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Author(s):  
Debanjan Sen ◽  
Samhita Bhaumik ◽  
Gourav Roy ◽  
Ravikumar Muttineni ◽  
Rasbihari Hembram ◽  
...  

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly infectious and pathogenic virus. To date, there is a lack of proper medication against this virus, which has triggered the scientific community to find therapeutics. Searching of SARS-CoV-2 main protease inhibitors from anti-viral natural products based on traditional knowledge may be an effective approach. In this work, structure-based virtual screening of the compounds of Justicia adhatoda was performed against SARS-CoV-2 Mpro, followed by ADME filtration, molecular dynamics, and MMGBSA-based binding free energy calculation. On the basis of docking score, crucial interacting amino acid residues, molecular dynamics, and binding energy profile, three novel phenolic compounds JA_38b, JA_38c, and JA_39 were selected as potential binders against SARS-CoV-2 Mpro. This information may be used to develop potential therapeutics countermeasures against SARS-CoV-2 infection after in vitro and detailed pharmacological study.


Biomolecules ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 1329
Author(s):  
Cécilia Hognon ◽  
Emmanuelle Bignon ◽  
Guillaume Harle ◽  
Nadège Touche ◽  
Stéphanie Grandemange ◽  
...  

Maintaining iron homeostasis is fundamental for almost all living beings, and its deregulation correlates with severe and debilitating pathologies. The process is made more complicated by the omnipresence of iron and by its role as a fundamental component of a number of crucial metallo proteins. The response to modifications in the amount of the free-iron pool is performed via the inhibition of ferritin translation by sequestering consensus messenger RNA (mRNA) sequences. In turn, this is regulated by the iron-sensitive conformational equilibrium between cytosolic aconitase and IRP1, mediated by the presence of an iron–sulfur cluster. In this contribution, we analyze by full-atom molecular dynamics simulation, the factors leading to both the interaction with mRNA and the conformational transition. Furthermore, the role of the iron–sulfur cluster in driving the conformational transition is assessed by obtaining the related free energy profile via enhanced sampling molecular dynamics simulations.


2021 ◽  
Author(s):  
Ioannis Koskinas ◽  
Apostolos C. Tsolakis ◽  
Venizelos Venizelou ◽  
Dimosthenis Ioannidis ◽  
George E. Georghiou ◽  
...  

Energies ◽  
2021 ◽  
Vol 14 (17) ◽  
pp. 5445
Author(s):  
Simone Ferrari ◽  
Federica Zagarella ◽  
Paola Caputo ◽  
Giuliano Dall’O’

Assessing the existing building stock’s hourly energy demand and predicting its variation due to energy efficiency measures are fundamental for planning strategies towards renewable-based Smart Energy Systems. However, the need for accurate methods for this purpose in the literature arises. The present article describes a GIS-based procedure developed for estimating the energy demand profiles of urban buildings based on the definition of the volumetric consistency of a building stock, characterized by different ages of construction and the most widespread uses, as well as dynamic simulations of a set of Building Energy Models adopting different energy-related features. The simulation models are based on a simple Building Energy Concept where selected thermal zones, representative of different boundary conditions options, are accounted. By associating the simulated hourly energy density profiles to the geo-referenced building stock and to the surveyed thermal system types, the whole hourly energy profile is estimated for the considered area. The method was tested on the building stock of Milan (Italy) and validated with the data available from the annual energy balance of the city. This procedure could support energy planners in defining urban energy demand profiles for energy policy scenarios.


2021 ◽  
Vol 16 (4) ◽  
pp. 796-803
Author(s):  
Suci Zulaikha Hildayani ◽  
Muhamad Abdulkadir Martoprawiro ◽  
Yana Maolana Syah

Flavanones are one of the flavonoid group that has wide variety of applications such as a precursors in drug discovery. In the laboratory, flavanone is often synthesized from chalcone compounds. The conversion of chalcone to flavanone can be catalyzed by bronsted acid. The reaction mechanism for this process is proposed through the Michael addition reaction, however, the energetic details and the rate determining step for this reaction is not certainly known. This research aimed to investigate the reaction mechanism for chalcone-flavanone conversion with the present of bronsted acid as catalyst and also studied the effect of the solvent on the reaction energy profile with computational method. In this study, the modeling of the reaction mechanism for the said reaction was carried out using the DFT computational method with M06-2X functional. The computation was done both in the gas phase and in present of the solvent effect using the PCM models. The results showed that the mechanism of chalcone-flavanone conversion occurred in three steps which are protonation, cyclization, and then tautomerization. Based on these calculations, the rate determining step was the tautomerization reaction, which exhibited the same results with or without the solvent effects. Copyright © 2021 by Authors, Published by BCREC Group. This is an open access article under the CC BY-SA License (https://creativecommons.org/licenses/by-sa/4.0). 


