scholarly journals Computational estimation of potential inhibitors from known drugs against the main protease of SARS-CoV-2

RSC Advances ◽  
2021 ◽  
Vol 11 (28) ◽  
pp. 17478-17486
Author(s):  
Nguyen Minh Tam ◽  
Minh Quan Pham ◽  
Nguyen Xuan Ha ◽  
Pham Cam Nam ◽  
Huong Thi Thu Phung
Keyword(s):  
Binding Site ◽  
Substrate Binding ◽  
Substrate Binding Site ◽  
Computational Estimation ◽  
Main Protease ◽  
Critical Residues ◽  
Approved Drugs ◽  
Potential Inhibitors

Approved drugs predicted to interact with critical residues in the substrate-binding site of SARS-CoV-2 Mpro can be promising inhibitors.

The Structural Landscape of SARS-CoV-2 Main Protease: Hints for Inhibitor Search.

2020 ◽  
Author(s):  
Luigi Leonardo Palese
Keyword(s):  
Comparative Analysis ◽  
Global Health ◽  
Binding Site ◽  
Causative Agent ◽  
Data Set ◽  
Substrate Binding Site ◽  
Global Pandemic ◽  
Main Protease ◽  
Crystallographic Structures ◽  
Structural Aspects

In 2019, an outbreak occurred which resulted in a global pandemic. The causative agent of this serious global health threat was a coronavirus similar to the agent of SARS, referred to as SARS-CoV-2. In this work an analysis of the available structures of the SARS-CoV-2 main protease has been performed. From a data set of crystallographic structures the dynamics of the protease has been obtained. Furthermore, a comparative analysis of the structures of SARS-CoV-2 with those of the main protease of the coronavirus responsible of SARS (SARS-CoV) was carried out. The results of these studies suggest that, although main proteases of SARS-CoV and SARS-CoV-2 are similar at the backbone level, some plasticity at the substrate binding site can be observed. The consequences of these structural aspects on the search for effective inhibitors of these enzymes are discussed, with a focus on already known compounds. The results obtained show that compounds containing an oxirane ring could be considered as inhibitors of the main protease of SARS-CoV-2.

Comprehensive in silico Study of GLUT10: Prediction of Possible Substrate Binding Sites and Interacting Molecules

2020 ◽  
Vol 21 (2) ◽  
pp. 117-130 ◽  
Author(s):  
Mohammad J. Hosen ◽  
Mahmudul Hasan ◽  
Sourav Chakraborty ◽  
Ruhshan A. Abir ◽  
Abdullah Zubaer ◽  
...  
Keyword(s):  
Virtual Screening ◽  
Binding Site ◽  
Glucose Transporter ◽  
Substrate Binding ◽  
Mutation Screening ◽  
Homology Model ◽  
Connective Tissue Disorder ◽  
Crystallographic Structure ◽  
Substrate Binding Site

Objectives: The Arterial Tortuosity Syndrome (ATS) is an autosomal recessive connective tissue disorder, mainly characterized by tortuosity and stenosis of the arteries with a propensity towards aneurysm formation and dissection. It is caused by mutations in the SLC2A10 gene that encodes the facilitative glucose transporter GLUT10. The molecules transported by and interacting with GLUT10 have still not been unambiguously identified. Hence, the study attempts to identify both the substrate binding site of GLUT10 and the molecules interacting with this site. Methods: As High-resolution X-ray crystallographic structure of GLUT10 was not available, 3D homology model of GLUT10 in open conformation was constructed. Further, molecular docking and bioinformatics investigation were employed. Results and Discussion: Blind docking of nine reported potential in vitro substrates with this 3D homology model revealed that substrate binding site is possibly made with PRO531, GLU507, GLU437, TRP432, ALA506, LEU519, LEU505, LEU433, GLN525, GLN510, LYS372, LYS373, SER520, SER124, SER533, SER504, SER436 amino acid residues. Virtual screening of all metabolites from the Human Serum Metabolome Database and muscle metabolites from Human Metabolite Database (HMDB) against the GLUT10 revealed possible substrates and interacting molecules for GLUT10, which were found to be involved directly or partially in ATS progression or different arterial disorders. Reported mutation screening revealed that a highly emergent point mutation (c. 1309G>A, p. Glu437Lys) is located in the predicted substrate binding site region. Conclusion: Virtual screening expands the possibility to explore more compounds that can interact with GLUT10 and may aid in understanding the mechanisms leading to ATS.

The role of Glu196 in the environment around the substrate binding site of leucine aminopeptidase fromStreptomyces griseus

FEBS Letters ◽  
2006 ◽  
Vol 580 (3) ◽  
pp. 912-917 ◽  
Author(s):  
Jiro Arima ◽  
Yoshiko Uesugi ◽  
Misugi Uraji ◽  
Masaki Iwabuchi ◽  
Tadashi Hatanaka
Keyword(s):  
Binding Site ◽  
Leucine Aminopeptidase ◽  
Substrate Binding ◽  
Substrate Binding Site

Identification of Significant Residues in the Substrate Binding Site ofBacillus stearothermophilusFarnesyl Diphosphate Synthase†

Biochemistry ◽  
1996 ◽  
Vol 35 (29) ◽  
pp. 9533-9538 ◽  
Author(s):  
Tanetoshi Koyama ◽  
Masaya Tajima ◽  
Hiroaki Sano ◽  
Takashi Doi ◽  
Ayumi Koike-Takeshita ◽  
...  
Keyword(s):  
Binding Site ◽  
Substrate Binding ◽  
Substrate Binding Site
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