scholarly journals In vitro study of Hesperetin and Hesperidin as inhibitors of zika and chikungunya virus proteases

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0246319
Author(s):  
Raphael J. Eberle ◽  
Danilo S. Olivier ◽  
Carolina C. Pacca ◽  
Clarita M. S. Avilla ◽  
Mauricio L. Nogueira ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Chikungunya Virus ◽  
In Vitro Study ◽  
3D Models ◽  
Binding Pocket ◽  
Starting Point ◽  
Low Cytotoxicity ◽  
Inhibitory Potential ◽  
Dynamics Simulations

The potential outcome of flavivirus and alphavirus co-infections is worrisome due to the development of severe diseases. Hundreds of millions of people worldwide live under the risk of infections caused by viruses like chikungunya virus (CHIKV, genus Alphavirus), dengue virus (DENV, genus Flavivirus), and zika virus (ZIKV, genus Flavivirus). So far, neither any drug exists against the infection by a single virus, nor against co-infection. The results described in our study demonstrate the inhibitory potential of two flavonoids derived from citrus plants: Hesperetin (HST) against NS2B/NS3pro of ZIKV and nsP2pro of CHIKV and, Hesperidin (HSD) against nsP2pro of CHIKV. The flavonoids are noncompetitive inhibitors and the determined IC50 values are in low µM range for HST against ZIKV NS2B/NS3pro (12.6 ± 1.3 µM) and against CHIKV nsP2pro (2.5 ± 0.4 µM). The IC50 for HSD against CHIKV nsP2pro was 7.1 ± 1.1 µM. The calculated ligand efficiencies for HST were > 0.3, which reflect its potential to be used as a lead compound. Docking and molecular dynamics simulations display the effect of HST and HSD on the protease 3D models of CHIKV and ZIKV. Conformational changes after ligand binding and their effect on the substrate-binding pocket of the proteases were investigated. Additionally, MTT assays demonstrated a very low cytotoxicity of both the molecules. Based on our results, we assume that HST comprise a chemical structure that serves as a starting point molecule to develop a potent inhibitor to combat CHIKV and ZIKV co-infections by inhibiting the virus proteases.

scholarly journals The Repurposed Drugs Suramin and Quinacrine Cooperatively Inhibit SARS-CoV-2 3CLpro In Vitro

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 873
Author(s):  
Raphael J. Eberle ◽  
Danilo S. Olivier ◽  
Marcos S. Amaral ◽  
Ian Gering ◽  
Dieter Willbold ◽  
...  
Keyword(s):  
Binding Mode ◽  
Drug Candidates ◽  
Main Protease ◽  
Ic50 Values ◽  
Repurposed Drugs ◽  
Antiparasitic Drugs ◽  
Inhibitory Potential ◽  
Dynamics Simulations ◽  
Micromolar Range

Since the first report of a new pneumonia disease in December 2019 (Wuhan, China) the WHO reported more than 148 million confirmed cases and 3.1 million losses globally up to now. The causative agent of COVID-19 (SARS-CoV-2) has spread worldwide, resulting in a pandemic of unprecedented magnitude. To date, several clinically safe and efficient vaccines (e.g., Pfizer-BioNTech, Moderna, Johnson & Johnson, and AstraZeneca COVID-19 vaccines) as well as drugs for emergency use have been approved. However, increasing numbers of SARS-Cov-2 variants make it imminent to identify an alternative way to treat SARS-CoV-2 infections. A well-known strategy to identify molecules with inhibitory potential against SARS-CoV-2 proteins is repurposing clinically developed drugs, e.g., antiparasitic drugs. The results described in this study demonstrated the inhibitory potential of quinacrine and suramin against SARS-CoV-2 main protease (3CLpro). Quinacrine and suramin molecules presented a competitive and noncompetitive inhibition mode, respectively, with IC50 values in the low micromolar range. Surface plasmon resonance (SPR) experiments demonstrated that quinacrine and suramin alone possessed a moderate or weak affinity with SARS-CoV-2 3CLpro but suramin binding increased quinacrine interaction by around a factor of eight. Using docking and molecular dynamics simulations, we identified a possible binding mode and the amino acids involved in these interactions. Our results suggested that suramin, in combination with quinacrine, showed promising synergistic efficacy to inhibit SARS-CoV-2 3CLpro. We suppose that the identification of effective, synergistic drug combinations could lead to the design of better treatments for the COVID-19 disease and repurposable drug candidates offer fast therapeutic breakthroughs, mainly in a pandemic moment.

