scholarly journals Identifikasi Peptida Bioaktif dari Protein Kedelai sebagai Inhibitor Enzim α-glukosidase untuk Kandidat Antidiabetes

2020 ◽  
Vol 17 (2) ◽  
pp. 101-109
Author(s):  
Taufik Muhammad Fakih ◽  
Mentari Luthfika Dewi
Keyword(s):  
Molecular Interactions ◽  
Metabolic Disorders ◽  
Enzyme Inhibitor ◽  
Therapeutic Potential ◽  
Binding Free Energy ◽  
Peptide Sequencing ◽  
Bioactive Peptide ◽  
Suitable Candidate ◽  
Discovery Studio ◽  
Peptide Docking

Diabetes mellitus is one of the endocrine metabolic disorders that has caused morbidity and mortality worldwide. Α-glucosidase inhibitor which plays an important role in carbohydrate metabolism is needed to avoid postprandial hyperglycemia. A bioactive peptide derived from soy protein was chosen as an alternative treatment for diabetes because of its therapeutic potential. Several bioactive peptides have been shown to inhibit the α-glucosidase enzyme, such as the bioactive peptide LLPLPVLK, SWLRL, and WLRL. This study aims to identify and evaluate molecular interactions that occur between bioactive peptide molecules and α-glucosidase enzyme macromolecules using protein-peptide docking methods through in silico. Bioactive peptide sequencing was first modeled using the PEP-FOLD software. The best conformation was chosen for an interaction study of the α-glucosidase enzyme macromolecule using HPEPDock software. Further exploration was carried out on the molecular interactions formed using BIOVIA Discovery Studio 2020 software. Based on the results of molecular docking, the WLRL bioactive peptide has the best affinity against the α-glucosidase enzyme, with a binding free energy value of −748.12 kJ/mol. Therefore, the bioactive peptide is predicted to be a suitable candidate for the α-glucosidase enzyme inhibitor.

scholarly journals Pemodelan Molekuler Peptida Bioaktif Laut sebagai Antikoagulan Alami terhadap Enzim Sitokrom P450 (CYP) 2C9

2020 ◽  
Vol 6 (2) ◽  
Author(s):  
Taufik Muhammad Fakih ◽  
Mentari Luthfika Dewi
Keyword(s):  
Cytochrome P450 ◽  
Bioactive Peptides ◽  
Blue Mussel ◽  
Enzyme Inhibitor ◽  
Therapeutic Potential ◽  
Peptide Sequencing ◽  
Bioactive Peptide ◽  
Bleeding Complications ◽  
Peptide Docking ◽  
Yellowfin Sole

Anticoagulants are very important for the treatment and prevention of thrombotic disorders. The use of conventional anticoagulants like heparin and warfarin can cause bleeding complications. To find safer anticoagulant therapy agents, the development of isolation of new anticoagulant compounds has shifted towards natural sources. Bioactive peptides can be considered a better alternative because of their therapeutic potential in the treatment of various diseases. Several peptide molecules have been shown to inhibit the cytochrome P450 (CYP) 2C9 enzyme as a natural anticoagulant, such as bioactive peptides produced by yellowfin sole (Limanda aspera) and bioactive peptides in blue mussel (Mytilus edulis). This study aims to identify and evaluate the interactions that occur between peptide molecules with the cytochrome P450 (CYP) 2C9 enzyme using protein-peptide docking methods. Bioactive peptide sequencing was modeled using the PEP-FOLD software. The best conformation was chosen for an interaction study against the macromolecule of cytochrome P450 (CYP) 2C9 enzyme using PatchDock software. Further observations were made of interactions formed using BIOVIA Discovery Studio 2020 software. Based on the results of protein-peptide docking, the yellowfin sole peptide molecule has a good affinity against the macromolecule of cytochrome P450 (CYP) 2C9 enzyme, with an ACE score of −2527.01 kJ / mol. Therefore, the bioactive peptide is predicted to be used as a candidate for the cytochrome P450 (CYP) 2C9 enzyme inhibitor.

scholarly journals The design of bioactive marine peptides as a HIV-1 protease inhibitor

2021 ◽  
Vol 17 (2) ◽  
pp. 160-171
Author(s):  
Taufik Muhammad Fakih ◽  
Mentari Luthfika Dewi
Keyword(s):  
Protease Inhibitor ◽  
Molecular Interactions ◽  
In Silico ◽  
Bioactive Peptides ◽  
Bioactive Peptide ◽  
Human Immune System ◽  
Discovery Studio ◽  
Peptide Molecule ◽  
Immunodeficiency Syndrome ◽  
Hiv 1

