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 Prediksi Asam Kuinat Sebagai Anti-Inflamasi Terhadap COX-2 Secara Virtual

2019 ◽  
Vol 4 (3) ◽  
pp. 124
Author(s):  
Yohanes Bare ◽  
Agustina Dua Kuki ◽  
Apriani Herni Rophi ◽  
Gabriella Candrakirana Krisnamurti ◽  
Margaretha Rika Wahyu Gabrella Lorenza ◽  
...  
Keyword(s):  
Protein Data Bank ◽  
Data Bank ◽  
Protein Domain ◽  
Discovery Studio ◽  
Cox 2 ◽  
Domain Protein

Inflamasi merupakan mekanisme pertahanan tubuh terhadap terhadap rangsangan berbahaya, seperti patogen, sel-sel yang rusak, senyawa beracun, atau iradiasi. Selama inflamasi dalam tubuh terdapat COX-2 mediator inflamasi yang peran meningkatkan inflamasi.  Sistem imun anti-inflamasi yang mengalami mutasi menyebabkan inflmasi meningkat. Oleh karena itu untuk menurnkannya menggunakan bioaktif alam. Asam kuinat memiliki toksisitas yang sangat rendah dan tidak memberikan efek negatif terhadap organ tubuh manusia. Asam kuinat memiliki potensi yang besar sebagai kandidat obat tertinggi dalam terapi. Akan tetapi kurangnya kajiannya. Penelitian ini bertujuan unutk memprediksi potensi serta menganalisis asam kuinat sebagai agen inflamasi dengan cara menghambat COX-2. Metode yang digunakan terdiri atas pengunduhan protein COX-2 dari protein data bank (PDB) dan asam kuinat diperoleh dari database PubChem, persiapan protein (COX-2) dan ligan (asam Kuinat) dengan program PyRx, analisis interaksi protein dan ligan menggunakan program Hex 8.0.0 dan Discovery Studio client 4.  Interaksi antara protein dan ligan menunjukan hasil positif dengan ditemukan 2 domain protein yang berikatan dengan asam kuinat. Protein domain A (GLU140, ASN144, SER143, dan TRP139) dan protein domain B (GLU236, THR237, LYS333, GLN241, GLN330, PHE329, dan LEU238). Ikatan yang terbentuk ada ikatan hidrogen dengan energi sebesar -198.95cal/mol. Asam kuinat diprediksi memiliki potensi sebagai terapi anti-inflamasi, hal ini ditunjukan karena ada ikatan yang terbentuk antara ligan dan 11 residu asam amino.

Combinatorial Screening of COX-2 Inhibitors from Chinese Herbs Based on Multiple Structure-Based Pharmacophores

2013 ◽  
Vol 791-793 ◽  
pp. 269-273
Author(s):  
Yan Ling Zhang ◽  
Yuan Ming Wang ◽  
Yan Jiang Qiao
Keyword(s):  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Protein Data Bank ◽  
Data Bank ◽  
Chinese Herbs ◽  
Combinatorial Screening ◽  
Cox 2 ◽  
Appraisal Index ◽  
Cox 2 Inhibitors ◽  
Pharmacophore Models

Ten structure-based pharmacophore models of Cyclooxygenase 2 (COX-2) inhibitors were generated by LigandScout based on COX-2 inhibitor complexes from the Protein Data Bank (PDB). The potential COX-2 inhibitors were identified from traditional Chinese medicine with the method of combinatorial screening with ten models. Based on the screening results of MDDR and the metrics of E, A% and comprehensive appraisal index (CAI), the threshold of hit frequency of molecules was defined and used to identify the active molecules from Chinese herbs. The molecules hit by not less than six pharmacophore models were taken as the screening objects of COX-2 inhibitor, and 1103 molecules were obtained.

