), myricetin (- 8,7 kcal/mol), quercetin (-8,5 kcal/mol), (−)-epicatechin (-8,3 kcal/mol), (−)- epigallocatechin (-8,3 kcal/mol), kaempferol (-8,3 kcal/mol), procyanidin B2 (-8,1), and theflavindigallate (-7,6 kcal/mol) also have the potential to inhibit MRSA due to its low binding energy. Key words : Molecular docking, MRSA, PBP2a, Tea polyphenols.

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