scholarly journals DOCKING MOLEKULER SENYAWA METABOLIT SEKUNDER Lantana camara SEBAGAI ANTIINFLAMASI TERHADAP ENZIM COX-1

Jurnal Biota ◽  
2018 ◽  
Vol 4 (2) ◽  
pp. 79-83
Author(s):  
Atim Febry Masula ◽  
Dian Puspitasari ◽  
Eili Supriatin S.W ◽  
Khoirul Ummah ◽  
Dinik Rokhmatin ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Protein Data Bank ◽  
In Silico ◽  
Data Bank ◽  
Lantana Camara ◽  
Lantadene A ◽  
Cox 1

Lantana camara mengandung beberapa jenis flavonoid seperti Umuhengerin, Lantadene A, Lantadene B, Ictero -genin. Salah satu mekanisme kerja flavonoid sebagai antiinflammatoryis dengan menghambat ceptor siklooksigenase (COX). Penelitian ini bertujuan untuk mengetahui afinitas senyawa flavonoid yang terkandung dalam L. camara dengan reseptor COX-1 sebagai antiinflamasi dan untuk mengetahui ikatan hidrogen yang dapat dibentuk dengan metode molecular docking. Pengujian in silico dilakukan berdasarkan metode desain obat yang dibantu komputer. Alat-alat yang digunakan dalam penelitian ini, perangkat lunak PyRx, perangkat lunak PyMol, Pubchem (senyawa database), PDB (Protein Data Bank), dan Po-seView. Berdasarkan hasil docking dan pembahasan di atas dapat disimpulkan bahwa Icterogenin com-pound dan senyawa Umuhengerin adalah senyawa yang paling efektif dalam proses antiinflamasi, Icterogenin com-pound memiliki nilai RMSD 41,1 Å dan nilai afinity mengikat -8,8 dan senyawa Umuhengerin memiliki val-ue RMSD 1, 61 Å dan nilai afinitas pengikatan -8.0. Ini menunjukkan bahwa senyawa tersebut memiliki nilai RMSD dari senyawa Icterogenin. Namun, senyawa Icterogenin memiliki ikatan hidrogen yang lebih kuat dan lebih efisien daripada senyawa Umuhengerin karena nilai afinitas pengikatan terendah.

scholarly journals ANALYSIS OF MOLECULAR DOCKING EFFICIENCY OF CLEISTANTHIN-A, AS AN ALTERNATIVE FOR NICOTINE ADDICTION

2018 ◽  
Vol 10 (4) ◽  
pp. 98
Author(s):  
A. Amala Lourthuraj ◽  
M. Masilamani Selvam ◽  
Bharathi Ravikrishnan ◽  
M. Vinoth ◽  
Waheeta Hopper
Keyword(s):  
Molecular Docking ◽  
Virtual Screening ◽  
Protein Data Bank ◽  
Acetylcholine Receptor ◽  
Nicotinic Acetylcholine Receptor ◽  
High Throughput ◽  
In Silico ◽  
Data Bank ◽  
Tobacco Consumption ◽  
Nicotinic Acetylcholine

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.

scholarly journals Investigation of molecular mechanisms of cannabinoids with neuromodulator activity using in silico tools

2021 ◽  
Vol 7 (19) ◽  
Author(s):  
Aline Lins da Silva ◽  
Thais Linhares Silva ◽  
Leonardo Luiz Borges
Keyword(s):  
Molecular Docking ◽  
Protein Data Bank ◽  
In Silico ◽  
Molecular Mechanisms ◽  
Cannabis Sativa ◽  
Target Identification ◽  
Data Bank ◽  
Biological Properties ◽  
Potential Interaction ◽  
The Central Nervous System