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 In Silico Insight the Prediction of Chlorogenic Acid in Coffee through Cyclooxygenase-2 (COX2) Interaction

2019 ◽  
Vol 7 (2) ◽  
Author(s):  
Yohanes Bare ◽  
Dewi Ratih Tirto Sari ◽  
Yoga Tribakti Rachmad ◽  
Gabriella Candrakirana Krisnamurti ◽  
Agustina Elizabeth
Keyword(s):  
Chlorogenic Acid ◽  
Potential Role ◽  
Interaction Model ◽  
Data Bank ◽  
High Permeability ◽  
Discovery Studio ◽  
Docking Approach ◽  
Cox 2 ◽  
Therapeutic Compound

Inflammation was signs of pathological or abnormality in tissue to give an alert as a trouble signal to the system. Therapeutic using NSAIDs has some side effects. This research explored the potential role of chlorogenic acid as natural therapeutic compound to inhibit the inflammation target such as COX-2 by interaction model. The research method used in this study was the molecular docking approach, which binds ligand and protein. Protein data provided by Protein Data Bank (ID: 6cox) while, chlorogenic acid obtain from PubChem (CID: 1794427). We docked COX-2 and chlorogenic acid using Hex 8.0.0. Visualization and analysis of the molecular interactions of chlorogenic acid and COX-2 conducted by the Discovery Studio Client 4.1 software. Chlorogenic acid has a high permeability and is easily absorbed based on five Lipinski Rule. Interestingly, we found Fifteen amino acid was binding with chlorogenic acid that formed by hydrogen bond and van der Waals.The interaction between ligand-protein results in energy binding -327.59cal/mol. Chlorogenic acid has a potential role to inhibit inflammation pathway by inhibiting COX-2. We predicted chlorogenic acid has a potential as therapy anti-inflammatory to suppress COX-2 as mediator inflammation.

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.

ANÁLISE COMPUTACIONAL DA INTERAÇÃO ENTRE O CANAL IÔNICO DE α-HL E COMPOSTOS TIAZOLIDÍNICOS

2021 ◽  
Author(s):  
Maria Isabel dos Santos Cavalcanti ◽  
Débora Brígida Moura de Freitas ◽  
Dijanah Cota Machado ◽  
Cláudio Gabriel Rodrigues
Keyword(s):  
Staphylococcus Aureus ◽  
Protein Data Bank ◽  
Data Bank ◽  
Discovery Studio

Introdução: Staphylococcus aureus (S. aureus) é uma bactéria associada a diversas infecções, tanto na comunidade quanto em ambiente hospitalar, ocasionando desde infecção cutânea até septicemia(1). Um importante fator de virulência é a exotoxina alfa-hemolisina (α-HL), que oligomeriza e forma canais iônicos transmembranares nas células-alvo, permitindo o fluxo livre de várias espécies químicas, resultando na morte celular(2). Diversas cepas de S. aureus exibem multirresistência aos antibióticos, limitando as opções de tratamento. Os derivados tiazolidínicos podem ser uma boa alternativa para bloquear a α-HL, pois possuem amplas propriedades bioativas, como por exemplo a antimicrobiana para cepas multirresistentes, sendo eficazes contra o S. aureus e inibindo o seu crescimento(3). Objetivos: Dada a importância da busca de compostos com ação antibacteriana, via bloqueio da α-HL, este trabalho visa analisar, via docagem molecular, a interação de derivados tiazolidínicos 5-benzilideno com o canal iônico formado pela toxina. Métodos: A estrutura cristalográfica da α-HL de S. aureus foi obtida pelo Protein Data Bank (PDB) e utilizou-se o MolView para modelagem dos compostos denominados GQ294 e GQ443, posteriormente submetidos ao Avogadro 1.1.1 para minimização de energia molecular. A docagem foi realizada pelo DockThor e os resultados foram analisados utilizando o Discovery Studio Visualizer. Resultados: A partir dos resultados de docagem pelo DockThor, foi obtida uma classificação dos compostos de acordo com suas energias totais e scores de afinidade com a toxina. Os valores de energia total do GQ443 e GQ294 foram iguais a -15,152 KJ/ mol e -19,009 KJ/ mol, respectivamente. Enquanto o score de afinidade de GQ443 e GQ294 foi de -6,820 Kcal/ mol e -5,902 Kcal/ mol respectivamente. As análises obtidas a partir do Discovery Studio Visualizer demonstraram que os dois compostos interagem com a região de constrição do canal iônico, principalmente com os resíduos GLU 111 e LYS 147, sendo estas interações mediadas principalmente por ligações de hidrogênio, além de interações do tipo cátionpi, pi-alquila, pi-enxofre. Esses dados corroboram com outros trabalhos já encontrados na literatura(4). Conclusões: Os resultados indicam, preditivamente, que os compostos GQ443 e GQ294 interagem com o canal da α-HL na região de constrição, sugerindo um bloqueio de sua atividade. São necessários dados experimentais para elucidar os dados teóricos já obtidos.