scholarly journals The repurposed drugs suramin and quinacrine inhibit cooperatively in vitro SARS-CoV-2 3CLpro

2020 ◽  
Author(s):  
Raphael J. Eberle ◽  
Danilo S. Olivier ◽  
Marcos S. Amaral ◽  
Dieter Willbold ◽  
Raghuvir K. Arni ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Drug Repositioning ◽  
Binding Mode ◽  
Main Protease ◽  
Repurposed Drugs ◽  
Inhibitory Potential ◽  
Dynamics Simulations ◽  
Synergistic Drug Combinations

AbstractSince the first report of a new pneumonia disease in December 2019 (Wuhan, China) up to now WHO reported more than 50 million confirmed cases and more than one million losses, globally. The causative agent of COVID-19 (SARS-CoV-2) has spread worldwide resulting in a pandemic of unprecedented magnitude. To date, no clinically safe drug or vaccine is available and the development of molecules to combat SARS-CoV-2 infections is imminent. A well-known strategy to identify molecules with inhibitory potential against SARS-CoV-2 proteins is the repurposing of clinically developed drugs, e.g., anti-parasitic drugs. The results described in this study demonstrate the inhibitory potential of quinacrine and suramin against SARS-CoV-2 main protease (3CLpro). Quinacrine and suramin molecules present a competitive and non-competitive mode of inhibition, respectively, with IC50 and KD values in low μM range. Using docking and molecular dynamics simulations we identified a possible binding mode and the amino acids involved in these interactions. Our results suggested that suramin in combination with quinacrine showed promising synergistic efficacy to inhibit SARS-CoV-2 3CLpro. The identification of effective, synergistic drug combinations could lead to the design of better treatments for the COVID-19 disease. Drug repositioning offers hope to the SARS-CoV-2 control.

scholarly journals Camel Hemorphins Exhibit a More Potent Angiotensin-I Converting Enzyme Inhibitory Activity than Other Mammalian Hemorphins: An In Silico and In Vitro Study

Biomolecules ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 486 ◽  
Author(s):  
Amanat Ali ◽  
Seham Abdullah Rashed Alzeyoudi ◽  
Shamma Abdulla Almutawa ◽  
Alya Nasir Alnajjar ◽  
Yusra Al Dhaheri ◽  
...  
Keyword(s):  
Binding Affinity ◽  
Active Site ◽  
Inhibitory Activity ◽  
In Vitro Study ◽  
Ace Inhibition ◽  
Converting Enzyme ◽  
Angiotensin I ◽  
Angiotensin I Converting Enzyme ◽  
Dynamics Simulations

Angiotensin-I converting enzyme (ACE) is a zinc metallopeptidase that has an important role in regulating the renin-angiotensin-aldosterone system (RAAS). It is also an important drug target for the management of cardiovascular diseases. Hemorphins are endogenous peptides that are produced by proteolytic cleavage of beta hemoglobin. A number of studies have reported various therapeutic activities of hemorphins. Previous reports have shown antihypertensive action of hemorphins via the inhibition of ACE. The sequence of hemorphins is highly conserved among mammals, except in camels, which harbors a unique Q>R variation in the peptide. Here, we studied the ACE inhibitory activity of camel hemorphins (LVVYPWTRRF and YPWTRRF) and non-camel hemorphins (LVVYPWTQRF and YPWTQRF). Computational methods were used to determine the most likely binding pose and binding affinity of both camel and non-camel hemorphins within the active site of ACE. Molecular dynamics simulations showed that the peptides interacted with critical residues in the active site of ACE. Notably, camel hemorphins showed higher binding affinity and sustained interactions with all three subsites of the ACE active site. An in vitro ACE inhibition assay showed that the IC50 of camel hemorphins were significantly lower than the IC50 of non-camel hemorphins.

scholarly journals ATP hydrolysis and nucleotide exit enhance maltose translocation in the MalFGK2E importer

