scholarly journals Study of SARS-nCOV2 Indian isolates gaining insights into mutation frequencies, protein stability and prospective effect on its pathogenicity

Coronaviruses ◽  
2021 ◽  
Vol 02 ◽  
Author(s):  
Akshay Uttarkar ◽  
Vidya Niranjan ◽  
Shivam Pandit ◽  
Srividya Subash
Keyword(s):  
Protein Stability ◽  
Drug Binding ◽  
Spike Glycoprotein ◽  
Genomic Variations ◽  
3C Protease ◽  
Binding Pockets ◽  
Mutation Pattern ◽  
The Will ◽  
Host Jumping ◽  
The Impact

Background: SARS-nCOV-2 is a variant of the known SARS coronavirus family. The mutations in viruses are very rapid and can play a crucial role in the evolution or devolution of the organism. This has a direct impact on “host jumping” and pathogenicity of the virus. Objective: The study aims to understand the frequency of genomic variations that have occurred in the virus affecting the Indian sub-population. The impact of variations translating to proteins and its consequences affecting protein stability and interaction were studied. Method: Phylogenetic analysis of the 140 genomes from the India region was performed, followed by SNP and Indel analysis of both CDS and non-CDS regions. This effort was followed by a prediction of mutations occurring in 8 proteins of interest and the impact on protein stability and prospective drug interactions. Results: Genomes showed variability in origin, and major branches can be mapped to the 2002 outbreak of SARS. The mutation frequency in CDS regions showed that 241 C >T, 3037 C >T, 2836 C >T, and 6312 C >A occurred in 81.5 % of genomes mapping to major genes. Corresponding mutations were mapped to protein sequences. The effect of mutations occurring in spike glycoprotein, RNA dependent RNA polymerase, nsp8, nucleocapsid and 3c protease were also mapped. Conclusion: Whilst the mutations in spike glycoprotein showcased an increase in protein stability, the residues undergoing mutations were also a part of drug binding pockets for hydroxychloroquine. Mutations occurring in other proteins of interest were leading to a decrease in protein stability. The mutations were also a part of drug binding pockets for Favipiravir, Remdesivir and Dexamethasone. The work promotes the will to analyse larger datasets to understand mutation pattern globally.

A First Step towards a Tribological Approach to Investigate Cutting Tool Wear

2014 ◽  
Vol 611-612 ◽  
pp. 452-459 ◽  
Author(s):  
Giovenco Axel ◽  
Frédéric Valiorgue ◽  
Cédric Courbon ◽  
Joël Rech ◽  
Ugo Masciantonio
Keyword(s):  
Tool Wear ◽  
Cutting Tool ◽  
304L Stainless Steel ◽  
Fe Modelling ◽  
Wear Model ◽  
Cutting Tool Wear ◽  
The Will ◽  
Preliminary Study ◽  
The Impact ◽  
Macroscopic Parameters

The present work is motivated by the will to improve Finite Element (FE) Modelling of cutting tool wear. As a first step, the characterisation of wear mechanisms and identification of a wear model appear to be fundamental. The key idea of this work consists in using a dedicated tribometer, able to simulate relevant tribological conditions encountered in cutting (pressure, velocity). The tribometer can be used to estimate the evolution of wear versus time for various tribological conditions (pressure, velocity, temperature). Based on this design of experiments, it becomes possible to identify analytically a wear model. As a preliminary study this paper will be focused on the impact of sliding speed at the contact interface between 304L stainless steel and tungsten carbide (WC) coated with titanium nitride (TiN) pin. This experiment enables to observe a modification of wear phenomena between sliding speeds of 60 m/min and 180 m/min. Finally, the impact on macroscopic parameters has been observed.

scholarly journals INPS: predicting the impact of non-synonymous variations on protein stability from sequence

