In silico approach on sequential and structural variability in oryzacystatin and its interaction with cysteine protease enzymes of insect

2021 ◽  
Vol 186 ◽  
pp. 112728
Author(s):  
Krishnamanikumar Premachandran ◽  
Thanga Suja Srinivasan ◽  
Carlton Ranjith Wilson Alphonse
Keyword(s):  
Cysteine Protease ◽  
In Silico ◽  
Structural Variability

scholarly journals Cruzain structures: apocruzain and cruzain bound to S-methyl thiomethanesulfonate and implications for drug design

2019 ◽  
Vol 75 (6) ◽  
pp. 419-427 ◽  
Author(s):  
Elany Barbosa da Silva ◽  
Elfriede Dall ◽  
Peter Briza ◽  
Hans Brandstetter ◽  
Rafaela Salgado Ferreira
Keyword(s):  
Drug Design ◽  
Trypanosoma Cruzi ◽  
Chagas Disease ◽  
Cysteine Protease ◽  
In Silico ◽  
Structural Information ◽  
Mass Spectrometric ◽  
Catalytic Cysteine ◽  
Reversible Covalent ◽  
Covalent Inhibitor

Chagas disease, which is caused by Trypanosoma cruzi, affects more than six million people worldwide. Cruzain is the major cysteine protease involved in the survival of this parasite. Here, the expression, purification and crystallization of this enzyme are reported. The cruzain crystals diffracted to 1.2 Å resolution, yielding two novel cruzain structures: apocruzain and cruzain bound to the reversible covalent inhibitor S-methyl thiomethanesulfonate. Mass-spectrometric experiments confirmed the presence of a methylthiol group attached to the catalytic cysteine. Comparison of these structures with previously published structures indicates the rigidity of the cruzain structure. These results provide further structural information about the enzyme and may help in new in silico studies to identify or optimize novel prototypes of cruzain inhibitors.

scholarly journals In Silico Molecular Characterization of Cysteine Protease YopT from Yersinia pestis by Homology Modeling and Binding Site Identification

2014 ◽  
Vol 8 (1) ◽  
Author(s):  
Md. Anayet Hasan ◽  
S. M. Alauddin ◽  
Mohammad Al Amin ◽  
Suza Mohammad Nur ◽  
Adnan Mannan
Keyword(s):  
Homology Modeling ◽  
Binding Site ◽  
Yersinia Pestis ◽  
Molecular Characterization ◽  
Cysteine Protease ◽  
In Silico ◽  
Binding Site Identification ◽  
Site Identification

Abstract non disponibile

scholarly journals STUDI IN SILICO SIFAT FARMAKOKINETIK, TOKSISITAS, DAN AKTIVITAS IMUNOMODULATOR BRAZILEIN KAYU SECANG TERHADAP ENZIM 3-CHYMOTRYPSIN-LIKE CYSTEINE PROTEASE CORONAVIRUS

2020 ◽  
Vol 1 (1) ◽  
pp. 76-85
Author(s):  
Dwi Krihariyani Dwi ◽  
Retno Sasongkowati ◽  
Edy Haryanto
Keyword(s):  
Cysteine Protease ◽  
In Silico ◽  
Online Tool ◽  
Molegro Virtual Docker

