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

The Protein Data Bank (PDB), Its Related Services and Software Tools as Key Components for In Silico Guided Drug Discovery

2008 ◽  
Vol 51 (22) ◽  
pp. 7021-7040 ◽  
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 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.

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 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 Penambatan In Siliko Senyawa Ester Naringenin Sebagai Antidiabetes

2018 ◽  
Vol 1 (1) ◽  
pp. 245-250
Author(s):  
Nerdy Nerdy ◽  
Effendy De Lux Putra ◽  
Ginda Haro ◽  
Urip Harahap
Keyword(s):  
Diabetes Mellitus ◽  
Protein Data Bank ◽  
Bond Energy ◽  
In Silico ◽  
Phosphoenolpyruvate Carboxykinase ◽  
Parent Compound ◽  
Data Bank ◽  
Mean Square ◽  
In Silico Docking ◽  
Diabetes Melitus

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.

scholarly journals POTENSI SENYAWA AKTIF BUNGA, KULIT DAUN DAN GETAH Aloe barbadensis Miller. TERHADAP PENGHAMBATAN ENZIM TYROSINASE

2019 ◽  
Vol 1 (1) ◽  
Author(s):  
Nur Aji
Keyword(s):  
Ferulic Acid ◽  
Protein Data Bank ◽  
In Silico ◽  
Sinapic Acid ◽  
Aloe Vera ◽  
Data Bank ◽  
Gentisic Acid ◽  
Aloe Barbadensis ◽  
Molegro Virtual Docker

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.

scholarly journals PROSPECÇÃO DE CANDIDATOS A FÁRMACOS PARA TRATAMENTO DE TUMORES MALIGNOS

2021 ◽  
Author(s):  
Lis Mariana da Silva Menezes ◽  
Liliane Rodrigues Garcia ◽  
Gabrieli Carolina Favacho Gonçalves ◽  
Ronaldo Correia da Silva ◽  
Adonis de Melo Lima
Keyword(s):  
Protein Data Bank ◽  
In Silico ◽  
Data Bank ◽  
Erwinia Billingiae

Introdução: A principal característica do câncer é o crescimento descontrolado de células neoplásicas, formando tumores. Tecidos tumorais apresentam dependência do aminoácido L-asparagina para se desenvolver, sendo a obtenção desse aminoácido feita do meio extracelular. Alguns medicamentos quimioterápicos hidrolisam a asparagina em amônia e aspartato, eliminando a fonte sérica de asparagina das células tumorais, causando uma apoptose seletiva. Esse efeito é possível pela presença da enzima asparaginase utilizada como princípio ativo dos medicamentos anticancerígenos. Ess molécula é isolada principalmente da bactéria E.coli, porém pacientes têm apresentado efeitos colaterais ao uso de medicamentos que a contem, sendo necessárias novas alternativas farmacológicas. Objetivo: Realizar análise in silico do potencial biotecnológico de asparaginase de Erwinia billingiae, a partir da construção 3D da proteína, identificação do sítio ativo e validação do modelo proposto. Materiais e métodos: Foi realizada uma busca a partir da sequência FASTA da L asparaginase de Erwinia billingiae no Protein Data Bank (PDB), para aquisição de um molde proteíco. Posteriormente foi realizado o alinhamento entre as sequências alvo e molde. Foram construídos cinco modelos proteicos no progama modeller 9v8, e estes foram submetidos à validação através do diagrama de Ramachandran, QMEAN, Prosa e ProQ. Resultados: Foi escolhido o PDB 4O0E para ser utilizado como referência para gerar os candidatos a fármaco, sendo construído diversos modelos, validados e escolhido aquele com melhores resultados. O modelo proposto possui 320 aminoácidos, sendo sua estrutura secundária caracterizada por 11 ẞ-folhas, 8 α-hélices e 20 loops, todos equivalentes às estruturas do modelo de referência (4O0E). Foi observada a presença da tríade catalítica T168, T186 e T219 do modelo de referência em posições equivalentes no modelo construído, sugerindo conservação de sua função. Conclusão: A asparaginase de Erwinia billingiae mantém a tríade catalítica de treoninas conservada sugerindo preservação de sua função proteolítica. Estudos adicionais de acoplamento e dinâmica molecular devem ser realizados para observar se ocorrem interações no complexo enzima-substrato.

Structure Assessment Analysis of Core Domain of Seven Protein Data Bank Entries of HIV-1 Protease Using Different in-silico Techniques

2015 ◽  
Vol 10 (2) ◽  
pp. 98-104
Author(s):  
Mymoona Akhter ◽  
Kalicharan Sharma ◽  
M. M. Alam ◽  
M. S. Zaman ◽  
A. Husain ◽  
...  
Keyword(s):  
Protein Data Bank ◽  
In Silico ◽  
Data Bank ◽  
Core Domain ◽  
Structure Assessment ◽  
Hiv 1
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