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Bárbara Abreu ◽  
Carlos Cruz ◽  
A. Sofia F. Oliveira ◽  
Cláudio M. Soares
Keyword(s):  
Conformational Changes ◽  
Abc Transporters ◽  
Atp Hydrolysis ◽  
Binding Pocket ◽  
Potential Of Mean Force ◽  
Type I ◽  
Concomitant Increase ◽  
Transport Cycle ◽  
Dynamics Simulations ◽  
Key Residues

AbstractATP binding cassette (ABC) transporters employ ATP hydrolysis to harness substrate translocation across membranes. The Escherichia coli MalFGK2E maltose importer is an example of a type I ABC importer and a model system for this class of ABC transporters. The MalFGK2E importer is responsible for the intake of malto-oligossacharides in E.coli. Despite being extensively studied, little is known about the effect of ATP hydrolysis and nucleotide exit on substrate transport. In this work, we studied this phenomenon using extensive molecular dynamics simulations (MD) along with potential of mean force calculations of maltose transport across the pore, in the pre-hydrolysis, post-hydrolysis and nucleotide-free states. We concluded that ATP hydrolysis and nucleotide exit trigger conformational changes that result in the decrease of energetic barriers to maltose translocation towards the cytoplasm, with a concomitant increase of the energy barrier in the periplasmic side of the pore, contributing for the irreversibility of the process. We also identified key residues that aid in positioning and orientation of maltose, as well as a novel binding pocket for maltose in MalG. Additionally, ATP hydrolysis leads to conformations similar to the nucleotide-free state. This study shows the contribution of ATP hydrolysis and nucleotide exit in the transport cycle, shedding light on ABC type I importer mechanisms.

scholarly journals In Vitro Assays for the Discovery of PCSK9 Autoprocessing Inhibitors

2016 ◽  
Vol 21 (10) ◽  
pp. 1034-1041 ◽  
Author(s):  
Scott P. Salowe ◽  
Lei Zhang ◽  
Hratch J. Zokian ◽  
Jennifer J. Gesell ◽  
Deborah L. Zink ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Low Density Lipoprotein ◽  
Ldl Receptor ◽  
Resonance Energy Transfer ◽  
Density Lipoprotein ◽  
Resonance Energy ◽  
In Vitro Study ◽  
In Vitro Assays ◽  
Time Resolved

PCSK9 plays a significant role in regulating low-density lipoprotein (LDL) cholesterol levels and has become an important drug target for treating hypercholesterolemia. Although a member of the serine protease family, PCSK9 only catalyzes a single reaction, the autocleavage of its prodomain. The maturation of the proprotein is an essential prerequisite for the secretion of PCSK9 to the extracellular space where it binds the LDL receptor and targets it for degradation. We have found that a construct of proPCSK9 where the C-terminal domain has been truncated has sufficient stability to be expressed and purified from Escherichia coli for the in vitro study of autoprocessing. Using automated Western analysis, we demonstrate that autoprocessing exhibits the anticipated first-order kinetics. A high-throughput time-resolved fluorescence resonance energy transfer assay for autocleavage has been developed using a PCSK9 monoclonal antibody that is sensitive to the conformational changes that occur upon maturation of the proprotein. Kinetic theory has been developed that describes the behavior of both reversible and irreversible inhibitors of autocleavage. The analysis of an irreversible lactone inhibitor validates the expected relationship between potency and the reaction end point. An orthogonal liquid chromatography–mass spectrometry assay has also been implemented for the confirmation of hits from the antibody-based assays.

scholarly journals Screening of in vitro antiviral activity of purified terpenoid extracts of selected sea weeds against chikungunya virus

2020 ◽  
pp. 320-324
Author(s):  
Sabira Siraj Sumayya ◽  
Abdulhadeef Shereefa Lubaina ◽  
Kumaraswamy Murugan
Keyword(s):  
Antiviral Activity ◽  
Chikungunya Virus ◽  
Kappaphycus Alvarezii ◽  
Inhibitory Effect ◽  
Hypnea Musciformis ◽  
High Incidence ◽  
Medicinal Properties ◽  
Inhibitory Potential ◽  
Layer Chromatography

