scholarly journals DOCKING STUDIES OF CURCUMIN AS A POTENTIAL LEAD COMPOUND TO DEVELOP NOVEL DIPEPTYDYL PEPTIDASE-4 INHIBITORS

2010 ◽  
Vol 9 (1) ◽  
pp. 132-136 ◽  
Author(s):  
Enade Perdana Istyastono
Keyword(s):  
Docking Studies ◽  
Lead Compound ◽  
Reference Compound ◽  
Operating Environment ◽  
Molecular Operating Environment ◽  
Software Applications ◽  
Small Compound ◽  
Docking Method ◽  
Conformational Spaces ◽  
Free Energy Of Binding

Interaction of curcumin to dipeptydyl peptidase-4 (DPP-4) has been studied by employing docking method using Molecular Operating Environment (MOE) and AutoDock as the docking software applications. Although MOE can sample more conformational spaces that represent the original interaction poses than AutoDock, both softwares serve as valid and acceptable docking applications to study the interactions of small compound to DPP-4. The calculated free energy of binding (DGbinding) results from MOE and AutoDock shows that curcumin is needed to be optimized to reach similar or better DGbinding compare to the reference compound. Curcumin can be considered as a good lead compound in the development of new DPP-4 inhibitor. The results of these studies can serve as an initial effort of the further study.     Keywords: curcumin, docking, molecular operating environment (MOE), AutoDock, dipeptydyl peptidase-4 (DPP-4)

In silico discovery of novel flavonoids as poly ADP ribose polymerase (PARP) inhibitors

2020 ◽  
Vol 16 ◽  
Author(s):  
Ashish Shah ◽  
Ghanshyam Parmar ◽  
Avinash Kumar Seth
Keyword(s):  
Virtual Screening ◽  
In Silico ◽  
Synthetic Lethality ◽  
Parp Inhibitor ◽  
Parp Inhibitors ◽  
Docking Studies ◽  
Docking Score ◽  
Docking Method ◽  
Anti Cancer ◽  
In Silico Toxicity

Background: The concept of synthetic lethality is emerging field in the treatment of cancer and can be applied for new drug development of cancer as it has been already represented by Poly (ADP-ribose) polymerase (PARPs) inhibitors. Objectives: In this study we performed virtual screening of 329 flavonoids obtained from Naturally Occurring Plant-based Anti-cancer Compound-Activity-Target (NPACT) database to identify novel PARP inhibitors. Materials and methods: Virtual screening carried out using different In Silico methods which includes molecular docking studies, prediction of druglikeness and In Silico toxicity studies. Results: Fifteen out of 329 flavonoids achieved better docking score as compared to rucaparib which is an FDA approved PARP inhibitor. These 15 hits were again rescored using accurate docking mode and drug-likeliness properties were evaluated. Accuracy of docking method was checked using re-docking. Finally NPACT00183 and NPACT00280 were identified as potential PARP inhibitors with docking score of -139.237 and -129.36 respectively. These two flavonoids were also showed no AMES toxicity and no carcinogenicity which was predicted using admetSAR. Conclusion: Our finding suggests that NPACT00183 and NPACT00280 have promising potential to be further explored as PARP inhibitors.

scholarly journals Approach Towards Drugs Repurposing: Docking Studies with Multiple Target Proteins Associated with SARS-CoV-2

2020 ◽  
Author(s):  
Shiwani Rana ◽  
Meghali Panwar ◽  
Kalyan Sundar Ghosh
Keyword(s):  
Viral Infections ◽  
Molecular Targets ◽  
Drug Repurposing ◽  
Docking Studies ◽  
Extreme Situation ◽  
Angiotensin Converting Enzyme 2 ◽  
Viral Proteases ◽  
Docking Tool ◽  
Free Energy Of Binding ◽  
3Cl Protease