This work aims to complement the investigations of the molecular mechanisms of cannabinoids and their receptors, elucidating molecular targets that explain the effect of chemical compounds present in Cannabis sativa on central neuromodulation through in silico methods. Cannabis sativa metabolites were collected bibliographically, and the coding of molecules to perform the predictions were obtained from the PubChem website. Bioactivity screening was then performed with SwissADME, ProToxII, PASS, and Molinspiration programs and target search with SuperPred Webserver servers. After target identification, the selected structure was obtained from the Protein Data Bank (PDB) site for molecular docking with the GOLD program. Cannabis sativa metabolites had their physicochemical and biological properties analyzed. The targets for molecular docking were identified and verified for each compound, with their respective structures crystallized in the Protein Data Bank (PDB). The tetrahydrocannabivarin (THCV) molecule was selected because it predicted interaction with the N-arachidonylglycine receptor (PDB ID: 4UUQ). Docking reveals a potential interaction of THCV with the N-arachidonylglycine receptor. Furthermore, the binding structure of this study showed pharmacophoric alignment with the five most potent molecules capable of antagonizing the monoglycerate lipase receptor. TCHV docking showed anchoring of this molecule in the active site of the N-arachidonylglycine receptor due to the activities of this species. Thus, this marker could act as an antagonist of this receptor, behaving as an active metabolite with neuromodulatory activity through a possible alteration of microglial activity in the central nervous system, which may act as a therapeutic agent in neurodegenerative pathologies.

Virtual Screening, Molecular docking and in-silico ADME-Tox analysis for identification of potential main protease (Mpro) enzyme inhibitors

2020 ◽  
Vol 18 ◽  
Author(s):  
Debadash Panigrahi ◽  
Ganesh Prasad Mishra
Keyword(s):  
Molecular Docking ◽  
Virtual Screening ◽  
In Silico ◽  
Data Bank ◽  
Future Research ◽  
Reference Compound ◽  
Unexpected Death ◽  
Main Protease ◽  
In Silico Admet

Objective:: Recent pandemic caused by SARS-CoV-2 described in Wuhan China in December-2019 spread widely almost all the countries of the world. Corona virus (COVID-19) is causing the unexpected death of many peoples and severe economic loss in several countries. Virtual screening based on molecular docking, drug-likeness prediction, and in silico ADMET study has become an effective tool for the identification of small molecules as novel antiviral drugs to treat diseases. Methods:: In the current study, virtual screening was performed through molecular docking for identifying potent inhibitors against Mpro enzyme from the ZINC library for the possible treatment of COVID-19 pandemic. Interestingly, some compounds are identified as possible anti-covid-19 agents for future research. 350 compounds were screened based on their similarity score with reference compound X77 from ZINC data bank and were subjected to docking with crystal structure available of Mpro enzyme. These compounds were then filtered by their in silico ADME-Tox and drug-likeness prediction values. Result:: Out of these 350 screened compounds, 10 compounds were selected based on their docking score and best docked pose in comparison to the reference compound X77. In silico ADME-Tox and drug likeliness predictions of the top compounds were performed and found to be excellent results. All the 10 screened compounds showed significant binding pose with the target enzyme main protease (Mpro) enzyme and satisfactory pharmacokinetic and toxicological properties. Conclusion:: Based on results we can suggest that the identified compounds may be considered for therapeutic development against the COVID-19 virus and can be further evaluated for in vitro activity, preclinical, clinical studies and formulated in a suitable dosage form to maximize their bioavailability.

scholarly journals La acelerada búsqueda de candidatos terapéuticos contra SARS-CoV-2, métodos in silico: Revisión

2020 ◽  
Vol 7 (3) ◽  
pp. 347-362
Author(s):  
Oscar Cobar ◽  
Rodrigo J. Vargas
Keyword(s):  
Protein Data Bank ◽  
In Silico ◽  
Data Bank

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.

scholarly journals BUSCA DE MOLÉCULAS COM ATIVIDADE BRONCODILATADORA NA ESPÉCIE MIKANIA GLOMERATA SPRENG EMPREGANDO FERRAMENTAS IN SILICO

2020 ◽  
Vol 6 (15) ◽  
Author(s):  
Letícia Fernandes Fraga ◽  
Leonardo Luiz Borges
Keyword(s):  
Protein Data Bank ◽  
In Silico ◽  
Data Bank ◽  
Mikania Glomerata

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.

