Identification of Fungal Bioactive Compounds Targeting MMP-9 for Endometriosis- An In silico Approach

Background: Endometriosis is a chronic inflammatory disease of the female reproductive system characterized by the presence of endometrial tissue outside the uterus that affects 5 to 10% of women of reproductive age, which is approximately 176 million women in the world. The women suffering from endometriosis have been reported to have high levels of matrix metalloproteinase (especially MMP-9) which regulates the inflammatory process. Thus, the aim of this study is to investigate the naturally available anti-inflammatory fungal compounds that can target the MMP-9 by various in silico approaches. Methodology: A wide variety of anti-inflammatory bioactive compounds were screened and five compounds were further selected based on ‘Lipinski’s rule of five’ using the PubChem database. The bioavailability, pharmacokinetics, ADMET properties and biological activity of these compounds were predicted computationally using databases such as SWISS-ADME, PubChem, pkCSM and PASS. The target 1L6J (Crystal structure of human matrix metalloproteinase MMP-9) structure was retrieved from the PDB database. Comparative analysis of the bioactive compounds with the target was performed by AutoDock 4.2.6 and further visualisation of the target residues interacting with the compounds was performed using LigPlot v.2. 2. tool. Results: Based on the docking results, the compounds namely, Ergosterol peroxide, Lovastatin, Javanicin, Asperlin and Ergothioneine exhibited binding energy value of -10.25 kcal/mol, -8.4 kcal/mol, -7.64 kcal/mol, -7.07 kcal/mol and -6.19 kcal/mol respectively whereas Elagolix (control drug) exhibited binding energy value of -4.88 kcal/mol, thus, indicating that the selected bioactive compounds were seen to have better binding energy comparative to the control drug. Conclusion: Ergosterol peroxide derived from edible mushroom might act as a potential lead compound for designing a therapeutic drug for treating endometriosis and this compound can further be explored to evaluate its level of toxicity and efficacy in the wet laboratory studies by in vitro and in vivo methods.

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Chemical analysis and in silico anticancer and anti-inflammatory potentials of bioactive compounds from Moringaoleifera seed oil

Advances in Traditional Medicine ◽

10.1007/s13596-020-00521-y ◽

2020 ◽

Author(s):

Victor O. Apeh ◽

Emeka Asogwa ◽

Felicia I. Chukwuma ◽

Obiora F. Okonkwo ◽

Florence Nwora ◽

...

Keyword(s):

Chemical Analysis ◽

Bioactive Compounds ◽

In Silico ◽

Seed Oil ◽

Anti Inflammatory

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In vitro and in silico elucidation of antidiabetic and anti-inflammatory activities of bioactive compounds from Momordica charantia L.

Bioorganic & Medicinal Chemistry ◽

10.1016/j.bmc.2019.05.035 ◽

2019 ◽

Vol 27 (14) ◽

pp. 3097-3109 ◽

Cited By ~ 4

Author(s):

Siddanagouda R. Shivanagoudra ◽

Wilmer H. Perera ◽

Jose L. Perez ◽

Giridhar Athrey ◽

Yuxiang Sun ◽

...

Keyword(s):

Bioactive Compounds ◽

In Silico ◽

Momordica Charantia ◽

Anti Inflammatory

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

Biomedicine ◽

10.51248/.v41i2.1038 ◽

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.

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An Insight of Co-Encapsulation Nigella sativa and Cosmos caudatus Kunth Extracts as Anti-Inflammatory Agent Through In Silico Study

Jurnal Kimia Sains dan Aplikasi ◽

10.14710/jksa.24.5.152-160 ◽

2021 ◽

Vol 24 (5) ◽

pp. 152-160

Author(s):

Nadiyah Zuhroh ◽

Zubaidah Ningsih ◽

Anna Safitri

Keyword(s):