<p>The current pandemic outbreak of COVID-19 due to viral infections by SARS-CoV-2 is now become associated with severe commotion on global healthcare and economy. In this extreme situation when vaccine or drugs against COVID-19 are not available, the only quick and feasible therapeutic alternative would be the drug repurposing approach. In the present work, <i>in silico</i> screening of some antiviral and antiprotozoal drugs using Autodock docking tool was performed. Two known antiviral drugs sorivudine and noricumazole B are predicted to bind to the active site of the viral proteases namely cysteine like protease or 3CL protease (3CLpro) and papain like protease (PLpro) respectively with a highly favorable free energy of binding. Further, the promising molecules were subjected for checking their activity on other molecular targets like spike protein S1, RNA dependent RNA polymerase (RdRp) and angiotensin converting enzyme 2 (ACE2) receptor. But the compounds were found not effective on rest other molecular targets. </p>

scholarly journals THE APPLICABILITY OF THE CRYSTAL STRUCTURE OF TERMOTOGA MARITIMA 4--GLUCANOTRANSFERASE AS THE TEMPLATE FOR SULOCHRIN AS -GLUCOSIDASE INHIBITORS

2010 ◽  
Vol 9 (3) ◽  
pp. 479-486
Author(s):  
Rizna Triana Dewi ◽  
Yulia Anita ◽  
Enade Perdana Istyastono ◽  
Akhmad Darmawan ◽  
Muhamad Hanafi
Keyword(s):  
Crystal Structure ◽  
Saccharomyces Cerevisiae ◽  
Thermotoga Maritima ◽  
Binding Pocket ◽  
Operating Environment ◽  
High Sequence Identity ◽  
Glucosidase Inhibitor ◽  
Glucosidase Inhibitors ◽  
Docking Method ◽  
Binding Residues

Interaction of sulochrin to active site of glucosidase enzyme of Termotoga maritime has been studied by employing docking method using Molecular Operating Environment (MOE), in comparison with those are reports of established inhibitor α-glucosidase such as acarbose, miglitol and voglibose, and salicinol, as reference compounds. The crystal structure T. maritima α-glucanotransferase (PDB code: 1LWJ) can be employed to serve as the template in the virtual screening of S. cerevisiae α-glucosidase. The comparison between the binding pocket residues of Thermotoga maritima α-glucanotransferase and Saccharomyces cerevisiae α-glucosidase show a high sequence identity and similarity. The result showed that sulochrin could be located in the binding pocket and formed some interactions with the binding residues. The ligands showed proper predicted binding energy (-6.74 - -4.13 kcal/mol) and predicted Ki values (0.011 - 0.939 mM). Sulochrin has a possibility to serve as a lead compound in the development of new α-glucosidase inhibitor.   Keywords: Docking, sulochrin, α-glucosidase Inhibitor, Thermotoga maritime α-glucotransferase, Saccharomyces cerevisiae α-glucosidase, MOE

scholarly journals Bioassay-Guided Isolation, Metabolic Profiling, and Docking Studies of Hyaluronidase Inhibitors from Ravenala madagascariensis

Molecules ◽  
2020 ◽  
Vol 25 (7) ◽  
pp. 1714 ◽  
Author(s):  
Esraa M. Mohamed ◽  
Mona H. Hetta ◽  
Mostafa E. Rateb ◽  
Mohamed A. Selim ◽  
Asmaa M. AboulMagd ◽  
...  
Keyword(s):  
Metabolic Profiling ◽  
Docking Study ◽  
Docking Studies ◽  
Operating Environment ◽  
Etoh Extract ◽  
Flavone Glycosides ◽  
Flower Stem ◽  
Bioassay Guided Fractionation ◽  
Rutin And Quercetin ◽  
Leaf N

Hyaluronidase enzyme (HAase) has a role in the dissolution or disintegration of hyaluronic acid (HA) and in maintaining the heathy state of skin. Bioassay-guided fractionation of Ravenala madagascariensis (Sonn.) organ extracts (leaf, flower, stem, and root) testing for hyaluronidase inhibition was performed followed by metabolic profiling using LC–HRMS. Additionally, a hyaluronidase docking study was achieved using Molecular Operating Environment (MOE). Results showed that the crude hydroalcoholic (70% EtOH) extract of the leaves as well as its n-butanol (n-BuOH) partition showed higher HAase activity with 64.3% inhibition. Metabolic analysis of R. madagascariensis resulted in the identification of 19 phenolic compounds ranging from different chemical classes (flavone glycosides, flavonol glycosides, and flavanol aglycones). Bioassay-guided purification of the leaf n-BuOH partition led to the isolation of seven compounds that were identified as narcissin, rutin, epiafzelechin, epicatechin, isorhamnetin 7-O-glucoside, kaempferol, and isorhamnetin-7-O-rutinoside. The docking study showed that narcissin, rutin, and quercetin 3-O-glucoside all interact with HAase through hydrogen bonding with the Asp111, Gln271, and/or Glu113 residues. Our results highlight Ravenala madagascariensis and its flavonoids as promising hyaluronidase inhibitors in natural cosmetology preparations for skin care.

