Cardoso, Wesley B Mendanha, Sebastião A
Published in
Journal of molecular structure
In this paper we investigate 10 different HIV protease inhibitors (HPIs) as possible repurposed-drugs candidates against SARS-CoV-2. To this end, we execute molecular docking and molecular dynamics simulations. The in silico data demonstrated that, despite their molecular differences, all HPIs presented a similar behavior for the parameters analyze...
Sankhe, Runali Rathi, Ekta Manandhar, Suman Kumar, Avinash Pai, Sreedhara Ranganath K Kini, Suvarna G Kishore, Anoop
Published in
Journal of molecular structure
Neprilysin (NEP) is a neutral endopeptidase with diverse physiological roles in the body. NEP's role in degradation of diverse classes of peptides such as amyloid beta, natriuretic peptide, substance P, angiotensin, endothelins, etc., is associated with pathologies of alzheimer's, kidney and heart diseases, obesity, diabetes and certain malignancie...
Pei, Qing-Xiang Sorkin, Viacheslav Liu, Ping Zhong, Yucheng Thitsartarn, Warintorn He, Chaobin Zhang, Yong-Wei
Published in
Journal of Polymer Research
We investigate the mechanical behavior of polypropylene/silica composites under mode I and II loading by using molecular dynamics simulations, focusing on the effects of two typical surface coupling agents of HMDZ and APTES on the interface deformation and failure. It is found that under mode I loading, the silica surface functionalized with APTES ...
Sharn, Hari Om Singh, Dev Bukhsh Singh, Satendra
Published in
In Silico Pharmacology
Bordetella pertussis and Bordetella parapertussis are Gram-negative, aerobic, and pathogenic bacteria and cause pertussis disease (whooping cough) in humans. Genomic island analysis indicated the presence of an important protein bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase (BMD/MC) in both B. pertussi...
Rai, Sumit Kumar Pathak, Rajesh Kumar Singh, Dev Bukhsh Bhatt, Arun Baunthiyal, Mamta
Published in
In Silico Pharmacology
Glaucoma, the most perilous disease leading to blindness is a result of optical neuropathy. Accumulation of aqueous humor in the posterior chamber due to a large difference in the rate of formation and its drainage in the anterior chamber causes an increase in intraocular pressure (IOP) leading to damage of nerve cells. A literature survey has reve...
Ibrahim, Mahmoud A. A. Abdelrahman, Alaa H. M. Allemailem, Khaled S. Almatroudi, Ahmad Moustafa, Mahmoud F. Hegazy, Mohamed-Elamir F.
Published in
The Protein Journal
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a recently emanating human infectious coronavirus that causes COVID-19 disease. On 11th March 2020, it has been announced as a pandemic by the World Health Organization (WHO). Recently, several repositioned drugs have been subjected to clinical investigations as anti-COVID-19 drugs. He...
Hu, Weidong Bhattacharya, Supriyo Hong, Teresa Wong, Patty Li, Lin Vaidehi, Nagarajan Kalkum, Markus Shively, John E
Published in
Biochimica et biophysica acta. Biomembranes
AIIt, a heterotetramer of S100A10 (P11) and Annexin A2, plays a key role in calcium dependent, membrane associations with a variety of proteins. We previously showed that AIIt interacts with the short cytoplasmic domain (12 amino acids) of CEACAM1 (CEACAM1-SF). Since the cytoplasmic domains of CEACAM1 help regulate the formation of cis- or trans-di...
Minicozzi, Velia Di Venere, Almerinda Nicolai, Eleonora Giuliani, Alessandro Caccuri, Anna Maria Di Paola, Luisa Mei, Giampiero
Published in
Journal of biomolecular structure & dynamics
The oligomeric state of TRAF2 (tumor necrosis factor-receptor associated factor 2), a TNF (tumor necrosis factor) receptor-associated factor, is crucial for membrane binding and probably plays a fundamental role in regulating the protein function in vivo. In this study we have combined molecular dynamics with the protein contact network approach to...
Claverie, Jérôme Kamali-Bernard, Siham Bernard, João Manuel Marques Cordeiro Fa...
The two most common polymorphs in industrial alite, $M_1$ and $M_3$, were characterized at the molecular scale. Different methods were employed and discussed to assess mechanical properties and specific heat of both polymorphs. The calculated homogenized elastic moduli and specific heat were found in good agreement with experimental measurements. A...
Priest, Chad VanGordon, Monika R Rempe, Caroline Chaudhari, Mangesh I Stevens, Mark J Rick, Steve Rempe, Susan B
Published in
Methods in molecular biology (Clifton, N.J.)
Umbrella sampling, coupled with a weighted histogram analysis method (US-WHAM), can be used to construct potentials of mean force (PMFs) for studying the complex ion permeation pathways of membrane transport proteins. Despite the widespread use of US-WHAM, obtaining a physically meaningful PMF can be challenging. Here, we provide a protocol to reso...