Bioactive Compounds ◽

In Silico ◽

Nigella Sativa ◽

In Vivo Studies ◽

Drug Candidate ◽

Active Compounds ◽

Cosmos Caudatus ◽

Cox 2 ◽

Anti Inflammatory ◽

Cox 1

This study analyzes anti-inflammatory activity from extracts of Nigella sativa and Cosmos caudatus Kunth co-encapsulated through in silico molecular docking. The LC-MS results revealed that extracts of N. sativa mostly contained thymoquinone and alpha-hederin, whereas quercetin and kaempferol were the major compounds in C. caudatus K. Nevertheless, the bioactive compounds are usually susceptible to degradation by exposure to light, heat, oxygen, which may limit its biological activity. Therefore, encapsulation is one of the promising techniques to protect bioactive compounds. Ligands were encapsulated with chitosan and sodium tripolyphosphate as wall materials. Cyclooxygenase-1 (COX-1) and cyclooxygenase-2 (COX-2) as the target enzymes were docked with a combination of these active compounds (non-encapsulated and encapsulated), using the HEX 8.0 program, and visualized using the Discovery studio visualizer software v16.1.0.15350. Interestingly, docking results of the combination of encapsulated ligands showed no interactions to COX-1 but interacted with COX-2. Therefore, co-encapsulation of extracts combinations has been suggested to act as anti-inflammatory agents targeted specifically to the COX-2 enzyme. The total energy of the encapsulated of combination of extract compounds to COX-2 were -1425.88 (mol/cal) for thymoquinone + quercetin; -1435.87 (mol/cal) for thymoquinone + kaempferol; 1175.97 (mol/cal) for quercetin + alpha hederin; -957.74 (mol/cal) for kaempferol + alpha hederin; and -283.3 (mol/cal) for diclofenac sodium, as a control NSAID drug. These suggest that encapsulated active compounds in N. sativa and C. caudatus K. have potency as a drug candidate for the selective NSAIDs category, which can be subjected to further in vitro and in vivo studies.

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STUDI MOLECULAR DOCKING SENYAWA GOLONGAN FLAVONOL SEBAGAI ANTIBAKTERI

JOPS (Journal Of Pharmacy and Science) ◽

10.36341/jops.v1i2.489 ◽

2018 ◽

Vol 1 (2) ◽

pp. 20-27

Author(s):

Isna Wardaniati ◽

Muhammad Azhari Herli

Keyword(s):

Molecular Docking ◽

Binding Energy ◽

Binding Affinity ◽

Bioactive Compounds ◽

In Silico ◽

Three Dimensional ◽

Dimensional Structure ◽

Three Dimensional Structure ◽

Receptor Interactions

In this paper we studied the bioactive compounds of Flavonol-D-alanil D-alanin dekarboksipeptidase receptor interactions In silico. First, prepared three dimensional structure of D-alanil D-alanin dekarboksipeptidase as receptor. Preparation of fourth bioactive compounds of flavonol which will be as ligands, klokasilin and D-alanil D-alanin as a comparison. The fourth bioactive compounds of flavonol, klokasilin and D-alanil D-alanin were docked with D-alanil D-alanin dekarboksipeptidase until energy values were obtained. The fourth bioactive compounds of flavonol had lesser binding energy values than D-alanil D-alanin, Quercitrine and rutin also predicted to have greater binding energy and binding affinity than klokasilin (antibiotic) and D-alanil D-alanin (nature ligand).

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Scrophularia lucida L. as a valuable source of bioactive compounds for pharmaceutical applications: In vitro antioxidant, anti-inflammatory, enzyme inhibitory properties, in silico studies, and HPLC profiles

Journal of Pharmaceutical and Biomedical Analysis ◽

10.1016/j.jpba.2018.09.035 ◽

2019 ◽

Vol 162 ◽

pp. 225-233 ◽

Cited By ~ 35

Author(s):

Gokhan Zengin ◽

Azzurra Stefanucci ◽

Maria João Rodrigues ◽

Adriano Mollica ◽

Luisa Custodio ◽

...

Keyword(s):

Bioactive Compounds ◽

In Silico ◽

Valuable Source ◽

Pharmaceutical Applications ◽

In Silico Studies ◽

Hplc Profiles ◽

Anti Inflammatory

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In silico study of anthocyanin and ternatin flavonoids for the treatment of inflammation-related diseases using molecular docking analysis

Food Research ◽

10.26656/fr.2017.4(3).378 ◽

2020 ◽

Vol 4 (3) ◽

pp. 780-785

Author(s):

Y.T. Wijaya ◽

A. Yulandi ◽

A.W. Gunawan ◽

Yanti

Keyword(s):

Molecular Docking ◽

Binding Energy ◽

Active Site ◽

In Silico ◽

Protein Crystal ◽

Drug Candidate ◽

Inflammatory Drugs ◽

Cox 2 ◽

Anti Inflammatory ◽

Cox 1

Inflammatory markers such as cyclooxygenase (COX)-2, inducible nitric oxide synthase (iNOS), myeloperoxidase (MPO), and prostaglandin (PEG) are widely known as major targets in discovering natural anti-inflammatory drugs for the treatment of inflammationrelated diseases. Non-steroidal anti-inflammatory drugs (NSAIDs) such as ibuprofen and aspirin are mostly used at present, however, some NSAIDS have been reported to cause gastrointestinal side effect due to ligand-protein interaction. Molecular docking is a promising tool to study such modes of interaction. In this study, we evaluated the potential use of anthocyanin and ternatin flavonoids as natural anti-inflammatory agents for treatment of inflammatory-related diseases using in silico molecular docking assay. Automated docking study using Protein-Ligand ANT System (PLANTS) and AutoDock Vina was performed with various ligand molecules, including ibuprofen, anthocyanin, and ternatin against the protein crystal structures of COX-1, COX-2, iNOS, and MPO. The in silico data demonstrated that ibuprofen bound effectively to the active site of COX-1 and MPO with minimum binding energy, yet the compound required more energy to bind the active site of COX-2. Ternatin flavonoid was bound to COX-2 and iNOS with minimum binding energy. In terms of binding energy, anthocyanin flavonoid was found to be effective for inhibiting COX-1, COX-2, and iNOS. These results suggested that anthocyanin and ternatin flavonoids may potentially be developed as anti-inflammatory drug candidate for the treatment of inflammatory-related diseases.