scholarly journals ФАРМАКОФОРНЕ МОДЕЛЮВАННЯ РЯДУ 3,5-ДИЗАМІЩЕНИХ ПОХІДНИХ (4-МЕТИЛ/R-ФЕНІЛ-3H-ТІАЗОЛ-2-ІЛІДЕН)-R1-ФЕНІЛ/ЦИКЛОГЕКСИЛ-АМІНІВ ІЗ КАРДІОПРОТЕКТОРНОЮ АКТИВНІСТЮ

2019 ◽  
pp. 11-18
Author(s):  
I. V. Drapak
Keyword(s):  
In Silico ◽  
Operating Environment ◽  
Molecular Operating Environment

Мета роботи. Фармакофорне моделювання для ряду 3,5-дизаміщених похідних (4-метил/R-феніл-3H-тіазол-2-іліден)-R1-феніл/циклогексил-амінів із встановленими кардіопротекторними властивостями. Матеріали і методи. Об’єктами дослідження були 3,5-дизаміщені похідні (4-метил/R-феніл-3H-тіазол-2-іліден)-R1-феніл/циклогексил-амінів із встановленою кардіопротекторною активністю. Фармакофорне моделювання проводили в програмному середовищі для обчислювальних хімічних досліджень Molecular Operating Environment (MOE) версії 2007.09. У даному дослідженні використовували силове поле MMFF94x, оптимізацію геометрії конформерів проводили методом стохастичного пошуку. Результати й обговорення. У процесі фармакофорного моделювання розроблено 8 моделей, які характеризуються різним складом та координатами фармакофорних центрів, а також точністю класифікації. У всіх моделях ключову роль відіграють наявні в активних молекулах акцептори водневого зв’язку та гідрофобні області. Створена фармакофорна модель містить дві пари фармакофорних центрів, які знаходяться на протилежних краях та однієї гідрофобної області розташованої біля центру фармакофора. Кожна з цих пар сформована з близько розташованих (відстані 2,85 та 3,79 Å відповідно) гідрофобного фармакофорного центру та проекції донора водневого зв’язку. Висновки. Проведене фармакофорне моделювання ряду 3,5-дизаміщених похідних (4-метил/R-феніл-3H-тіазол-2-іліден)-R1-феніл/циклогексил-амінів з дослідженими in vivo кардіопротекторними властивостями дало змогу виділити можливий фармакофор, що складається із трьох гідрофобних областей та двох проекцій акцепторів водневого зв’язку. Точність класифікації активних та неактивних сполук даною моделлю становить 0,73. На основі аналізу узгодженої з фармакофорною моделлю конформації сполуки з найбільшою кардіопротекторною активністю висунуто гіпотезу про участь ацетильної групи, іміно-групи та можливо дистального атома Нітрогену піперазинового фрагменту у взаємодії з амінокислотами – донорами Гідрогену біомішені. Подальші дослідження потрібні для ідентифікації біомішені, відповідальної за прояв кардіопротекторних властивостей. Одержана фармакофорна модель буде в подальшому використовуватись для in silico скринінгу молекулярних баз даних з метою ідентифікації віртуальних хітів та цілеспрямованого пошуку нових кардіопротекторів.

scholarly journals PENELUSURAN MEKANISME FLAVONOID KULIT JERUK KEPROK (Citrus reticulata) SEBAGAI AGEN KEMOPREVENTIF MELALUI DOCKING MOLEKULER PADA PROTEIN TARGET CYP1A2