Background: Human immunodeficiency virus/acquired immunodeficiency syndrome (HIV or AIDS) is a disease related to the human immune system. Given its important role in viral replication, HIV1 protease (HIV1 PR) becomes the major therapeutic target in the treatment of AIDS. In this case, we need a dynamic aspect of molecular interactions that can demonstrate the important role of conformational variability in the design of HIV1 PR inhibitors. There are several inhibitor candidates from marine organisms, such as the LLEYSL and LLEYSI bioactive peptides produced by oysters (Crassostrea gigas). Objective: Proteinpeptide docking method was used in silico to identify, evaluate, and explore the molecular interactions between bioactive peptide molecules and HIV-1 protease macromolecules. Methods: The sequencing of bioactive peptide molecules was modeled into 3D conformation using the PEPFOLD software. The best conformation was chosen for the study of molecular interactions against HIV1 protease macromolecules using the PatchDock software. The molecular interactions formed were further observed using the BIOVIA Discovery Studio 2020 software. Results: The results of this study indicated that the LLEYSL bioactive peptide had the best affinity with an ACE score of minus 1284.70 kJ per mol. Conclusion: Bioactive peptide molecule is predicted to be a candidate for HIV1 protease inhibitor. Keywords: AIDS, HIV1 protease, bioactive peptides, protein-peptide docking, in silico

scholarly journals Prediction of GluN2B-CT1290-1310/DAPK1 Interaction by Protein–Peptide Docking and Molecular Dynamics Simulation

Molecules ◽  
2018 ◽  
Vol 23 (11) ◽  
pp. 3018 ◽  
Author(s):  
Gao Tu ◽  
Tingting Fu ◽  
Fengyuan Yang ◽  
Lixia Yao ◽  
Weiwei Xue ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Electrostatic Interactions ◽  
Binding Free Energy ◽  
Computational Simulation ◽  
Critical Role ◽  
Dynamics Simulation ◽  
Peptide Docking ◽  
C Terminus ◽  
Free Energy Decomposition

The interaction of death-associated protein kinase 1 (DAPK1) with the 2B subunit (GluN2B) C-terminus of N-methyl-D-aspartate receptor (NMDAR) plays a critical role in the pathophysiology of depression and is considered a potential target for the structure-based discovery of new antidepressants. However, the 3D structures of C-terminus residues 1290–1310 of GluN2B (GluN2B-CT1290-1310) remain elusive and the interaction between GluN2B-CT1290-1310 and DAPK1 is unknown. In this study, the mechanism of interaction between DAPK1 and GluN2B-CT1290-1310 was predicted by computational simulation methods including protein–peptide docking and molecular dynamics (MD) simulation. Based on the equilibrated MD trajectory, the total binding free energy between GluN2B-CT1290-1310 and DAPK1 was computed by the mechanics generalized born surface area (MM/GBSA) approach. The simulation results showed that hydrophobic, van der Waals, and electrostatic interactions are responsible for the binding of GluN2B-CT1290–1310/DAPK1. Moreover, through per-residue free energy decomposition and in silico alanine scanning analysis, hotspot residues between GluN2B-CT1290-1310 and DAPK1 interface were identified. In conclusion, this work predicted the binding mode and quantitatively characterized the protein–peptide interface, which will aid in the discovery of novel drugs targeting the GluN2B-CT1290-1310 and DAPK1 interface.

scholarly journals Climbing up and down binding landscapes: a high-throughput study of mutational effects in homologous protein-protein complexes

2020 ◽  
Author(s):  
Michael Heyne ◽  
Jason Shirian ◽  
Itay Cohen ◽  
Yoav Peleg ◽  
Evette S. Radisky ◽  
...  
Keyword(s):  
Binding Affinity ◽  
Protein Interactions ◽  
Enzyme Inhibitor ◽  
Binding Free Energy ◽  
Hot Spot ◽  
Cold Spot ◽  
Binding Affinities ◽  
High Affinity ◽  
Binding Interface ◽  
Biological Complexes