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 The POTENTIAL OF BUTTERFLY PEA FLOWER METHANOL EXTRACT AS AN ANTIOXIDANT BY IN SILICO

2020 ◽  
Vol 1 (3) ◽  
pp. 163-169
Author(s):  
Tiana Fitrilia ◽  
M. Fakih Kurniawan ◽  
Febryana Rahayu Kurniawati ◽  
Tirta Setiawan
Keyword(s):  
Nadph Oxidase ◽  
In Silico ◽  
Methanol Extract ◽  
Data Bank ◽  
Computational Method ◽  
Flowering Plant ◽  
Chemical Components ◽  
Discovery Studio ◽  
Butterfly Pea ◽  
G Value

Abstract: Butterfly pea flower (Clitoria ternatea L.) is a flowering plant from the Fabecea family that can grow vines. Butterfly pea flower are known to have chemical components that can act as antioxidants. This study aims to predict the potential of active compounds from methanol extract of butterfly pea flower in inhibiting reactive oxygen species (ROS) based on bond affinity (∆G), the value of Root Mean Square Deviation (RMSD) and their interactions. The method used was a computational method with in silico technique. The software used was Autodock Vina with visualization using the Biovia Discovery Studio Visualizer 2020. The enzyme receptor was NADPH Oxidase (NOX) obtained from Protein Data Bank and the test ligands were a chemical compound from methanol extract of butterfly pea flower. The results of the in silico study showed that the NO had a innate ligand, namely the GTP ligand which has a ∆G value of -7.3 kcal/mol, an RMSD value of 3.1111 Å and the interaction with the receptor that involves the presence of hydrogen bonds. Based on the results of the analysis of 11 test ligands, the chemical component of caffeine was predicted to have the most potential in inhibiting ROS compounds with a value of ∆G -5.4, RMSD value of 1.328 Å and had the same amino acid residue in hydrogen bonding, namely ASP118, and GLY15. The test ligand had the ability to inhibit ROS compounds with a lower level of stability than the innate ligand. Keywords: antioxidant; butterfly pea flower; in silico; NADPH oxidase, ROS

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 Targeting Omp-A Protein of Acinetobacter Baumannii with the Bio-Active Compounds from Azadirachta Indica - an in-silico Approach

2021 ◽  
pp. 323-334
Author(s):  
R. Nandita ◽  
A. S. Smiline Girija ◽  
P. Sankar Ganesh ◽  
J. Vijayashree Priyadharsini
Keyword(s):  
Crystal Structure ◽  
Acinetobacter Baumannii ◽  
Azadirachta Indica ◽  
In Silico ◽  
3D Structure ◽  
Data Bank ◽  
Binding Energies ◽  
Active Compounds ◽  
Discovery Studio ◽  
Ompa Protein

Background: Acinetobacter baumannii is a gram negative bacterium which is typically short, round, coccobacillus and was named after the bacteriologist Paul Baumann. It is an emerging dental pathogen since it acquires  drug resistance and expression of several virulence genes. It is an opportunistic pathogen in humans, affecting people with compromised immune systems. Acinetobacter baumannii is an arising nosocomial microorganism causing serious complications because of the propensity of its multi-drug resistant property. Aim: The aim of the present study was to target omp-A protein of Acinetobacter baumannii with the bio active compounds from Azadirachta indica an in-silico approach. Materials and Methods: The crystal structure of ompA protein was obtained from the PDB protein data bank. The structures of the bio-active derivatives of A. indica were obtained from the chemsketch software. The generated 3D structures were then optimised. Auto Dock instrument was utilized for docking investigation to interpret the affinity between bio-compounds of A. indica against ompA protein of A. baumannii. Results: The 3D crystal structure of OmpA-like domain from A.baumannii was retrieved from PDB database and its PDB ID was 3TD3 – A chain. 3D Structure of OmpA visualization using Biovia-Discovery studio visualizer. The 2D structure of compounds from Azadirachta indica was drawn using ACD chemsketch and saved in MDL-mol format and converted to PDB format using open babel converter. The final docked structures for the drug ligand interactions were assessed for their binding energies and hydrogen bonds. Conclusion: The present study had achieved the anti-biofilm inhibitory effect of imidazole-2-carboxylic acid from A. indica exhibiting a great interaction between activity with ompA utilizing computational investigation.

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