scholarly journals In Silico Analyses and Cytotoxicity Study of Asiaticoside and Asiatic Acid from Malaysian Plant as Potential mTOR Inhibitors

Molecules ◽  
2020 ◽  
Vol 25 (17) ◽  
pp. 3991
Author(s):  
Ninie Nadia Zulkipli ◽  
Rahimah Zakaria ◽  
Idris Long ◽  
Siti Fadilah Abdullah ◽  
Erma Fatiha Muhammad ◽  
...  

Natural products remain a popular alternative treatment for many ailments in various countries. This study aimed to screen for potential mammalian target of rapamycin (mTOR) inhibitors from Malaysian natural substance, using the Natural Product Discovery database, and to determine the IC50 of the selected mTOR inhibitors against UMB1949 cell line. The crystallographic structure of the molecular target (mTOR) was obtained from Protein Data Bank, with Protein Data Bank (PDB) ID: 4DRI. Everolimus, an mTOR inhibitor, was used as a standard compound for the comparative analysis. Computational docking approach was performed, using AutoDock Vina (screening) and AutoDock 4.2.6 (analysis). Based on our analysis, asiaticoside and its derivative, asiatic acid, both from Centella asiatica, revealed optimum-binding affinities with mTOR that were comparable to our standard compound. The effect of asiaticoside and asiatic acid on mTOR inhibition was validated with UMB1949 cell line, and their IC50 values were 300 and 60 µM, respectively, compared to everolimus (29.5 µM). Interestingly, this is the first study of asiaticoside and asiatic acid against tuberous sclerosis complex (TSC) disease model by targeting mTOR. These results, coupled with our in silico findings, should prompt further studies, to clarify the mode of action, safety, and efficacy of these compounds as mTOR inhibitors.

2020 ◽  
Vol 7 (3) ◽  
pp. 347-362
Author(s):  
Oscar Cobar ◽  
Rodrigo J. Vargas

El reposicionamiento de fármacos como la derivatización química, que se han aplicado en los estudios de descubrimiento y diseño de fármacos contra el SARS-CoV-2, dependen del ciclo de vida del virus, las dianas moleculares identificadas y un diseño basado en su estructura e interacciones moleculares. Se realizó una revisión extensa en las bases de datos públicas e institucionales RSCB-Protein Data Bank, ZINC, NCBI (PubMed, PMC), PubChem, Science Direct e instituciones como CDC, NIH y revistas científicas especializadas sobre los avances en la búsqueda de nuevas moléculas contra el nuevo coronavirus basadas en estudios in silico, detectándose más de 40,000 publicaciones sobre SARS-CoV-2 y cerca de 200 relacionadas a dichos estudios, las consideradas más relevantes fueron analizadas e incluidas en este artículo. Su análisis evidencia el avance acelerado de las herramientas computacionales y fortaleza del diseño de fármacos asistido por computadora (in silico approach) para la generación de nuevas moléculas con posibilidad de ser activas contra COVID-19 y presenta las principales dianas moleculares sobre la que actúan estos agentes con potencial antiviral.


Author(s):  
Dominique MIAS-LUCQUIN ◽  
Isaure Chauvot de Beauchêne

We explored the Protein Data-Bank (PDB) to collect protein-ssDNA structures and create a multi-conformational docking benchmark including both bound and unbound protein structures. Due to ssDNA high flexibility when not bound, no ssDNA unbound structure is included. For the 143 groups identified as bound-unbound structures of the same protein , we studied the conformational changes in the protein induced by the ssDNA binding. Moreover, based on several bound or unbound protein structures in some groups, we also assessed the intrinsic conformational variability in either bound or unbound conditions, and compared it to the supposedly binding-induced modifications. This benchmark is, to our knowledge, the first attempt made to peruse available structures of protein – ssDNA interactions to such an extent, aiming to improve computational docking tools dedicated to this kind of molecular interactions.