Currently, the search of novel phytochemicals with unique biological potentialities is a pre-requisite for the designing ideal drugs for the human kind. Sea weeds are bioresources with a broad spectrum of medicinal properties with minimal side effects. Kerala, the Southern state of India reported high incidence of Chikungunya virus (CHIKV) infections in the last several tears. No specific virucidal therapy or effective vaccines are available. This emphasizes the need of searching for phytochemicals as drugs with less cost and more effective. Therefore, an attempt was made in screening purified terpenoid extracts of selected sea weeds as anti-CHIKV potential. In this study the terpenoids composition from the red algae Hypnea musciformis, Kappaphycus alvarezii and Gracillaria dura were identified and analyzed by thin layer chromatography and Gas chromatography- Mass spectrum. The methanolic extract of seaweeds was purified by column chromatography and each fraction was eluted by using petroleum ether and ethyl acetate as solvent combination. The analysis of the purified fraction of H. musciformis and K. alvarezii revealed the presence of 8 terpenoid fractions, and G. dura showed only 4 major components respectively. Vero cell lines were employed in the antiviral assays, infected to CHIKV, and treated with varied doses of purified terpenoid extracts. In the antiviral activity, terpenoid extracts of G. dura showed remarkable and promising EC50 inhibitory effect at 1.25 μg/ml. Further, the terpenoid extracts displayed efficient virucidal activity against CHIKV (inhibit around 90%) with 5 μg/ml dosage. As the last phase, terpenoid extracts added at time intervals of 0, 1, 2, 3 post-infection periods still maintained a significant inhibitory potential against CHIKV viral replication. Thus, the overall study suggests that the terpenoid extracts of G. dura may be effectively used in the prevention and treatment of CHIKV infections. Clinical studies may be warranted for designing a promising new anti-CHIKV drug.

scholarly journals 3-(5-Nitrofuran-2-yl)prop-2-en-1-one Derivatives, with Potent Antituberculosis Activity, Inhibit A Novel Therapeutic Target, Arylamine N-acetyltransferase, in Mycobacteria

Antibiotics ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 368
Author(s):  
Neha Agre ◽  
Nilesh Tawari ◽  
Arundhati Maitra ◽  
Antima Gupta ◽  
Tulika Munshi ◽  
...  
Keyword(s):  
Cell Lines ◽  
Therapeutic Target ◽  
Therapeutic Index ◽  
Multidrug Resistant ◽  
Mycobacterium Tuberculosis H37rv ◽  
Mammalian Cell Lines ◽  
Low Cytotoxicity ◽  
Inhibitory Potential ◽  
Novel Target

In this study, the inhibitory potential of 3-(5-nitrofuran-2-yl)prop-2-en-1-one derivatives was evaluated against a panel of bacteria, as well as mammalian cell lines to determine their therapeutic index. In addition, we investigated the mechanism of antibiotic action of the derivatives to identify their therapeutic target. We discovered compound 2 to be an extremely potent inhibitor of Mycobacterium tuberculosis H37Rv growth (MIC: 0.031 mg/L) in vitro, performing better than the currently used first-line antituberculosis drugs such as isoniazid, rifampicin, ethambutol, and pretomanid in vitro. Furthermore, compound 3 was equipotent to pretomanid against a multidrug-resistant M. tuberculosis clinical isolate. The derivatives were selective and bactericidal towards slow-growing mycobacteria. They showed low cytotoxicity towards murine RAW 264.7 and human THP-1 cell lines, with high selectivity indices. Compound 1 effectively eliminated the intracellular mycobacteria in a mycobacteria-infected macrophage model. The derivatives were assessed for their potential to inhibit mycobacterial arylamine N-acetyltransferase (NAT) and were identified as good inhibitors of recombinant mycobacterial NAT, a novel target essential for the intracellular survival of M. tuberculosis. This study provided hits for designing new potent and selective antituberculosis leads, having mycobacterial NAT inhibition as their possible endogenous mechanisms of action.

scholarly journals A mechanism for the activation of the mechanosensitive Piezo1 channel by the small molecule Yoda1

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Wesley M. Botello-Smith ◽  
Wenjuan Jiang ◽  
Han Zhang ◽  
Alper D. Ozkan ◽  
Yi-Chun Lin ◽  
...  
Keyword(s):  
Small Molecule ◽  
Conformational Changes ◽  
Calcium Imaging ◽  
Rational Design ◽  
Binding Pocket ◽  
Mechanical Forces ◽  
Biological Processes ◽  
Clinical Value ◽  
Mechanical Threshold ◽  
Dynamics Simulations