AbstractEach protein-protein interaction (PPI) has evolved to possess binding affinity that is compatible with its cellular function. As such, cognate enzyme/inhibitor interactions frequently exhibit very high binding affinities, while structurally similar non-cognate PPIs possess substantially weaker binding affinities. To understand how slight differences in sequence and structure could lead to drastic changes in PPI binding free energy (ΔΔGbind), we study three homologous PPIs that span nine orders of magnitude in binding affinity and involve a serine protease interacting with an inhibitor BPTI. Using state-of-the-art methodology that combines protein randomization and affinity sorting coupled to next-generation sequencing and data normalization, we report quantitative binding landscapes consisting of ΔΔGbind values for the three PPIs, gleaned from tens of thousands of single and double mutations in the BPTI binding interface. We demonstrate that the three homologous PPIs possess drastically different binding landscapes and lie at different points in respect to the landscape maximum. Furthermore, the three PPIs demonstrate distinct patterns of coupling energies between two simultaneous mutations that depend not only on positions involved but also on the nature of the mutation. Interestingly, we find that in all three PPIs positive epistasis is frequently observed at hot-spot positions where mutations lead to loss of high affinity, while conversely negative epistasis is observed at cold-spot positions, where mutations lead to affinity enhancement. The new insights on PPI evolution revealed in this study will be invaluable in understanding evolution of other biological complexes and can greatly facilitate design of novel high-affinity protein inhibitors.SignificanceProtein-protein interactions (PPIs) have evolved to display binding affinities that can support their function. As such, cognate and non-cognate PPIs could be highly similar structurally but exhibit huge differences in binding affinities. To understand this phenomenon, we studied the effect of tens of thousands of single and double mutations on binding affinity of three homologous protease-inhibitor complexes. We show that binding landscapes of the three complexes are strikingly different and depend on the PPI evolutionary optimality. We observe different patterns of couplings between mutations for the three PPIs with negative and positive epistasis appearing most frequently at hot-spot and cold-spot positions, respectively. The evolutionary trends observed here are likely to be universal to all biological complexes in the cell.

scholarly journals The Therapeutic Potential of Nuclear Receptor Modulators for Treatment of Metabolic Disorders: PPARγ, RORs, and Rev-erbs

2014 ◽  
Vol 19 (2) ◽  
pp. 193-208 ◽  
Author(s):  
David P. Marciano ◽  
Mi Ra Chang ◽  
Cesar A. Corzo ◽  
Devrishi Goswami ◽  
Vinh Q. Lam ◽  
...  
Keyword(s):  
Nuclear Receptor ◽  
Metabolic Disorders ◽  
Therapeutic Potential ◽  
Receptor Modulators

scholarly journals Determining the Effect of Pterostilbene on Insulin Secretion Using Chemoproteomics

Molecules ◽  
2020 ◽  
Vol 25 (12) ◽  
pp. 2885
Author(s):  
Chiara Cassiano ◽  
Daniela Eletto ◽  
Alessandra Tosco ◽  
Raffaele Riccio ◽  
Maria Chiara Monti ◽  
...  
Keyword(s):  
Insulin Secretion ◽  
Pancreatic Beta Cells ◽  
Metabolic Disorders ◽  
Therapeutic Potential ◽  
Pharmacological Profile ◽  
Biological Targets ◽  
Cell Assays ◽  
Potential Applications ◽  
Insulin Dependent

Pterostilbene, the 3,5-dimethoxy derivative of resveratrol, is a well-known polyphenolic compound, mainly found in blueberries, grapevines, and Pterocarpus marsupium heartwood, which has recently attracted a great deal of attention due to its wide bio-pharmacological profile. Moreover, pterostilbene is more lipophilic than resveratrol, with a consequently better bioavailability and a more interesting therapeutic potential. In this work, a chemoproteomic approach, based on affinity chromatography, was applied on pterostilbene in the attempt to identify the biological targets responsible for its bioactivity. On this basis, syntaxins, a group of proteins involved in the formation of SNARE complexes mediating vesicles exocytosis, were selected among the most interesting pterostilbene interactors. In vitro and in cell assays gave evidence of the pterostilbene ability to reduce insulin secretion on glucose-stimulated pancreatic beta cells, opening the way to potential applications of pterostilbene as a supplement in the care of insulin-dependent metabolic disorders.

Chronic effects of an endothelin-converting enzyme inhibitor on cardiorenal and hormonal function in heart failure

2002 ◽  
Vol 103 (s2002) ◽  
pp. 254S-257S ◽  
Author(s):  
Atsuyuki WADA ◽  
Masato OHNISHI ◽  
Takayoshi TSUTAMOTO ◽  
Masanori FUJII ◽  
Takehiro MATSUMOTO ◽  
...  
Keyword(s):  
Heart Failure ◽  
Enzyme Inhibitor ◽  
Therapeutic Potential ◽  
Renal Plasma Flow ◽  
Urinary Sodium Excretion ◽  
Converting Enzyme ◽  
Hormonal Function ◽  
Chronic Effects ◽  
Significant Difference ◽  
Body Fluid Balance

Endothelin (ET)-converting enzyme (ECE) is a rate-limiting step in ET-1 generation, and its expression and activity are increased significantly with the development of congestive heart failure (CHF). The selective enzymic inhibition of ET-1 formation thus seems to be a very important target in the prevention of CHF. We evaluated the chronic effects of a specific ECE inhibitor, FR901533 (0.3mg·kg-1·h-1, n = 5) on cardiac, hormonal, and body fluid balance in dogs with CHF induced by rapid right ventricular pacing (270beats/min, 22 days). Vehicle dogs were given placebo (n = 5). Despite no significant difference in blood pressure, FR901533 decreased pulmonary capillary wedge pressure and increased cardiac output compared with the vehicle. FR901533 prevented the reduction of urine flow rate and urinary sodium excretion in association with an increase in the glomerular filtration rate and renal plasma flow compared with the vehicle. FR901533 also suppressed significantly the elevation of plasma atrial natriuretic peptide and aldosterone levels which is an established prognostic factor in CHF. These results indicate that the role of ECE in CHF is important and that chronic ECE inhibition could possess therapeutic potential in the treatment of CHF not only on haemodynamics but also in the prevention of fluid retention.

