Structure-Based Virtual Screening Reveals Ibrutinib and Zanubrutinib as Potential Repurposed Drugs against COVID-19

Coronavirus disease (COVID)-19 is the leading global health threat to date caused by a severe acute respiratory syndrome coronavirus (SARS-CoV-2). Recent clinical trials reported that the use of Bruton’s tyrosine kinase (BTK) inhibitors to treat COVID-19 patients could reduce dyspnea and hypoxia, thromboinflammation, hypercoagulability and improve oxygenation. However, the mechanism of action remains unclear. Thus, this study employs structure-based virtual screening (SBVS) to repurpose BTK inhibitors acalabrutinib, dasatinib, evobrutinib, fostamatinib, ibrutinib, inositol 1,3,4,5-tetrakisphosphate, spebrutinib, XL418 and zanubrutinib against SARS-CoV-2. Molecular docking is conducted with BTK inhibitors against structural and nonstructural proteins of SARS-CoV-2 and host targets (ACE2, TMPRSS2 and BTK). Molecular mechanics-generalized Born surface area (MM/GBSA) calculations and molecular dynamics (MD) simulations are then carried out on the selected complexes with high binding energy. Ibrutinib and zanubrutinib are found to be the most potent of the drugs screened based on the results of computational studies. Results further show that ibrutinib and zanubrutinib could exploit different mechanisms at the viral entry and replication stage and could be repurposed as potential inhibitors of SARS-CoV-2 pathogenesis.

Spectroscopic evidence of superconductivity pairing at 83 K in single-layer FeSe/SrTiO3 films

Single-layer FeSe films grown on the SrTiO3 substrate (FeSe/STO) have attracted much attention because of their possible record-high superconducting critical temperature (Tc) and distinct electronic structures. However, it has been under debate on how high its Tc can really reach due to the inconsistency of the results from different measurements. Here we report spectroscopic evidence of superconductivity pairing at 83 K in single-layer FeSe/STO films. By preparing high-quality single-layer FeSe/STO films, we observe strong superconductivity-induced Bogoliubov back-bending bands that extend to rather high binding energy ~ 100 meV by high-resolution angle-resolved photoemission measurements. They provide a new definitive benchmark of superconductivity pairing that is directly observed up to 83 K. Moreover, we find that the pairing state can be further divided into two temperature regions. These results indicate that either Tc as high as 83 K is achievable, or there is a pseudogap formation from superconductivity fluctuation in single-layer FeSe/STO films.

Synthesis, molecular docking calculation, fluorescence and bioimaging of mitochondria-targeted ratiometric fluorescent probes for sensing hypochlorite in vivo

A novel mitochondria-targeted ratio fluorescent probe Mi-OCl-RP was constructed. High binding energy may explain the mitochondria selectivity of the probe. The probe has excellent spectral properties and as a robust tool for monitoring OCl−in vivo.

Boron “gluing” nitrogen heteroatoms in a prepolymerized ionic liquid-based carbon scaffold for durable supercapacitive activity

Doped boron atoms are bridged to glue more electroactive nitrogen sites on the carbon surface, and the high binding energy of the consequent B–C bonds further consolidates the porous carbon scaffold for durable ion/electron transfer.

The Influence of Calcium toward Order/Disorder Conformation of Repeat-in-Toxin (RTX) Structure of Family I.3 Lipase from Pseudomonas fluorescens AMS8

Calcium-binding plays a decisive role in the folding and stabilization of many RTX proteins, especially for the RTX domain. Although many studies have been conducted to prove the contribution of Ca2+ ion toward the folding and stabilization of RTX proteins, its functional dynamics and conformational structural changes remain elusive. Here, molecular docking and molecular dynamics (MD) simulations were performed to analyze the contribution of Ca2+ ion toward the folding and stabilization of the RTX lipase (AMS8 lipase) structure. AMS8 lipase contains six Ca2+ ions (Ca1–Ca6). Three Ca2+ ions (Ca3, Ca4, and Ca5) were bound to the RTX parallel β-roll motif repeat structure (RTX domain). The metal ion (Ca2+) docking analysis gives a high binding energy, especially for Ca4 and Ca5 which are tightly bound to the RTX domain. The function of each Ca2+ ion is further analyzed using the MD simulation. The removal of Ca3, Ca4, and Ca5 caused the AMS8 lipase structure to become unstable and unfolded. The results suggested that Ca3, Ca4, and Ca5 stabilized the RTX domain. In conclusion, Ca3, Ca4, and Ca5 play a crucial role in the folding and stabilization of the RTX domain, which sustain the integrity of the overall AMS8 lipase structure.