Enzim 3-chymotrypsin-like cysteine protease (3CLpro) adalah enzim yang berfungsi  mengendalikan replikasi dalam siklus hidup coronavirus. Enzim 3CLproadalah target biologis (reseptor) yang akan berinteraksi dengan obat (ligan). Brazilein merupakan kandungan senyawa mayor dalam kayu secang yang secara empiris digunakan sebagai imunomodulator. Penelitian ini bertujuan untuk memprediksi secara in silico aktivitas imunomodulator senyawa brazilein terhadap enzim 3CLpro, dengan senyawa pembanding kurkumin. Uji in silico digunakan untuk memprediksi aktivitas imunomodulator dengan melakukan docking menggunakan program komputer Molegro Virtual Docker. Reseptor yang digunakan adalah 3CLpro, kode PDB: 6M2N, dengan ligan 3WL_401[C]. Prediksi sifat farmakokinetik (ADME) dan toksisitas brazilein dan kurkumin dilakukan menggunakan program pkCSM online tool. Analisis data dilakukan dengan membandingkan energi ikatan hasil docking antara brazilein, ligan, dan kurkumin pada reseptor target. Semakin rendah energi ikatan ligan dengan reseptor target, semakin stabil ikatan yang terbentuk. Hasil uji in silico menunjukkan bahwa energi ikatan ligan = -83.1153kkal/mol, brazilein = -82.0583kkal/mol, dan kurkumin = -115.852kkal/mol. Hasil uji di atas menunjukkan bahwa brazilein memiliki potensi sebagai imunomodulator meskipun lebih rendah dibanding ligan dan kurkumin. Hasil uji in silico menggunakan program pkCSM online tool menunjukkan bahwa senyawa brazilein mempunyai sifat farmakokinetik yang baik, dan menimbulkan toksisitas yang relatif rendah.

scholarly journals Drug repurposing against MERS CoV and SARS-COV-2 PLpro in silico

2020 ◽  
Author(s):  
Abdo Elfiky ◽  
Noha Ibrahim ◽  
Wael Elshemey
Keyword(s):  
Molecular Docking ◽  
Middle East ◽  
Protease Inhibitors ◽  
Binding Affinity ◽  
Cysteine Protease ◽  
In Silico ◽  
Drug Repurposing ◽  
Middle East Respiratory Syndrome ◽  
Interaction Pattern ◽  
Structural Protein

Abstract Aim: The Middle East Respiratory Syndrome coronavirus (MERS-CoV) and COVID-19 cause severe acute, deadly, pneumonia. Papain-like protease (PLpro), is HCoV cysteine protease encoded within the Non-Structural protein 3. Materials and Methods: Molecular docking is performed to test the binding performance of six protease inhibitors against MERS CoV and SARS-CoV-2 PLpro. Results: The compound, GRL-0667, shows the highest binding affinity to MERS CoV PLpro, while Grazoprevir shows the highest binding affinity against HCV NS3. Moreover, the interaction pattern in the case of HCV NS3 is the same as in the case of coronaviruses. Conclusion: The present study shows the ability of some anti-SARS CoV and anti-HCV NS3 drugs to inhibit MERS CoV PLpro, interestingly, including the newly emerged SARS-COV-2 PLpro.

scholarly journals In-Silico evaluation of Anti-Leishmanial compounds of selected pharmacophore

2018 ◽  
Vol 8 (6-s) ◽  
pp. 227-229
Author(s):  
Sindhuprava Rana ◽  
R Sivaperumal
Keyword(s):  
Hydrogen Bonding ◽  
Visceral Leishmaniasis ◽  
Cysteine Protease ◽  
Inhibitory Activity ◽  
In Silico ◽  
Cathepsin B ◽  
Leishmania Donovani ◽  
Software Tool ◽  
Lead Compounds ◽  
Amastigote Stage

In this study, out of sixteen compounds, only thirteen compounds have shown hydrogen bonding with the modeled cathepsin B protein of L donovani, remaining compound (C1D13416238, Posaconazole. and CID 6082033) did not show any hydrogen bonding with ligands. So, these 13 compounds which show hydrogen bonding with modeled protein could be considered as most potent lead compounds having inhibitory activity at either promastigote stage or amastigote stage of Leishmania donovani. Few compounds demonstrated better docking score to either AutoDock4.0 or GOLD v2.l but some compound did not show any hydrogen bonding with modeled protein in either docking software tool. Thus, it could be concluded that generated experimental compounds could have potential as pharmacological tool against Visceral Leishmaniasis. Keywords: Cysteine Protease, Vinyl Hydrazide, Antileishmanial Drugs, Licochalcone, Visceral Leishmaniasis.

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