POTENSI DAUN ASAM JAWA (Tamarindus indica L.) SEBAGAI ALTERNATIF ANTIINFLAMASI: STUDI IN SILICO

2019 ◽  
pp. 42-50
Author(s):  
Erma Yunita ◽  
Siti Fatimah ◽  
Deni Yulianto ◽  
Vedy Trikuncahyo ◽  
Zihan Khodijah
Keyword(s):  
Molecular Docking ◽  
Root Mean Square ◽  
Root Mean Square Deviation ◽  
In Silico ◽  
Mean Square ◽  
Mean Square Deviation ◽  
Tamarindus Indica ◽  
Protein Target ◽  
Cox 2 ◽  
Cox 1

  Daun asam jawa (Tamarindus indica L.) merupakan tanaman yang memiliki banyak khasiat. Kandungan senyawa kimia yang terkandung salah satunya Kuersetin. Kuersetin merupakan senyawa flavonoid yang dapat digunakan sebagai anti inflamasi. Penelitian ini bertujuan untuk mengetahui potensi aktivitas Kuersetin dari daun asam jawa sebagai anti inflamasi terhadap protein COX-1 dan COX-2 secara in silico. Ekstrak daun asam jawa diperoleh dengan maserasi bertingkat menggunakan heksan dan etanol. Kadar Kuersetinnya dihitung secara spektrofotometri UVVis. Konfirmasi aktivitas antiinflamasi dilakukan secara in silico. Protein yang digunakan adalah 6COX, 3PGH, dan 1EQH. Kuersetin sebagai senyawa aktif sedangkan Aspirin digunakan sebagai zat pembanding. Preparasi ligan Kuersetin menggunakan MarvinSketch kemudian preparasi protein target 6COX, 1EQH, dan 3PGH menggunakan YASARA. Selanjutnya melakukan molecular docking menggunakan program PLANTS. Parameter evaluasi validasi dapat dilihat dari nilai Root Mean Square Deviation (RMSD), dimana nilai RMSD yang diterima adalah kurang dari 2Å. Kadar Kuersetin yang diperoleh dalam ekstrak dalam daun asam jawa sebesar 31,26 mg/g. Hasil docking menunjukkan bahwa Kuersetin mampu berinteraksi dengan 1EQH, 3PGH, dan 6COX dimana skor dockingnya masing-masing adalah -77,6195; -75,1344; dan -82,2454, sedangkan hasil docking Aspirin masing-masing adalah -69,8784; -75,2421; dan - 72,0884. Kuersetin memiliki potensi sebagai anti inflamasi yang lebih baik dibandingkan dengan Aspirin namun memiliki resiko lebih tinggi menyebabkan ulkus lambung dibanding Aspirin.

ChemInform Abstract: The Protein Data Bank (PDB), Its Related Services and Software Tools as Key Components for in silico Guided Drug Discovery

ChemInform ◽  
2009 ◽  
Vol 40 (9) ◽  
Author(s):  
Johannes Kirchmair ◽  
Patrick Markt ◽  
Simona Distinto ◽  
Daniela Schuster ◽  
Gudrun M. Spitzer ◽  
...  
Keyword(s):  
Drug Discovery ◽  
Protein Data Bank ◽  
In Silico ◽  
Data Bank ◽  
Software Tools ◽  
Related Services

scholarly journals Anti-Arthritic and Anti-Inflammatory Potential of Spondias mangifera Extract Fractions: An In Silico, In Vitro and In Vivo Approach

Plants ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 825
Author(s):  
Mohammad Khalid ◽  
Mohammed H. Alqarni ◽  
Ambreen Shoaib ◽  
Muhammad Arif ◽  
Ahmed I. Foudah ◽  
...  
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Arthritis Score ◽  
Beneficial Effects ◽  
Tnf Α ◽  
Cox 2 ◽  
Anti Inflammatory ◽  
Cox 1

The fruits of Spondias mangifera (S. mangifera) have traditionally been used for the management of rheumatism in the northeast region of India. The present study explores the probable anti-arthritis and anti-inflammatory potential of S. mangifera fruit extract’s ethanolic fraction (EtoH-F). To support this study, we first approached the parameters in silico by means of the active constituents of the plant (beta amyrin, beta sitosterol, oleonolic acid and co-crystallised ligands, i.e., SPD-304) via molecular docking on COX-1, COX-2 and TNF-α. Thereafter, the absorption, distribution, metabolism, excretion and toxicity properties were also determined, and finally experimental activity was performed in vitro and in vivo. The in vitro activities of the plant extract fractions were evaluated by means of parameters like 1,1-Diphenyl-2- picrylhydrazyl (DPPH), free radical-reducing potential, albumin denaturation, and protease inhibitory activity. The in vivo activity was evaluated using parameters like COX, TNF-α and IL-6 inhibition assay and arthritis score in Freund Adjuvant (CFA) models at a dose of 400 mg/kg b.w. per day of different fractions (hexane, chloroform, alcoholic). The molecular docking assay was performed on COX-1, COX-2 and TNF-α. The results of in vitro studies showed concentration-dependent reduction in albumin denaturation, protease inhibitors and scavenging activity at 500 µg/mL. Administration of the S. mangifera alcoholic fraction at the abovementioned dose resulted in a significant reduction (p < 0.01) in arthritis score, paw diameters, TNF-α, IL-6 as compared to diseased animals. The docking results showed that residues show a critical binding affinity with TNF-α and act as the TNF-α antagonist. The alcoholic fraction of S. mangifera extract possesses beneficial effects on rheumatoid arthritis as well as anti-inflammatory potential, and can further can be used as a possible agent for novel target-based therapies for the management of arthritis.