2015 ◽  
Vol 31 (17) ◽  
pp. 2816-2821 ◽  
Author(s):  
Piero Fariselli ◽  
Pier Luigi Martelli ◽  
Castrense Savojardo ◽  
Rita Casadio
Keyword(s):  
Protein Stability ◽  
The Impact

scholarly journals Engineered disulfide bonds in recombinant human interferon-γ: the impact of the N-terminal helix A and the AB-loop on protein stability

1996 ◽  
Vol 9 (10) ◽  
pp. 905-912 ◽  
Author(s):  
Gero Waschütza ◽  
Volkhart Li ◽  
Thomas Schäfer ◽  
Dietmar Schomburg ◽  
Carmen Villmann ◽  
...  
Keyword(s):  
Protein Stability ◽  
Disulfide Bonds ◽  
Interferon Γ ◽  
Human Interferon ◽  
The Impact

scholarly journals Structure-based inhibitor design of mutant RAS proteins—a paradigm shift

2020 ◽  
Vol 39 (4) ◽  
pp. 1091-1105
Author(s):  
Kinga Nyíri ◽  
Gergely Koppány ◽  
Beáta G. Vértessy
Keyword(s):  
Covalent Modification ◽  
Small Gtpase ◽  
Drug Binding ◽  
Ras Proteins ◽  
Structure Based Drug Design ◽  
Lung Cancers ◽  
Long Time ◽  
Binding Pockets ◽  
Cancer Types ◽  
Kras Protein

AbstractAs a member of small GTPase family, KRAS protein is a key physiological modulator of various cellular activities including proliferation. However, mutations of KRAS present in numerous cancer types, most frequently in pancreatic (> 60%), colorectal (> 40%), and lung cancers, drive oncogenic processes through overactivation of proliferation. The G12C mutation of KRAS protein is especially abundant in the case of these types of malignancies. Despite its key importance in human disease, KRAS was assumed to be non-druggable for a long time since the protein seemingly lacks potential drug-binding pockets except the nucleotide-binding site, which is difficult to be targeted due to the high affinity of KRAS for both GDP and GTP. Recently, a new approach broke the ice and provided evidence that upon covalent targeting of the G12C mutant KRAS, a highly dynamic pocket was revealed. This novel targeting is especially important since it serves with an inherent solution for drug selectivity. Based on these results, various structure-based drug design projects have been launched to develop selective KRAS mutant inhibitors. In addition to the covalent modification strategy mostly applicable for G12C mutation, different innovative solutions have been suggested for the other frequently occurring oncogenic G12 mutants. Here we summarize the latest advances of this field, provide perspectives for novel approaches, and highlight the special properties of KRAS, which might issue some new challenges.

scholarly journals Effective Inhibition of SARS-CoV-2 Entry by Heparin and Enoxaparin Derivatives

2020 ◽  
Author(s):  
Ritesh Tandon ◽  
Joshua S. Sharp ◽  
Fuming Zhang ◽  
Vitor H. Pomin ◽  
Nicole M. Ashpole ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Heparan Sulfate ◽  
Mammalian Cells ◽  
Sulfated Polysaccharides ◽  
Transduction Efficiency ◽  
Pseudotyped Virus ◽  
Spike Glycoprotein ◽  
Viral Activity ◽  
Recent Emergence ◽  
The Impact

Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) has caused a pandemic of historic proportions and continues to spread globally, with enormous consequences to human health. Currently there is no vaccine, effective therapeutic or prophylactic. Like other betacoronaviruses, attachment and entry of SARS-CoV-2 is mediated by the spike glycoprotein (SGP). In addition to its well-documented interaction with its receptor, human angiotensin converting enzyme 2 (hACE2), SGP has been found to bind to glycosaminoglycans like heparan sulfate, which is found on the surface of virtually all mammalian cells. Here, we pseudotyped SARS-CoV-2 SGP on a third generation lentiviral (pLV) vector and tested the impact of various sulfated polysaccharides on transduction efficiency in mammalian cells. The pLV vector pseudotyped SGP efficiently and produced high titers on HEK293T cells. Various sulfated polysaccharides potently neutralized pLV-S pseudotyped virus with clear structure-based differences in anti-viral activity and affinity to SGP. Concentration-response curves showed that pLV-S particles were efficiently neutralized by a range of concentrations of unfractionated heparin (UFH), enoxaparin, 6-O-desulfated UFH and 6-O-desulfated enoxaparin with an IC50 of 5.99 μg/L, 1.08 mg/L, 1.77 μg/L, and 5.86 mg/L respectively. In summary, several sulfated polysaccharides show potent anti-SARS-CoV-2 activity and can be developed for prophylactic as well as therapeutic purposes. Importance The recent emergence of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) in Wuhan, China in late 2019 and its subsequent spread to the rest of the world has created a pandemic situation unprecedented in modern history. While ACE2 has been identified as the viral receptor, cellular polysaccharides have also been implicated in virus entry. The SARS-CoV-2 spike glycoprotein (SGP) binds to glycosaminoglycans like heparan sulfate, which is found on the surface of virtually all mammalian cells. Here, we report structure-based differences in anti-viral activity and affinity to SGP for several sulfated polysaccharides, including both well-characterized FDA-approved drugs and novel marine sulfated polysaccharides, which can be developed for prophylactic as well as therapeutic purposes.

scholarly journals Multidrug Resistance in Neisseria gonorrhoeae: Identification of Functionally Important Residues in the MtrD Efflux Protein

mBio ◽  
2019 ◽  
Vol 10 (6) ◽  
Author(s):  
Mohsen Chitsaz ◽  
Lauren Booth ◽  
Mitchell T. Blyth ◽  
Megan L. O’Mara ◽  
Melissa H. Brown
Keyword(s):  
Molecular Dynamics ◽  
Multidrug Resistance ◽  
Neisseria Gonorrhoeae ◽  
Molecular Dynamics Simulations ◽  
Docking Studies ◽  
Drug Binding ◽  
Multidrug Efflux ◽  
Content Type ◽  
Binding Pockets ◽  
Dynamics Simulations

ABSTRACT A key mechanism that Neisseria gonorrhoeae uses to achieve multidrug resistance is the expulsion of structurally different antimicrobials by the MtrD multidrug efflux protein. MtrD resembles the homologous Escherichia coli AcrB efflux protein with several common structural features, including an open cleft containing putative access and deep binding pockets proposed to interact with substrates. A highly discriminating N. gonorrhoeae strain, with the MtrD and NorM multidrug efflux pumps inactivated, was constructed and used to confirm and extend the substrate profile of MtrD to include 14 new compounds. The structural basis of substrate interactions with MtrD was interrogated by a combination of long-timescale molecular dynamics simulations and docking studies together with site-directed mutagenesis of selected residues. Of the MtrD mutants generated, only one (S611A) retained a wild-type (WT) resistance profile, while others (F136A, F176A, I605A, F610A, F612C, and F623C) showed reduced resistance to different antimicrobial compounds. Docking studies of eight MtrD substrates confirmed that many of the mutated residues play important nonspecific roles in binding to these substrates. Long-timescale molecular dynamics simulations of MtrD with its substrate progesterone showed the spontaneous binding of the substrate to the access pocket of the binding cleft and its subsequent penetration into the deep binding pocket, allowing the permeation pathway for a substrate through this important resistance mechanism to be identified. These findings provide a detailed picture of the interaction of MtrD with substrates that can be used as a basis for rational antibiotic and inhibitor design. IMPORTANCE With over 78 million new infections globally each year, gonorrhea remains a frustratingly common infection. Continuous development and spread of antimicrobial-resistant strains of Neisseria gonorrhoeae, the causative agent of gonorrhea, have posed a serious threat to public health. One of the mechanisms in N. gonorrhoeae involved in resistance to multiple drugs is performed by the MtrD multidrug resistance efflux pump. This study demonstrated that the MtrD pump has a broader substrate specificity than previously proposed and identified a cluster of residues important for drug binding and translocation. Additionally, a permeation pathway for the MtrD substrate progesterone actively moving through the protein was determined, revealing key interactions within the putative MtrD drug binding pockets. Identification of functionally important residues and substrate-protein interactions of the MtrD protein is crucial to develop future strategies for the treatment of multidrug-resistant gonorrhea.

