Pharmaceutical interest of in-silico approaches

2022 ◽  
Vol 0 (0) ◽  
Author(s):  
Dinesh Kumar ◽  
Pooja Sharma ◽  
Ayush Mahajan ◽  
Ravi Dhawan ◽  
Kamal Dua
Keyword(s):  
Molecular Modeling ◽  
In Silico ◽  
Three Dimensional ◽  
Gene Sequencing ◽  
New Drugs ◽  
Dimensional Structure ◽  
Pharmaceutical Applications ◽  
Drug Designing ◽  
Different Types

Abstract The virtual environment within the computer using software performed on the computer is known as in-silico studies. These drugs designing software play a vital task in discovering new drugs in the field of pharmaceuticals. These designing programs and software are employed in gene sequencing, molecular modeling, and in assessing the three-dimensional structure of the molecule, which can further be used in drug designing and development. Drug development and discovery is not only a powerful, extensive, and an interdisciplinary system but also a very complex and time-consuming method. This book chapter mainly focused on different types of in-silico approaches along with their pharmaceutical applications in numerous diseases.

Demystifying the three dimensional structure of G protein-coupled receptors (GPCRs) with the aid of molecular modeling

2003 ◽  
pp. 2949 ◽  
Author(s):  
Stefano Moro ◽  
Francesca Deflorian ◽  
Giampiero Spalluto ◽  
Giorgia Pastorin ◽  
Barbara Cacciari ◽  
...  
Keyword(s):  
Molecular Modeling ◽  
G Protein ◽  
Three Dimensional ◽  
G Protein Coupled Receptors ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
G Protein Coupled

Molecular Modeling of the Three-Dimensional Structure of Human Sphingomyelin Synthase

2011 ◽  
Vol 29 (8) ◽  
pp. 1567-1575 ◽  
Author(s):  
Ya Zhang ◽  
Fu Lin ◽  
Xiaodong Deng ◽  
Renxiao Wang ◽  
Deyong Ye
Keyword(s):  
Molecular Modeling ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Sphingomyelin Synthase

scholarly journals In Silico Characterization of Surface Glycoprotein [QHD43416] of Severe Acute Respiratory Syndrome-Coronavirus 2

2020 ◽  
Vol 3 (2) ◽  
pp. 32-36
Author(s):  
Rajneesh Prajapat ◽  
◽  
Suman Jain ◽  
Manish K Vaishnav ◽  
Sonal Sogani ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
In Silico ◽  
Three Dimensional ◽  
Surface Glycoprotein ◽  
Dimensional Structure ◽  
Model Quality ◽  
Core Section ◽  
Novel Coronavirus ◽  
And Function ◽  
Tools And Techniques

The novel coronavirus (SARS-CoV-2) reported from Wuhan, China, that spread rapidly and cause severe acute respiratory syndrome. The disease associated with infection of SARS-CoV-2 that is referred as COVID-19 (Coronavirus Disease 2019). In the present study, the surface glycoprotein [QHD43416] of SARS-CoV-2 was characterized for structure analysis and validation to provide information about its three-dimensional structure by using in silico tools and techniques. The surface glycoprotein [QHD43416] sequence of SARS-CoV-2 was retrieved from NCBI and its PDB file was designed by using phyre2 server. The RAMPAGE and UCLA-DOE (Verify 3D) was used for analysis and validation of structure model of protein. The model quality estimation based on the ProSA. Alignment of surface glycoprotein [QHD43416], revealed homology (72% identity) with spike protein of bat coronavirus [BM48-31/BGR/2008]. The model corresponding to probability conformation with 90.5% residue of core section, 9.1 % of allowed section and 0.4 % residue of outer section in φ-ψ plot, that specifies accuracy of prediction model. The Verify 3D results shows that 59.53% residues have average 3D-1D score >= 0.2 this determines compatibility of 3D model with its amino acid sequence (1D). ProSA Z-score -11.19 represents the good quality of the model. The structure and function of coronavirus surface glycoprotein could be predicted by in silico modeling studies. The protein model will be further used for designing of vaccine / drug development against coronavirus infection.

scholarly journals MECHANICAL CHARACTERISTICS FOR COMPOSITE MATERIALS USING COMMERCIAL EPOXY RESINS AND DIFFERENT FILLERS

2021 ◽  
Vol 56 (5) ◽  
pp. 179-185
Author(s):  
Omar A. Amin ◽  
S. A. Hassan ◽  
M. A. Sadek ◽  
M. A. Radwan ◽  
Hany A. Elazab
Keyword(s):  
Mechanical Properties ◽  
Epoxy Resin ◽  
Epoxy Resins ◽  
Three Dimensional ◽  
Mechanical Tests ◽  
Diglycidyl Ether ◽  
Dimensional Structure ◽  
Polymeric Chain ◽  
Hydroxyl Groups ◽  
Different Types