Abstract Mechanosensitive Piezo1 and Piezo2 channels transduce various forms of mechanical forces into cellular signals that play vital roles in many important biological processes in vertebrate organisms. Besides mechanical forces, Piezo1 is selectively activated by micromolar concentrations of the small molecule Yoda1 through an unknown mechanism. Here, using a combination of all-atom molecular dynamics simulations, calcium imaging and electrophysiology, we identify an allosteric Yoda1 binding pocket located in the putative mechanosensory domain, approximately 40 Å away from the central pore. Our simulations further indicate that the presence of the agonist correlates with increased tension-induced motions of the Yoda1-bound subunit. Our results suggest a model wherein Yoda1 acts as a molecular wedge, facilitating force-induced conformational changes, effectively lowering the channel’s mechanical threshold for activation. The identification of an allosteric agonist binding site in Piezo1 channels will pave the way for the rational design of future Piezo modulators with clinical value.

scholarly journals Molecular dynamics simulations of nucleotide release from the circadian clock protein KaiC reveal atomic-resolution functional insights

2018 ◽  
Vol 115 (49) ◽  
pp. E11475-E11484 ◽  
Author(s):  
Lu Hong ◽  
Bodhi P. Vani ◽  
Erik H. Thiede ◽  
Michael J. Rust ◽  
Aaron R. Dinner
Keyword(s):  
Molecular Dynamics ◽  
Conformational Changes ◽  
Bound States ◽  
Large Scale ◽  
Nucleotide Exchange ◽  
Terminal Domain ◽  
Nucleotide Exchange Factor ◽  
Nucleotide Release ◽  
Dynamics Simulations

The cyanobacterial clock proteins KaiA, KaiB, and KaiC form a powerful system to study the biophysical basis of circadian rhythms, because an in vitro mixture of the three proteins is sufficient to generate a robust ∼24-h rhythm in the phosphorylation of KaiC. The nucleotide-bound states of KaiC critically affect both KaiB binding to the N-terminal domain (CI) and the phosphotransfer reactions that (de)phosphorylate the KaiC C-terminal domain (CII). However, the nucleotide exchange pathways associated with transitions among these states are poorly understood. In this study, we integrate recent advances in molecular dynamics methods to elucidate the structure and energetics of the pathway for Mg·ADP release from the CII domain. We find that nucleotide release is coupled to large-scale conformational changes in the KaiC hexamer. Solvating the nucleotide requires widening the subunit interface leading to the active site, which is linked to extension of the A-loop, a structure implicated in KaiA binding. These results provide a molecular hypothesis for how KaiA acts as a nucleotide exchange factor. In turn, structural parallels between the CI and CII domains suggest a mechanism for allosteric coupling between the domains. We relate our results to structures observed for other hexameric ATPases, which perform diverse functions.

scholarly journals Quinolone-Binding Pocket of DNA Gyrase: Role of GyrB

2002 ◽  
Vol 46 (6) ◽  
pp. 1805-1815 ◽  
Author(s):  
Jonathan Heddle ◽  
Anthony Maxwell
Keyword(s):  
Conformational Changes ◽  
Structural Data ◽  
Dna Gyrase ◽  
Binding Pocket ◽  
Quinolone Resistance ◽  
Resistance Mutations ◽  
Mutant Proteins ◽  
Close Proximity ◽  
To Come

ABSTRACT DNA gyrase is a prokaryotic type II topoisomerase and a major target of quinolone antibacterials. The majority of mutations conferring resistance to quinolones arise within the quinolone resistance-determining region of GyrA close to the active site (Tyr122) where DNA is bound and cleaved. However, some quinolone resistance mutations are known to exist in GyrB. Present structural data suggest that these residues lie a considerable distance from the quinolone resistance-determining region, and it is not obvious how they affect quinolone action. We have made and purified two such mutant proteins, GyrB(Asp426→Asn) and GyrB(Lys447→Glu), and characterized them in vitro. We found that the two proteins behave similarly to GyrA quinolone-resistant proteins. We showed that the mutations exert their effect by decreasing the amount of quinolone bound to a gyrase-DNA complex. We suggest that the GyrB residues form part of a quinolone-binding pocket that includes DNA and the quinolone resistance-determining region in GyrA and that large conformational changes during the catalytic cycle of the enzyme allow these regions to come into close proximity.

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