2020 ◽  
Vol 6 (15) ◽  
Author(s):  
Letícia Fernandes Fraga ◽  
Leonardo Luiz Borges

Este estudo tem por objetivo avaliar os principais compostos que expliquem a atividade broncodilatadora da Mikania glomerata Spreng, empregando ferramentas in silico. Os metabólitos do guaco foram levantados bibliograficamente e a codificação das moléculas para a realização das predições foi obtida no site Pubchem. Realizou-se então triagem de bioatividade com os programas SwissADME, ProToxII, PASS e Molinspiration e pesquisa de alvos, com os servidores SuperPred Webserver. Após a identificação do alvo, a estrutura selecionada foi obtida pelo site Protein Data Bank (PDB) para o docking molecular com o programa GOLD. Os metabólitos da Mikania glomerata Spreng tiveram suas propriedades físico-químicas e biológicas analisadas. Os alvos para o docking molecular foram identificados e verificados para cada composto, com suas respectivas estruturas cristalografadas no Protein Data Bank (PDB). A molécula de cumarina foi selecionada pois apresentou predição de interação com o receptor muscarínico M3 (ID: 4DAJ). O docking revelou interação da cumarina com o receptor M3, o que poderia auxiliar na explicação para os efeitos broncodilatadores desta espécie vegetal. O estudo in silico do guaco, abordado neste trabalho, elegeu a cumarina como principal metabólito ativo com possível atividade broncodilatadora presente na Mikania glomerata Spreng. O docking da cumarina mostrou ancoragem desta molécula no sítio ativo do receptor muscarínico M3 devido as atividades desta espécie, assim, este marcador poderia atuar como antagonista desse receptor, apresentando possível atividade parassimpatolítica e, portanto, broncodilatadora.


Author(s):  
A. Amala Lourthuraj ◽  
M. Masilamani Selvam ◽  
Bharathi Ravikrishnan ◽  
M. Vinoth ◽  
Waheeta Hopper

Objective: The present research was aimed to understand the molecular docking efficiency of a plant-derived compound cleistanthin-A and a common ingredient in tobacco consumption nicotine with nicotinic acetylcholine receptor (nAChR).Methods: The 3-D structure of nAChR was retrieved from the protein data bank (ID 5AFH). Ligand was obtained from the PUBCHEM. The in silico protocol comprised of three steps: high-throughput virtual screening (HTVS), standard preci­sion (SP) and extra precision (XP). The screened molecules were ranked accordingly using glide score. Schrödinger tool was used to perform the docking analysis.Results: The binding efficiency of the nicotine and cleistanthin-A was found to be docked at the cys-cys loop of the receptor. Based upon the glide score and glide energy it can be reported that, nicotine binding can be inhibited by the binding of cleistanthin-A to the nAChR.Conclusion: The docking efficiency of cleistanthin-A was good compared to nicotine towards nAChR. Hence, cleistanthin–A was derived as a better choice as an alternative for nicotine in smoke therapy.


Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 1740-1740 ◽  
Author(s):  
Kerstin M Kampa ◽  
Sandra Mueller ◽  
Katharina-Henriette Rasp ◽  
Lothar Kanz ◽  
Michael C Heinrich ◽  
...  