scholarly journals STUDI AKTIVITAS BIOLOGI SECARA IN SILICO SENYAWA NONIVAMIDE DAN NORDIHYDROCAPSAICIN SEBAGAI ANTI INFLAMASI

2021 ◽  
Vol 8 (2) ◽  
pp. 82
Author(s):  
Theresia Nona Elfi ◽  
Yohanes Nong Bunga ◽  
Yohanes Bare
Keyword(s):  
Protein Data Bank ◽  
In Silico ◽  
Data Bank ◽  
Discovery Studio ◽  
Capsicum Annum ◽  
Cox 2

<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>

scholarly journals POTENSI SENYAWA BIOAKTIF TANAMAN GENUS Phyllanthus SEBAGAI INHIBITOR REPLIKASI VIRUS HEPATITIS B

2017 ◽  
Vol 4 (2) ◽  
pp. 85
Author(s):  
. Firdayani ◽  
Susi Kusumaningrum ◽  
Yosephine Ria Miranti
Keyword(s):  
Molecular Docking ◽  
Amino Acid ◽  
Hepatitis B ◽  
Protein Data Bank ◽  
Bioactive Compounds ◽  
Core Protein ◽  
Data Bank ◽  
Amino Acid Residues ◽  
Virus Hepatitis ◽  
Molegro Virtual Docker

Potency of Plant Bioactive Compounds from the Genus Phyllanthus as Hepatitis B Virus Replication InhibitorIn this research, simulations of molecular docking of Phyllanthus bioactive compounds were performed into the core protein of HBV. This simulation aimed to predict the interaction between compounds with virus core protein causing disruption of capsid formation and inhibiting its replication. The docking simulation was completed by Molegro Virtual Docker 6.0. The 3D stable conformation of molecule structures were docked into HBV core protein downloaded from Protein Data Bank, then the results were analyzed to view the minimum energy and interactions that occurred. The coordinate docking was done at the same coordinate as the previously docked reference ligand position and was validated. From the results it was known that repandusinic acid formed the most stable affinity bond with amino acid residues of viral core proteins. Interaction of B chain forming hydrogen bonds with the amino acid residues of Thr 33, Trp 102, Phe 23, Leu 140, Tyr 118 and Ser 141, and C chain with Thr 128, Val 124 and Glu 117.These compounds can be used as marker for anti HBV.Keyword: Bioactive compounds, core protein, HBV , molecular docking, Phyllanthus ABSTRAKPada penelitian ini dilakukan simulasi penambatan molekul senyawa-senyawa bioaktif Phyllanthus ke dalam protein inti virus hepatitis B. Simulasi ini bertujuan untuk memprediksi interaksi terbentuk antara senyawa dengan protein yang menyebabkan terganggunya pembentukan kapsid virus dan menghambat replikasinya. Simulasi penambatan molekul dilakukan menggunakan program Molegro Virtual Docker 6.0. Sebagai reseptor target digunakan struktur 3D protein inti 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 asam repandusinat membentuk komplek dengan energi afinitas ikatan yang paling kecil dengan residu asam amino protein inti virus. Interaksi terjadi dengan rantai B yang membentuk ikatan hidrogen dengan asam amino Thr 33, Trp 102, Phe 23, Leu 140, Tyr 118 dan Ser 141, dan rantai C dengan asam amino Thr 128, Val 124 dan Glu 117. Senyawa ini dapat dijadikan sebagai marka untuk anti VHB.Kata kunci: Penambatan molekul, Phyllanthus, protein inti, senyawa bioaktif, VHBReceived: 11 December 2017                 Accepted: 27 December 2017           Published: 31 December 2017 

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