In-silico Design, ADMET Screening, MM-GBSA Binding Free Energy of Some Novel Isoxazole Substituted 9-Anilinoacridines as HER2 Inhibitors Targeting Breast Cancer

2019 ◽  
Vol 11 (2) ◽  
pp. 118-128 ◽  
Author(s):  
Rajagopal Kalirajan ◽  
Arumugasamy Pandiselvi ◽  
Byran Gowramma ◽  
Pandiyan Balachandran
Keyword(s):  
Breast Cancer ◽  
Free Energy ◽  
In Silico ◽  
Therapeutic Potential ◽  
Binding Free Energy ◽  
Breast Cancers ◽  
Molecular Docking Study ◽  
In Silico Admet

Background: Human Epidermal development factor Receptor-2 (HER2) is a membrane tyrosine kinase which is overexpressed and gene amplified in human breast cancers. HER2 amplification and overexpression have been linked to important tumor cell proliferation and survival pathways for 20% of instances of breast cancer. 9-aminoacridines are significant DNA-intercalating agents because of their antiproliferative properties. Objective: Some novel isoxazole substituted 9-anilinoacridines(1a-z) were designed by in-silico technique for their HER2 inhibitory activity. Docking investigations of compounds 1a-z are performed against HER2 (PDB id-3PP0) by using Schrodinger suit 2016-2. Methods: Molecular docking study for the designed molecules 1a-z are performed by Glide module, in-silico ADMET screening by QikProp module and binding free energy by Prime-MMGBSA module of Schrodinger suit. The binding affinity of designed molecules 1a-z towards HER2 was chosen based on GLIDE score. Results: Many compounds showed good hydrophobic communications and hydrogen bonding associations to hinder HER2. The compounds 1a-z, aside from 1z have significant Glide scores in the scope of - 4.91 to - 10.59 when compared with the standard Ethacridine (- 4.23) and Tamoxifen (- 3.78). The in-silico ADMET properties are inside the suggested about drug likeness. MM-GBSA binding of the most intense inhibitor is positive. Conclusion: The outcomes reveal that this study provides evidence for the consideration of isoxazole substituted 9-aminoacridine derivatives as potential HER2 inhibitors. The compounds, 1s,x,v,a,j,r with significant Glide scores may produce significant anti breast cancer activity and further in vitro and in vivo investigations may prove their therapeutic potential.

scholarly journals Sulfonanilide Derivatives in Identifying Novel Aromatase Inhibitors by Applying Docking, Virtual Screening, and MD Simulations Studies

2017 ◽  
Vol 2017 ◽  
pp. 1-17 ◽  
Author(s):  
Shailima Rampogu ◽  
Minky Son ◽  
Chanin Park ◽  
Hyong-Ha Kim ◽  
Jung-Keun Suh ◽  
...  
Keyword(s):  
Aromatase Inhibitors ◽  
Causes Of Death ◽  
Binding Free Energy ◽  
Chemical Compounds ◽  
Md Simulations ◽  
Free Energy Calculations ◽  
Lipinski’S Rule ◽  
Discovery Studio ◽  
Drug Candidates ◽  
Lipinski’S Rule Of Five

Breast cancer is one of the leading causes of death noticed in women across the world. Of late the most successful treatments rendered are the use of aromatase inhibitors (AIs). In the current study, a two-way approach for the identification of novel leads has been adapted. 81 chemical compounds were assessed to understand their potentiality against aromatase along with the four known drugs. Docking was performed employing the CDOCKER protocol available on the Discovery Studio (DS v4.5). Exemestane has displayed a higher dock score among the known drug candidates and is labeled as reference. Out of 81 ligands 14 have exhibited higher dock scores than the reference. In the second approach, these 14 compounds were utilized for the generation of the pharmacophore. The validated four-featured pharmacophore was then allowed to screen Chembridge database and the potential Hits were obtained after subjecting them to Lipinski’s rule of five and the ADMET properties. Subsequently, the acquired 3,050 Hits were escalated to molecular docking utilizing GOLD v5.0. Finally, the obtained Hits were consequently represented to be ideal lead candidates that were escalated to the MD simulations and binding free energy calculations. Additionally, the gene-disease association was performed to delineate the associated disease caused by CYP19A1.

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