Abstract Abstract 1740 Poster Board I-766 In ∼40% of de novo cases of acute myeloid leukemia (AML), autoactivating mutations in the class III receptor tyrosine kinases (RTK) KIT and FLT3 are observed and are closely linked to leukemogenesis. We and others previously demonstrated that leukemia-driving gain-of-function mutations of KIT and FLT3 consecutively activate AKT, MAPK1/2 (ERK1/2) and STAT signalling. We show that global AKT phosphorylation can be detected in AML patients. In contrast, RTK-inhibition only partially blocks PI3K/AKT/p70S6K signaling in our in vitro leukemia models, which suggests the existence of an escape mechanism that is not yet understood. Combination of tyrosine kinase inhibitors (TKI) with rapamycin, a specific MTOR inhibitor acting upstream of p70S6K, potentiates the antitumor activity of TKI. However, we show that upregulation of AKT-phophorylation – possibly by feedback loops – is observed in western blot analysis. In an attempt to globally block AKT signaling we tested the dual PI3K/MTOR inhibitors NVP-BEZ235 and NVP-BGT226 with regard to their antiproliferative and proapoptotic potential in a variety of mutant-KIT/FLT3 leukemia cell lines. Inhibition of PI3K and MTOR phosphorylation sites in the upper nanomolar range consequently lead to dephosphorylation of the threonine 308 as well as the serine 473 AKT phospho-sites - as well as the phospho p70S5kinase phospho-sites with both tested inhibitors. Moreover, global blockage of the PI3K/AKT/MTOR/p70S6K signal transduction pathway translated into a potent antitumor activity on the cellular level - with NVP-BGT226 being the more potent agent in antiproliferation and apoptosis assays with IC50s in the nanomolar range. Moreover, we also tested the blast crisis CML cell line K562 – which also revealed sensitivity towards PI3K/MTOR inhibition in the same dose range. To study the influence of different mutant isoforms of KIT/FLT3 on sensitivity to TKI, we created FLT3, KIT and BCR/ABL transfectants in a Ba/F3 cell line background. Both inhibitors displayed the most profound activity in cells transfected with an autoactivating FLT3 or KIT isoform with IC50s between 250-500 nanomolar. In contrast, the FLT3 wildtype isoform displayed decreased sensitivity towards both inhibitors. No sensitivity to NVP-BEZ235 and NVP-BGT226 was observed in BCR/ABL transfectants and the Ba/F3 parental cell line up to 5-10 micromolar. As expected, combination of the dual PI3K/MTOR inhibitors with TKI (Imatinib, Dasatinib, and Sunitinib) potentiated the antiproliferative and proapoptotic effects observed for the single agents. We conclude that the PI3K/AKT pathway is activated by mutant FLT3 and KIT isoforms - but not by BCR/ABL. In acute leukemias, including CML blast crisis, the PI3K/AKT pathway is further activated due to other yet unknown mechanisms. Thus, the PI3K/AKT pathway may provide an escape mechanism from TKI therapy contributing to the moderate/shorter response rates in acute forms of leukemia (including CML blast crisis) compared to TKI therapy in CML. NVP-BEZ235 and NVP-BGT226 display potent antiproliferative as well as proapoptotic effects in leukemia in vitro models alone and in combination with TKI and warrant clinical evaluation. Disclosures No relevant conflicts of interest to declare.


Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 4930-4930
Author(s):  
Joshua Acklin ◽  
Mitra Azadniv ◽  
Scott Portwood ◽  
Kimberly Lacagnina ◽  
Charlotte Beers ◽  
...  

Abstract Introduction : Mammalian target of rapamycin (mTOR) signaling has previously been identified as a possible therapeutic target in acute myelogenous leukemia (AML), as the PI3K/AKT/mTOR pathway has been shown to be upregulated in blasts of up to 90% of AML cases through the constitutive loss of the tumor suppressor PTEN. The activation of this pathway is implicated in synthesis of prosurvival transcription and translational factors responsible for cellular resistance to apoptosis, resistance to chemotherapy, and enhanced survival in the marrow microenvironment. Unfortunately, exploitation of this pathway has been largely ineffective in clinical studies. A second mTOR complex (mTORC2) will reestablish the activation of the first when the first mTOR complex (mTORC1) is shut down under treatment with traditional rapalogs, such as rapamycin and everolimus. Additionally, the cellular process of autophagy has been postulated to be a protective mechanism for leukemic blasts during treatment with mTOR inhibitors, therefore decreasing their efficacy. For these reasons, this work explores means to optimize mTOR pathway inhibition by examining effects of dual mTORC inhibition (OSI027), dual PI3K/mTOR inhibition (BEZ235/Dactilosib), combination of mTOR inhibitors with a histone deacetylase inhibitor with ability to inhibit AKT (LBH589/Panobinostat), and the combination of mTOR inhibitors with hypomethylating agents able to overcome the hypermethylation of mTOR pathway components such as TSC1, TSC2 and PTEN (decitabine/5-azacytidine). Materials and Methods : Primary AML leukapheresis samples obtained with informed consent were cultured for 48 hours in the presence of OSI027, LBH589 (Novartis), BEZ235 (Novartis), decitabine, or OSI027 in combination with each of these individual inhibitors and compared with control culture conditions. Cells were stained with annexinV and DAPI as previously described, and the percent of living, pre-apoptotic, necrotic and dead cells were determined via flow cytometry. Synergy calculations were completed using Calcusyn™ software as described by Chao and Talalay (1977). Autophagic flux was determined in the OSI027 and LBH589 combination exposure via flow cytometry using anti-LC3. Lastly, protein expression under treatment with various combinations was determined via standard western blotting techniques. Results: The MV411 AML cell line was utilized to establish efficacy of combination exposures. These cells expressed phosphorylated (p)Akt (ser 473), p4EBP1, and pmTOR. OSI027 10µM, LBH589 1µM, and BEZ235 10nM were able to inhibit pmTOR, pAKT, and p4EBP1 expression as determined by western blotting. In the MV411 cell line, IC50s were determined, and combination indices were determined for OSI027+BEZ235, panobinostat+BEZ235, and panobinostat+OSI027; all of which demonstrated synergy. In primary AML samples, the combination of OSI027 10uM and LBH589 10nM significantly increased the percentage of dead cells in comparison to OSI027 treatment alone. Additionally in primary AML blasts, pmTOR and pAKT expression were decreased in the combination of OSI027 and LBH589 when compared to single agent treatment via western blot. The combination of OSI027 and LBH589 demonstrated a significant reduction in the autophagic flux in comparison to OSI027 treatment alone, suggesting an anti-autophagic effect, which correlates with the increased rates of cellular death in the combination. It was also found in AML cell lines that the combination of 10 µM azacytidine and 100 nM rapamycin resulted in synergistic suppression of U937, MV411, and KG1a survival as measured by MTT. No synergy was noted in the HL60 cell line. This combination effectively suppressed CFU-L in primary AML cases and suppressed p70S6K and p4EBP1 expression more than either agent alone by western blotting. The combination of decitabine 500nM with OSI027 10uM did not demonstrate an increase in apoptotic cells in primary blasts compared to OSI027 alone. Conclusions : Based on these findings, we conclude that mTOR inhibition in AML cell lines and primary samples can be enhanced through dual mTORC inhibition, PI3K modulation, and histone deacetylase inhibition. This may occur through suppression of activated pathway mediators or through suppression of autophagic flux. These results suggest that there is merit in exploring these combinations for therapeutic potential in AML. Disclosures Portwood: ImmunoGen: Research Funding. Wang:ImmunoGen: Research Funding.