2010 ◽  
Vol 1 (1) ◽  
Author(s):  
Perdana Adhi Nugroho, Dyani P Sukamdi, Andita Pra Darma, Riris Istighfari Jenie, Edy Meiyanto
Keyword(s):  
Molecular Docking ◽  
Citrus Reticulata ◽  
Operating Environment ◽  
Molecular Operating Environment ◽  
Protein Target

Subklas flavonoid khususnya golongan polimetoksiflavon menunjukan aktivitas kemopreventif pada berbagai sel kanker secara in vitro dan beberapa studi in vivo. Pada tahapan inisiasi kanker, bioaktivasi karsinogen polisiklik aromatik hidrokarbon secara signifikan dapat direduksi oleh senyawaan polimetoksiflavon melalui penghambatan sistem enzim sitokrom P450 (CYP) dalam level transkripsi gen maupun interaksi langsung dengan enzim tersebut. Pada tahapan promosi kanker, berbagai studi menunjukan bahwa proliferasi sel kanker dihambat lebih kuat oleh golongan metoksiflavon dibandingkan hidroksiflavon. Tangeretin, nobiletin, naringin dan hesperidin adalah beberapa senyawa polimetoksiflavon dari kulit jeruk keprok yang dilaporkan memiliki efek kemopreventif melalui modulasi aktivitas CYP1A2. Penelitian ini bertujuan untuk mengetahui afinitas, konformasi dan interaksi senyawa berkerangka polimetoksiflavon kulit jeruk keprok (Citrus reticulata) terhadap protein target CYP1A2 menggunakan molecular docking. Optimasi geometri struktur polimetoksiflavon dilakukan dengan piranti lunak Molecular Operating Environment for Windows. Konformasi optimum struktur polimetoksiflavon dihasilkan menggunakan metode semiempirik AMBER99. Kemudian dilakukan proses docking senyawa uji dengan bindingsite CYP1A2 (PDB ID:2HI4) menggunakan piranti lunak Molecular Operating Environment for Windows dalam kondisi tanpa air. Hasil docking senyawa golongan polimetoksiflavon dibandingkan dengan native ligan pada target CYP1A2, menunjukkan interaksi polimetoksiflavon yang lebih kuat dibanding interaksi ligan pembanding á-naphtoflavon.  Kata kunci: Citrus reticulata, polimetoksiflavon, molecular docking, CYP1A2

Docking studies with multiple molecular targets associated with SARSCoV-2 for drug repurposing

Coronaviruses ◽  
2020 ◽  
Vol 01 ◽  
Author(s):  
Shiwani Rana ◽  
Meghali Panwar ◽  
Kalyan Sundar Ghosh
Keyword(s):  
Viral Infections ◽  
Molecular Targets ◽  
Drug Repurposing ◽  
Docking Studies ◽  
New Drugs ◽  
In Silico Screening ◽  
Angiotensin Converting Enzyme 2 ◽  
Viral Proteases ◽  
Free Energy Of Binding ◽  
3Cl Protease

Background: The current pandemic outbreak of COVID-19 due to viral infections by SARS-CoV-2 is now become associated with severe commotion on global healthcare and economy. Objective: In this extreme situation when vaccine or effective new drugs against COVID-19 are not available, the only quick and feasible therapeutic alternative would be the drug repurposing approach. Method: In the present work, in silico screening of some antiviral and antiprotozoal drugs was performed based on docking using Autodock. Results: Two known antiviral drugs sorivudine and noricumazole B are predicted to bind to the active site of the viral proteases namely cysteine like protease or 3CL protease (3CLpro) and papain like protease (PLpro) respectively with a highly favorable free energy of binding. Further, the promising molecules were subjected for checking their activity on other molecular targets in SARS-CoV-2 like spike protein S1, RNA dependent RNA polymerase (RdRp) and angiotensin converting enzyme 2 (ACE2) receptor. But the compounds were found non-effective on rest other molecular targets. Conclusion: Sorivudine alone or a combination of sorivudine and noricumazole B may be administered to impede viral replication though the predicted drug likeliness of noricumazole B is not very much satisfactory. These observations are solely based on the results from blind docking with protein molecules and that need to be further corroborated with experimental results.

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