scholarly journals Structural Basis of Enantioselective Inhibition of Cyclooxygenase-1 by S-α-Substituted Indomethacin Ethanolamides

2007 ◽  
Vol 282 (38) ◽  
pp. 28096-28105 ◽  
Author(s):  
Christine A. Harman ◽  
Melissa V. Turman ◽  
Kevin R. Kozak ◽  
Lawrence J. Marnett ◽  
William L. Smith ◽  
...  
Keyword(s):  
Binding Pocket ◽  
Drug Binding ◽  
Structural Basis ◽  
Cyclooxygenase 1 ◽  
Cox 2 ◽  
The Impact ◽  
First Time ◽  
Side Pocket ◽  
Cox 1 ◽  
Equal Efficacy

The modification of the nonselective nonsteroidal anti-inflammatory drug, indomethacin, by amidation presents a promising strategy for designing novel cyclooxygenase (COX)-2-selective inhibitors. A series of α-substituted indomethacin ethanolamides, which exist as R/S-enantiomeric pairs, provides a means to study the impact of stereochemistry on COX inhibition. Comparative studies revealed that the R- and S-enantiomers of the α-substituted analogs inhibit COX-2 with almost equal efficacy, whereas COX-1 is selectively inhibited by the S-enantiomers. Mutagenesis studies have not been able to identify residues that manifest the enantioselectivity in COX-1. In an effort to understand the structural impact of chirality on COX-1 selectivity, the crystal structures of ovine COX-1 in complexes with an enantiomeric pair of these indomethacin ethanolamides were determined at resolutions between 2.75 and 2.85Å. These structures reveal unique, enantiomer-selective interactions within the COX-1 side pocket region that stabilize drug binding and account for the chiral selectivity observed with the (S)-α-substituted indomethacin ethanolamides. Kinetic analysis of binding demonstrates that both inhibitors bind quickly utilizing a two-step mechanism. However, the second binding step is readily reversible for the R-enantiomer, whereas for the S-enantiomer, it is not. These studies establish for the first time the structural and kinetic basis of high affinity binding of a neutral inhibitor to COX-1 and demonstrate that the side pocket of COX-1, previously thought to be sterically inaccessible, can serve as a binding pocket for inhibitor association.

scholarly journals You Win Some, You Lose Some: Pension Reform in Bachelet’s First and Second Administrations

2019 ◽  
Vol 11 (2) ◽  
pp. 204-230 ◽  
Author(s):  
Silvia Borzutzky
Keyword(s):  
Political Ideology ◽  
Pension System ◽  
Pension Reform ◽  
Presidential Power ◽  
Pension Policy ◽  
The Will ◽  
The Government ◽  
The Impact ◽  
Government Coalition

This article analyses and compares President Bachelet’s successful efforts to reform the Chilean pension system in 2008 and her failure to achieve the same objective in 2017. The article addresses the impact of electoral promises, policy legacies, policy ideology, presidential power, the role of the private sector, and the role that the government coalitions had in the process of pension reform during the Bachelet administrations. We argue that the 2008 reform was possible because of Bachelet’s personal commitment to reform and the presence of a stable governing coalition that had the will and capacity to legislate. In the second administration, although the policy legacies and ideology had remained the same, the reform did not materialise due to intense conflict within the administration and within the government coalition, as well as conflict between the administration and the coalition. These conflicts, in turn, generated a vicious cycle responsible for Bachelet’s declining popularity, limited political capital, and reduced support for reform. A stagnant economy further undermined these efforts. In brief, this article argues that when assessing success and failure in pension policy reform it is important to analyse not only policy legacies and political ideology but also the strength of the executive, the cohesion of the governing coalition, and the country’s economic performance.

Sign in / Sign up

Export Citation Format

Share Document