ChemInform ◽  
2009 ◽  
Vol 40 (9) ◽  
Author(s):  
Johannes Kirchmair ◽  
Patrick Markt ◽  
Simona Distinto ◽  
Daniela Schuster ◽  
Gudrun M. Spitzer ◽  
...  

2021 ◽  
Vol 8 (2) ◽  
pp. 82
Author(s):  
Theresia Nona Elfi ◽  
Yohanes Nong Bunga ◽  
Yohanes Bare

<p>Cabai Merah Besar (<em>Capsicum Annum</em> L) merupakan tanaman holtikultura yang dibudidayakan dalam skala kecilnamun memiliki manfaat kesehatan. Cabai Merah Besar (<em>Capsicum Annum</em> L.) juga digunakan untuk pengobatan sakit gigi, bisul, anti parasit, anti inflamasi, antitusif dan juga digunakan sebagai antiseptik, nafsu makan. Penelitian ini memiliki tujuan untuk menganalisis potensi senyawa <em>nonivamide</em> dan <em>nordihydrocapsaicin </em>sebagai anti-inflamasi. Kajian penelitian metode in silico. Senyawa <em>Nonivamide</em> (CID :2998) dan <em>Nordihydrocapsaicin</em> (CID: 168836) diperoleh dari PubChem sedangkan COX-2 (6cox) dari Protein Data Bank. Analisis menggunakan HEX 8.0.0 dan ditampilkan Discovery studio client 4.1. Interaksi yang terjadi antara senyawa <em>Nonivamide</em> dan COX-2 membentuk ikatan hidrogen dengan tipe ikatan hidrogen konvensional (CYS47) dan ikatan hidrofobik (LEU152). Selain ikatan hidrogen, juga terdapat sembilan belas residu asam amino menunjukkan adanya gaya <em>V</em><em>an </em><em>D</em><em>er </em><em>W</em><em>aals</em> membentuk energi -339.48 cal/mol. Ikatan Nordihydrocapsaicin dengan COX-2 membentuk ikatan pada residu asam amino TRP139 bersifat Pi-Alkyl dan ikatan hidrogen sebagai donor dengan Residu asam amino SER143 energi ikatan sebesar -248.47 cal/mol.</p>


2018 ◽  
Vol 1 (1) ◽  
pp. 245-250
Author(s):  
Nerdy Nerdy ◽  
Effendy De Lux Putra ◽  
Ginda Haro ◽  
Urip Harahap

