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

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.

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>


2019 ◽  
Vol 4 (3) ◽  
pp. 124
Author(s):  
Yohanes Bare ◽  
Agustina Dua Kuki ◽  
Apriani Herni Rophi ◽  
Gabriella Candrakirana Krisnamurti ◽  
Margaretha Rika Wahyu Gabrella Lorenza ◽  
...  

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.


Author(s):  
Yohanes Bare ◽  
Mansur S ◽  
Sri Sulystyaningsih Natalia Daeng Tiring ◽  
Dewi Ratih Tirto Sari ◽  
Andri Maulidi

JNK adalah gen yang berperan dalam metabolisme DMT2. Dalam pengobatan T2DM digunakan JNK sebagai potensi terapi dengan menggunakan bahan alam. 8-shogaol adalah komponen kimia yang terkandung dalam jahe yang memiliki aktivitas antioksidan. Tujuan dari penelitina ini adalah menginversitagasi dan menganalisis peran 8-shogaol terhadap JNK. Protein JNK (ID: 464Y) diperoleh dari Protein Data Bank dan ligan 8-shogaol (CID:6442560 ) didapat dari pubchem. Ligan dan protein didocking menggunakan Hex 8.0.0. File dalam bentuk pdb divisualtisasi dan analisis menggunakan Discovery Studio Client 4.1 software. Interaksi ligan-protein menunjukan ikatan hidrogen pada residu asam amino LYS93 dan van der Waals pada 18 residu asam amino dengan energi ikatan-289.68cal/mol. Interkasi ini berpotensi sebagai penghambat kerja JNK dan dapat digunakan dalam terapi DMT2.Virtual screening: potential prediction of 8-shogaol againts c-Jun N-Terminal Kinase (JNK)AbstractJNK is one of gene that has a role in T2DM condition. To curve T2DM use JNK as potential healing using natural compounds. Eight-shogaol which found in ginger has function as a antioxidant.. The aim of the research is to investigate and analyze role 8-shogaol againts JNK. Protein JNK (ID: 464Y) was taken from Protein Data Bank and ligand 8-shogaol (CID:6442560 ) acquired from pubchem. Ligand and protein model were docked using Hex 8.0.0 software. Visualization and analysis molecular interactions by the Discovery Studio Client 4.1 software. Interaction ligand-protein showed one hydrogen bond in amino acid residue LYS93 and formed van der Waals in eighteen amino acid residues which energy binding -289.68cal/mol. This interaction has a potential to inhibit JNK role and lead to therapy T2DM.


2021 ◽  
Vol 2 (2) ◽  
pp. 187-192
Author(s):  
Mokhamad Syaban ◽  
◽  
Nabila Erwan ◽  
Muhamad Syamsuddin ◽  
Fatimah Zahra ◽  
...  

Background: β-lactamase is an enzyme that plays a role in the occurrence of antibiotic resistance against Methicillin-resistant Staphylococcus aureus (MRSA) bacteria. Viscosin is a lipopeptide biosurfactant produced by the Pseudomonas group bacteria. A study states that Viscosin has strong antibacterial properties. Aims: This study aims to determine the interactions that occur with Viscosin and β-lactamase enzymes. Methods: Researchers used the in-silico method to determine the molecular interactions that occurred computationally. The protein used was β-lactamase protein obtained from the Protein Data Bank and Viscosin ligand obtained from the PubChem web server, and we used native ligands as control. Pharma expert web server and Pyrx, Pymol, and Discovery Studio software were used in this research. Results: The results showed that Viscosin has high activity as an antibiotic and is predicted to be a membrane integrity antagonist. The binding affinity interaction that occurs between Viscosin-β-lactamase is -7.3 kcal/mol. The affinity is lower than the control. Conclusion: Viscosin was predicted to have strong antibacterial properties, but the binding interaction was lower than the control. However, exploration of Viscosin compounds and further research to determine the antibacterial effect of Viscosin against MRSA and other bacteria is needed to against antibiotic resistance.


2002 ◽  
Vol 58 (s1) ◽  
pp. c214-c214
Author(s):  
W. F. Bluhm ◽  
T. Battistuz ◽  
E. Clingman ◽  
N. Deshpande ◽  
W. Fleri ◽  
...  

2021 ◽  
pp. 166900
Author(s):  
Alexander Miguel Monzon ◽  
Paolo Bonato ◽  
Marco Necci ◽  
Silvio C.E. Tosatto ◽  
Damiano Piovesan
Keyword(s):  

2016 ◽  
Vol 72 (10) ◽  
pp. 1110-1118 ◽  
Author(s):  
Wouter G. Touw ◽  
Bart van Beusekom ◽  
Jochem M. G. Evers ◽  
Gert Vriend ◽  
Robbie P. Joosten

Many crystal structures in the Protein Data Bank contain zinc ions in a geometrically distorted tetrahedral complex with four Cys and/or His ligands. A method is presented to automatically validate and correct these zinc complexes. Analysis of the corrected zinc complexes shows that the average Zn–Cys distances and Cys–Zn–Cys angles are a function of the number of cysteines and histidines involved. The observed trends can be used to develop more context-sensitive targets for model validation and refinement.


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