Epoxy resins are thermoset polymers that consist of epoxide groups in their molecular structure. It shows many attractive characteristics like strong adhesion, excellent mechanical strength, low shrinkage, excellent insulator, excellent chemical stability for acidic and basic environments, and microbial resistance due to the presence of hydroxyl groups and ether bonds and its three-dimensional structure. Many of these characteristics can be modified by adding strong bindings in the polymeric chain to give more improved characteristics. This research aims to prepare a composite material using epoxy resin and different types of fillers to achieve resistance to high kinetic energy impact. Experimental work is focused on preparing cured epoxy resin samples by using diglycidyl ether of bisphenol A (DGEBA) resin with tertiary amine as a hardener. In order to obtain different samples with different properties, we add different types of fillers, then mechanical tests are used to measure the mechanical properties of the samples. The results have proved that fiberglass is the best filler added to epoxy resins to improve its mechanical properties.

scholarly journals Three‐dimensional structure of the stator subunits of ATP synthase from ESR spin labeling restraints and molecular modeling

2007 ◽  
Vol 21 (5) ◽  
Author(s):  
John G. Wise ◽  
Oleg Volkov ◽  
Tarek Zaida ◽  
Tassilo Hornung ◽  
Eric J. Hustedt ◽  
...  
Keyword(s):  
Molecular Modeling ◽  
Atp Synthase ◽  
Three Dimensional ◽  
Spin Labeling ◽  
Dimensional Structure ◽  
Three Dimensional Structure

scholarly journals Analisis In-Silico Struktur Tiga Dimensi Reseptor Trk A dan Trk B Protein Neurotrophin 3 Pada Gallus gallus (Chicken)

2020 ◽  
Vol 12 (2) ◽  
pp. 78-84
Author(s):  
Muhammad F. Rahman ◽  
Amiruddin Kasim ◽  
Muchlis L. Djirimu ◽  
I. Made Budiarsa
Keyword(s):  
Amino Acids ◽  
In Silico ◽  
Three Dimensional ◽  
Gallus Gallus ◽  
Dimensional Structure ◽  
Neurotrophin 3 ◽  
Trk A ◽  
And Function ◽  
Trk B ◽  
Ucsf Chimera

NT3 protein is expressed by Neurotrophin 3 (NTF-3) which plays a role in the process of differentiation, survival of peripheral and neuropathological of neurons. The information of structure and function of NT-3 proteins is still very limited, especially in Gallus gallus. This study aims to predict the three-dimensional structure of the Trk A and Trk B proteins in Gallus gallus. The target protein obtained from the UniProt server with access codes Q91009 (Trk A) and Q91987 (Trk B) using the 6kzc 1.A (PDB ID) template was analyzed in silico through a homology approach and describing the structural assessment using Chimera UCSF software. The analysis showed that the Trk A protein had a QMEAN value of -0.08, composed of 778 amino acids, mass 87334.30 Daltons, and Seq Identity 79.93%. Trk B had a QMEAN value of 0.16, consisting of 818 amino acids, mass 91732.05 Daltons, and Seq Identity 84.30%. Key words: NT3; homology; UCSF chimera; G. gallus

scholarly journals Homology Modeling and Docking Studies of TMPRSS2 with Experimentally Known Inhibitors Camostat Mesylate, Nafamostat and Bromhexine Hydrochloride to Control SARS-Coronavirus-2

2020 ◽  
Author(s):  
Kailas Sonawane ◽  
Sagar S. Barale ◽  
Maruti J. Dhanavade ◽  
Shailesh R. Waghmare ◽  
Naiem H. Nadaf ◽  
...  
Keyword(s):  
Host Cell ◽  
Human Cell ◽  
Structural Information ◽  
Three Dimensional ◽  
Catalytic Triad ◽  
New Drugs ◽  
Dimensional Structure ◽  
Inhibition Mechanism ◽  
Global Public Health ◽  
Sars Coronavirus

The rapid outbreak of SARS-Coronavirus 2 (SARS-CoV-2) caused a serious global public health threat. The spike ‘S’ protein of SARS-CoV-2 and ACE2 of the host cell are being targeted to design and discover new drugs to control Covid-19 disease. Similarly, a transmembrane serine protease, TMPRSS2 of the host cell has been found to play a significant role in proteolytic cleavage of viral spike protein priming to the receptor ACE2 present in human cell. However, three dimensional structure and inhibition mechanism of TMPRSS2 is yet to be explored experimentally. Hence, in the present study we have generated a homology model of TMPRSS2 and studied its binding properties with experimentally studied inhibitors <i>viz.</i> Camostat mesylate, Nafamostat and Bromhexine hydrochloride (BHH) using molecular docking technique. Docking analysis revealed that the Camostat mesylate and its structural analogue Nafamostat interacts strongly with residues His296, Ser441 and Asp435 present in catalytic triad of TMPRSS2. However, BHH interacts with Gln438 and other residues present in the active site pocket of TMPRSS2 through hydrophobic contacts effectively. Thus, these results revealed the inhibition mechanism of TMPRSS2 by known inhibitors Camostat mesylate, Nafamostat and Bromhexine hydrochloride in detail at the molecular level. However, Camostat mesylate shows strong binding as compared to other two inhibitors. This structural information could also be useful to design and discover new inhibitors of TMPRSS2, which may be helpful to prevent the entry to SARS-Coronavirus 2 in human cell.

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