Diabetes melitus merupakan penyakit yang diderita oleh banyak orang di dunia. Banyak obat sintetik yang tersedia untuk pengobatan diabetes melitus. Namun, ada kebutuhan yang mendesak untuk menghasilkan obat antidiabetes yang lebih baik khususnya dari bahan alam. Literatur menunjukkan bahwa flavonoid merupakan metabolit sekunder dari tumbuhan yang berkhasiat sebagai antidiabetes yang baik. Naringenin merupakan flavonoid dari jeruk yang memiliki aktivitas antidiabetes. Senyawa turunan lipofilik dari flavonoid naringenin yang dalam bentuk ester dapat meningkatkan aktivitas antidiabetes dari senyawa induk. Tujuan penelitian ini adalah untuk menentukan aktivitas antidiabetes dari senyawa naringenin dan senyawa ester dari naringenin. Penelitian ini dilakukan dengan penambatan secara in siliko dari molekul senyawa uji naringenin, serta turunan ester dari naringenin dengan penambatan secara in siliko terhadap Phosphoenolpyruvate Carboxykinase (PEPCK) yang diunduh via Protein Data Bank (PDB) dengan kode protein 1KHB. Selanjutnya dilakukan proses penambatan dengan program PLANTS, dan kemudian dilakukan evaluasi nilai energi ikatan hasil proses penambatan. Proses penambatan kembali molekul ligan asli ke dalam molekul kantung ikatan Phosphoenolpyruvate Carboxykinase (PEPCK) diperoleh nilai Root Mean Square Deviation (RMSD) 0,7670 Å. Penambatan molekul senyawa uji senyawa turunan ester dari naringenin menunjukkan aktivitas yang lebih baik dengan nilai energi ikatan yang lebih rendah bila dibandingkan dengan senyawa induk naringenin. Diabetes mellitus is a disease suffered by many around the world. There are many available synthetic medications for diabetes mellitus treatment. However, there are urgent needs to produce a better anti-diabetic especially from natural sources. Previous studiesindicated that flavonoid is asecondary metabolite from plants which has good anti-diabetic function. Naringenin is a flavonoid from orange which has anti-diabetic activity. The lipophilic derivative compound of naringenin flavonoid in ester form can increase the anti-diabetic activity from the parent compound. This research objectives were to determine the anti-diabetic activity of naringenin compounds and its ester compounds. This research was conducted using in silico docking ofcompound molecule of naringenin and also the ester derivation from naringenin with in silico docking to PhosphoenolpyruvateCarboxykinase (PEPCK) downloaded via Protein Data Bank (PDB) using 1 KHB protein code. Furthermore, docking process was conducted using PLANTS program, and also the bond energy value evaluation of the docking process. The ligand molecule docked in bag of bonds molecule (PhosphoenolpyruvateCarboxykinase (PEPCK) and the Root Mean Square Derivation (RMSD) with the value of 0.7670 Å was obtained. The naringenin ester derivation docking test indicated a better activity with a lower bond energy value than the naringenin parent compound.


2019 ◽  
Vol 1 (1) ◽  
Author(s):  
Nur Aji

Pada penelitian ini dilakukan simulasi penambatan molekul senyawa-senyawa aktif pada bunga, kulit daun dan getah tanaman Aloe barbadensis Miller . Simulasi ini bertujuan untuk memprediksi interaksi antara senyawa ligan uji dan protein yang menyebabkan terganggunya pembentukan melanin melalui interaksi kompetitif dengan enzim tirosinase. Simulasi penambatan molekul dilakukan menggunakan program Molegro Virtual Docker 6.0 dan prediksi permeabilitas dan sensitisasi kulit dengan pkCSM. Sebagai reseptor target digunakan struktur 3D protein 5M8P (tirosinase) dan ligan referensi TYR_516 (L-tirosin) yang diunduh dari Protein Data Bank. Posisi penambatan dilakukan pada koordinat yang sama dengan posisi ligan referensi yang sudah tertambat sebelumnya dan tervalidasi. Dari hasil simulasi diketahui bahwa dari 32 senyawa aktif dalam kulit daun, bunga dan getah aloe vera secara in silico terdapat tujuh senyawa yang potensial yang memiliki efek penghambatan tirosinase yaitu Aloesin, Cafeic Acid, Ferulic Acid, Galic Acid, Gentisic Acid, Protocathecuic Acid dan Sinapic Acid sedangkan berdasarkan energi interaksi potensi terbesar adalah Caffeic Acid.Kata kunci :Aloe barbadensis, Molegro, Enzim, Tirosinase, pkCSM.


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