2021 ◽  
Vol 3 (3) ◽  
pp. 135-148
Author(s):  
Nayana Shetty

For the purpose of high performance computation, several machines are developed at an exascale level. These machines can perform at least one exaflop calculations per second, which corresponds to a billion billon or 108. The universe and nature can be understood in a better manner while addressing certain challenging computational issues by using these machines. However, certain obstacles are faced by these machines. As huge quantity of components is encompassed in the exascale machines, frequent failure may be experienced and also the resilience may be challenging. High progress rate must be maintained for the applications by incorporating certain form of fault tolerance in the system. Power management has to be performed by incorporating the system in a parallel manner. All layers inclusive of fault tolerance layer must adhere to the power limitation in the system. Huge energy bills may be expected on installation of exascale machines due to the high power consumption. For various fault tolerance models, the energy profile must be analyzed. Parallel recovery, message-logging, and restart or checkpoint fault tolerance models for rollback recovery are evaluated in this paper. For execution with failure, the most energy efficient solution is provided by parallel recovery when programs with various programming models are used. The execution is performed faster with parallel recovery when compared to the other techniques. An analytical model is used for exploring these models and their behavior at extreme scales.


2021 ◽  
Author(s):  
Cecilia Hognon ◽  
Emmanuelle Bignon ◽  
Guillaume Harle ◽  
Nadege Touche ◽  
Stephanie Grandemange ◽  
...  

Maintaining iron homeostasis is fundamental for almost all living being, and its deregulation correlates with severe and debilitating pathologies. The process is made more complicated by the omnipresence of iron and by its role as a fundamental component of a number of crucial metallo proteins. The response to modifications in the amount of the free iron pool is performed via the inhibition of ferritin translation by sequestering consensus messenger RNA (mRNA) sequences. In turn this is regulated by the iron-sensitive conformational equilibrium between aconitase and IRP, mediated by the presence of an iron-sulfur cluster. In this contribution we analyze by full-atom molecular dynamics simulation, the factors leading to both the interaction with mRNA, and the conformational transition. Furthermore, the role of the iron-sulfur cluster in driving the confor-mational transition is assessed by obtaining the related free energy profile via enhanced sampling molecular dynamics simulations.


BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Ariadna Brito ◽  
Candice Merle ◽  
Pauline Lagarde ◽  
Benjamin Faustin ◽  
Anne Devin ◽  
...  

Abstract Background Cell-to-cell fusion is emerging as a key element of the metastatic process in various cancer types. We recently showed that hybrids made from the spontaneous merging of pre-malignant (IMR90 E6E7, i.e. E6E7) and malignant (IMR90 E6E7 RST, i.e. RST) mesenchymal cells recapitulate the main features of human undifferentiated pleomorphic sarcoma (UPS), with a highly rearranged genome and increased spreading capacities. To better characterize the intrinsic properties of these hybrids, we investigated here their metabolic energy profile compared to their parents. Results Our results unveiled that hybrids harbored a Warburg-like metabolism, like their RST counterparts. However, hybrids displayed a much greater metabolic activity, enhancing glycolysis to proliferate. Interestingly, modifying the metabolic environmental conditions through the use of 5-aminoimidazole-4-carbox-amide-1-β-D-ribofuranoside (AICAR), an activator of the 5′-adenosine monophosphate (AMP)-activated protein kinase (AMPK), specifically reduced the growth of hybrids, and also abrogated the invasive capacity of hybrids displaying enhanced glycolysis. Furthermore, AICAR efficiently blocked the tumoral features related to the aggressiveness of human UPS cell lines. Conclusion Altogether, our findings strongly suggest that hybrids rely on higher energy flux to proliferate and that a drug altering this metabolic equilibrium could impair their survival and be potentially considered as a novel therapeutic strategy.


2021 ◽  
Vol 15 ◽  
Author(s):  
Pundarikaksha Das ◽  
Venkata Satish Kumar Mattaparthi

Background: The Murine Double Minute 2 (MDM2) protein is a well-studied primary negative regulator of the tumor suppressor p53 molecule. Therefore, nowadays, many research studies have focused on the inhibition of MDM2 with potent inhibitors. Idasanutlin (RG7388) is a well-studied small molecule, the antagonist of MDM2 with potential antineoplastic activity. Nevertheless, the highly significant information about the free energy profile, intermediates, and the association of receptor and ligand components in the MDM2-idasanutlin complex remains unclear. Objective: To study the free energy profile of the MDM2-idasanutlin complex in terms of the Potential of Mean Force (PMF) method. Method: We have used the PMF method coupled with umbrella sampling simulations to generate the free energy profile for the association of N-Terminal Domain (NTD) of MDM2 and idasanutlin and a specific reaction coordinate for identifying transition states, intermediates as well as the relative stabilities of the endpoints. We have also determined the binding characteristics and interacting residues at the interface of the MDM2-idasanutlin complex from the Binding Free Energy (BFE) and Per Residue Energy Decomposition (PRED) analyses. Results: The PMF minima for the MDM2-idasanutlin complex was observed at a center of mass (CoM) distance of separation of 11 Å with dissociation energy of 17.5 kcal mol-1. As a function of the distance of separation of MDM2 from idasanutlin. We also studied the conformational dynamics and stability of the NTD of MDM2. We found a high binding affinity between MDM2 and idasanutlin (∆Grinding = -3.19 kcal mol-1). We found that in MDM2, the residues MET54, VAL67, and LEU58 provide the highest energy input for the interaction between MDM2 and idasanutlin. Conclusion: Our results in this study illustrate the significant structural and binding features of the MDM2-idasanutlin complex that may be useful in developing potent inhibitors of MDM2.


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