In-Silico Molecular Docking Show Mitocurcumin can Potentially Block Innate Immune Evasion Mechanism of SARS-CoV-2 and Enhance Viral Load Clearance

In the present work, we have employed a molecular docking approach to study the ability of mitocurcumin (MC), a triphenyl phosphonium conjugated curcumin derivative, to inhibit SARS-CoV-2 infection. Computational analysis revealed that MC can bind strongly to SARS-CoV-2 ADP Ribose Phosphatase (NSP3) with high binding energy of -10.3 kcal/mol and to SARS-CoV-2 methyltransferase (NSP10-NSP16 complex) with a high binding energy of -10.4 kcal/mol. We found that MC interacts with critical residues of viral NSP3 macro-domain, known to suppress host immune response, through hydrophobic interactions and occupies its active site. Furthermore, MC interacts with the critical residues of NSP10-NSP16 complex, known to prevent innate immune detection of viral mRNA, through hydrophobic and hydrogen bond interaction and occupies the methyl group donor site. MC is also found to bind to main protease of SARS-CoV-2 and may potentially act as an inhibitor of the viral protease. In conclusion, MC can potentially inhibit the activity of multiple SARS-CoV-2 proteins and may accentuate the innate immune system mediated clearance of viral load resulting in improved clinic outcome in COVID-19 patients.

In-Silico Molecular Docking Show Mitocurcumin can Potentially Block Innate Immune Evasion Mechanism of SARS-CoV-2 and Enhance Viral Load Clearance

In the present work, we have employed a molecular docking approach to study the ability of mitocurcumin (MC), a triphenyl phosphonium conjugated curcumin derivative, to inhibit SARS-CoV-2 infection. Computational analysis revealed that MC can bind strongly to SARS-CoV-2 ADP Ribose Phosphatase (NSP3) with high binding energy of -10.3 kcal/mol and to SARS-CoV-2 methyltransferase (NSP10-NSP16 complex) with a high binding energy of -10.4 kcal/mol. We found that MC interacts with critical residues of viral NSP3 macro-domain, known to suppress host immune response, through hydrophobic interactions and occupies its active site. Furthermore, MC interacts with the critical residues of NSP10-NSP16 complex, known to prevent innate immune detection of viral mRNA, through hydrophobic and hydrogen bond interaction and occupies the methyl group donor site. MC is also found to bind to main protease of SARS-CoV-2 and may potentially act as an inhibitor of the viral protease. In conclusion, MC can potentially inhibit the activity of multiple SARS-CoV-2 proteins and may accentuate the innate immune system mediated clearance of viral load resulting in improved clinic outcome in COVID-19 patients.

IN Silico Approach of Some Selected Honey Constituents as SARS-CoV-2 Main Protease (COVID-19) Inhibitors

<p>The huge attack of coronavirus disease 2019 (COVID-19) over all the world forces the researcher around the world to study the crystal structure of the main protease M^pro ( 3-chymotrypsin-like cysteine enzyme) which is the essential enzyme for coronavirus processing the polyproteins and its life cycles. And by the way, the inhibition of this enzyme active site becomes the target of all scientists of drug discovery in order to overcome this disease. In this study, we have used the molecular modeling approach to evaluate the activity of different active compounds from honeybee and propolis to inhibit the presented sars-cov-2 main protease via Schrödinger Maestro v10.1. the presented study resulted in six main compounds possess high binding energy with the receptor active site of COVID-19 main protease. we hope this study being the way for honeybee constitution as an effective ligand for sars-cov-2 main protease inhibition and be in the medicinal study of anti-COVID-19 therapeutic drugs.</p>

IN Silico Approach of Some Selected Honey Constituents as SARS-CoV-2 Main Protease (COVID-19) Inhibitors

<p>The huge attack of coronavirus disease 2019 (COVID-19) over all the world forces the researcher around the world to study the crystal structure of the main protease M^pro ( 3-chymotrypsin-like cysteine enzyme) which is the essential enzyme for coronavirus processing the polyproteins and its life cycles. And by the way, the inhibition of this enzyme active site becomes the target of all scientists of drug discovery in order to overcome this disease. In this study, we have used the molecular modeling approach to evaluate the activity of different active compounds from honeybee and propolis to inhibit the presented sars-cov-2 main protease via Schrödinger Maestro v10.1. the presented study resulted in six main compounds possess high binding energy with the receptor active site of COVID-19 main protease. we hope this study being the way for honeybee constitution as an effective ligand for sars-cov-2 main protease inhibition and be in the medicinal study of anti-COVID-19 therapeutic drugs.</p>

IN Silico Approach of Some Selected Honey Constituents as SARS-CoV-2 Main Protease (COVID-19) Inhibitors

<p>The huge attack of coronavirus disease 2019 (COVID-19) over all the world forces the researcher around the world to study the crystal structure of the main protease M^pro ( 3-chymotrypsin-like cysteine enzyme) which is the essential enzyme for coronavirus processing the polyproteins and its life cycles. And by the way, the inhibition of this enzyme active site becomes the target of all scientists of drug discovery in order to overcome this disease. In this study, we have used the molecular modeling approach to evaluate the activity of different active compounds from honeybee and propolis to inhibit the presented sars-cov-2 main protease via Schrödinger Maestro v10.1. the presented study resulted in six main compounds possess high binding energy with the receptor active site of COVID-19 main protease. we hope this study being the way for honeybee constitution as an effective ligand for sars-cov-2 main protease inhibition and be in the medicinal study of anti-COVID-19 therapeutic drugs.</p>