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Evaluation of Anti-inflammatory Effects of Choerospondias axillaris Fruit’s Methanolic Extract in Synoviocytes and CIA Rat Model

Current Pharmaceutical Biotechnology ◽

10.2174/1389201021666191210114127 ◽

2020 ◽

Vol 21 (7) ◽

pp. 596-604 ◽

Cited By ~ 1

Author(s):

Sonia Mann ◽

Ankita Sharma ◽

Ashish Sarkar ◽

Rupsi Kharb ◽

Rajesh Malhotra ◽

...

Keyword(s):

Binding Energy ◽

Bioactive Compounds ◽

Rat Model ◽

Methanolic Extract ◽

Systemic Disease ◽

Specific Treatment ◽

In Vivo Studies ◽

Collagen Induced Arthritis ◽

Anti Inflammatory

Background: Rheumatoid Arthritis (RA) is an autoimmune, systemic disease mainly affecting joints. Presently, there is no specific treatment/ drug available for curing RA except few supportive medicines. Therefore, the focus has been shifted to medicinal plants for the treatment of such diseases. Choerospondias axillaris commonly known as Lupsi/Lapsi and has been reported to have several properties for the treatment of various diseases. Objective: The present study has been conducted to explore the anti-inflammatory effects of Choerospondias axillaris fruit extract on Synoviocytes (FLS) and Collagen-Induced Arthritis (CIA) rat model. Methods: Methanolic extract of the Choerospondias axillaris fruit was used for determining phytochemical, antioxidant and anti-inflammatory properties. Antioxidant activity of Choerospondias axillaris fruit was determined by free radicals scavenging assays and bioactive compounds were identified via LC-MS/MS analysis. Anti-inflammatory effect was investigated in RA and Osteo Arthritis (OA) primary cells and also in Collagen Induced Arthritis (CIA) rat models. Further, the medicinal properties of anti-inflammatory bioactive compounds were supported by docking studies. Results: In-vitro and in-vivo studies showed significant decrease in the levels of inflammatory cytokines. Docking analysis revealed that quercetin inhibits TNF-α having -9.1 kcal/mol binding energy and 10.13 μM inhibitory constant. Quercetin also inhibits IL-6 having -6.6 kcal/mol binding energy and 21.9 μM inhibitory constant. Conclusion: Observed results suggest that the underutilized fruit Choerospondias axillaris can be used to reduce the inflammation of inflammatory diseases like RA.

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In-silico molecular docking analysis of some plant derived molecules for anti-inflammatory inhibitory activity

Current Botany ◽

10.25081/cb.2021.v12.6583 ◽

2021 ◽

pp. 22-27

Author(s):

L. Thamaraiselvi ◽

T. Selvankumar ◽

E.G. Wesely ◽

N. Vinod Kumar

Keyword(s):

Molecular Docking ◽

Binding Energy ◽

In Silico ◽

Novel Drugs ◽

In Silico Study ◽

Low Toxicity ◽

Cox 2 ◽

Anti Inflammatory ◽

In Silico Molecular Docking ◽

Oxide Synthase

Herbs are essential resources for drug discovery. However, numerous challenges stand in front of the scientific community to discover novel drugs from herbs. To explore the validation behind the precious knowledge of traditional medicine, we focused on achieving virtual screening to detect the potential medicines from the herbs. Five bioactive compounds from known anti-inflammatory medicinal plants were examined through molecular docking against cyclooxygenase-2 (COX-2) and inducible Nitric Oxide Synthase (iNOS), using AutoDock 4.2. The docking of selected ligands with COX-2 showed the binding energy varying from -6.15 Kcal/mol to ‑11.24 Kcal/mol. The docking energies of identified ligands with iNOS were generated ranges from -3.85kcal/mol to -6.99 kcal/mol. Among the tested ligands, it was noted that 6 urs-12-en-24-oic acid showed the best binding energy than other compounds with the lowest binding energy and highest binding affinity with both anti-inflammatory target proteins COX-2 and iNOS. The in silico study validates the potential phytochemical compound of the medicinal herb that contribute to anti-inflammatory activity with low toxicity and minimal side effects.

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