1,720,993 research outputs found
Identification of Inhibitors Binding Site of Ebola L Polymerase Based on its Homology Model
No full textCoumarins Isolated from Murraya paniculata in Vietnam and Their Inhibitory Effects against Enzyme Soluble Epoxide Hydrolase (sEH)
No full textIn the search for bioactive constituents from Vietnam medicinal plants, the leaves and stems of Murraya paniculata collected in HoaBinh Province, Vietnam were selected for chemical investigation. From the n-hexane fraction, two sterols, including β-sitosterol (6) and stigmasterol (7), and from the chloroform fraction, five coumarins, including mexoticin (1), omphalocarpin (2), murrangatin (3), kimcuongin (4), and murracarpin (5), were obtained. The structures of the isolated compounds were determined from ESI-MS, HR-ESI-MS, and NMR (1D and 2D) spectroscopic data. Coumarins (1–5) were elucidated for inhibitory effects against soluble epoxide hydrolase. Among them, coumarins (2–4) showed soluble epoxide hydrolase inhibitory activity with IC50 values 2.2 ± 4.7, 13.9 ± 6.5, and 3.2 ± 4.5 μM, respectively. A kinetic study of the five coumarins revealed the noncompetitive enzymatic mode for 3 and 4, and a mixture of competitive/noncompetitive enzymatic modes for coumarin 2. Using molecular modelling, the coumarin kimcuongin (4) showed the best binding outline into active sites of human soluble epoxide hydrolase
The surge of flavonoids as novel, fine regulators of cardiovascular Cav channels
Full text linkIon channels underlie a wide variety of physiological processes that involve rapid changes in cell dynamics, such as cardiac and vascular smooth muscle contraction. Overexpression or dysfunction of these membrane proteins are the basis of many cardiovascular diseases that represent the leading cause of morbidity and mortality for human beings. In the last few years, flavonoids, widely distributed in the plant kingdom, have attracted the interest of many laboratories as an emerging class of fine ion, in particular Cav, channels modulators. Pieces of in vitro evidence for direct as well as indirect effects exerted by various flavonoids on ion channel currents are now accumulating in the scientific literature. This activity may be responsible, at least in part, for the beneficial and protective effects of dietary flavonoids toward cardiovascular diseases highlighted in several epidemiological studies. Here we examine numerous studies aimed at analysing this feature of flavonoids, focusing on the mechanisms that promote their sometimes controversial activities at cardiovascular Cav channels. New methodological approaches, such as molecular modelling and docking to Cav1.2 channel α1c subunit, used to elucidate flavonoids intrinsic mechanism of action, are introduced. Moreover, flavonoid-membrane interaction, bioavailability, and antioxidant activity are taken into account and discussed
A possible strategy to fight COVID-19: Interfering with spike glycoprotein trimerization
No full textThe recent release of COVID-19 spike glycoprotein allows detailed analysis of the structural features that are required for stabilizing the infective form of its quaternary assembly. Trying to disassemble the trimeric structure of COVID-19 spike glycoprotein, we analyzed single protomer surfaces searching for concave moieties that are located at the three protomer-protomer interfaces. The presence of some druggable pockets at these interfaces suggested that some of the available drugs in Drug Bank could destabilize the quaternary spike glycoprotein formation by binding to these pockets, therefore interfering with COVID-19 life cycle. The approach we propose here can be an additional strategy to fight against the deadly virus. Ligands of COVID-19 spike glycoprotein that we have predicted in the present computational investigation, might be the basis for new experimental studies in vitro and in vivo
Applications of in silico Methods for Design and Development of Drugs Targeting Protein-Protein Interactions
No full textIdentification of protein-protein interactions (PPIs) is a major challenge in modern molecular biology and biochemistry research, due to the unquestionable role of proteins in cells, biological process and pathological states. Over the past decade, the PPIs have evolved from being considered a highly challenging field of research to being investigated and examined as targets for pharmacological intervention. Comprehension of protein interactions is crucial to known how proteins come together to build signalling pathways, to carry out their functions, or to cause diseases, when deregulated. Multiplicity and great amount of PPIs structures offer a huge number of new and potential targets for the treatment of different diseases. Computational techniques are becoming predominant in PPIs studies for their effectiveness, flexibility, accuracy and cost. As a matter of fact, there are effective in silico approaches which are able to identify PPIs and PPI site. Such methods for computational target prediction have been developed through molecular descriptors and data-mining procedures. In this review, we present different types of interactions between protein-protein and the application of in silico methods for design and development of drugs targeting PPIs. We described computational approaches for the identification of possible targets on protein surface and to detect of stimulator/inhibitor molecules. A deeper study of the most recent bioinformatics methodologies for PPIs studies is vital for a better understanding of protein complexes and for discover new potential PPI modulators in therapeutic intervention
A Focus on Ebola Virus Polymerase
No full textThe Ebola virus causes an acute, serious illness, which is often fatal if untreated. The 2014-2016 outbreak in West Africa was the largest and most complex Ebola outbreak since the first discovery of this virus in 1976. This chapter gives an overview about the Ebola virus RNA polymerase describing its structure, functions, and inhibitors. Ebola L-polymerase is an essential protein for the replication of the virus and thus it constitutes a good target for antiviral therapy. It is an RNA-dependent RNA polymerase that catalyzes the transcription of viral mRNAs, their capping and polyadenylation. Till now, no 3D structure of Ebola virus L-polymerase has been experimentally characterized, but its homology model based on crystal structures of other proteins, obtained theoretically, permitted to obtain its important functional and structural data. This chapter also summarizes the status quo of drugs currently used to treat Ebola virus infection
Identification of “on-off residues” in rat Cav1.2 α1C subunit channel using in silico analysis and docking simulation
No full textIntroduction
Voltage-dependent calcium channels (VSCC) is involved in important biological function as calcium ion transmembrane transport and cardiac contraction. VSCC is a multi-pass membrane protein, made up from α-1, α-2, β and δ subunits. α-1 subunit regulates the entry of ion calcium. Voltage-dependent L-type calcium channel subunit alpha-1C (Cav1.2 α1C subunit channel) is an isoform of VSCC, and is characterized from an high-voltage activation. Previous study have shown that class of molecules as benzothiazepines (Tikhonov D. et al, 2008), are able to block the alpha-1C subunit. Recent works have demonstrated that molecules belonged at the flavonoid class are able to inhibit or to raise channel activity (Saponara S. et al, 2011). In this work, we reported the sensing- residues that could play a key role in Cav1.2 α1C activity. Furthermore, we proposed a potential mechanism of action inside Cav1.2 α1C binding-site with differences between inhibitors and stimulants. Our work has clarifiedas the ligands operate on Cav1.2 α1C, this information could be useful in order to improve their usefulness.
Methods
The 3D structure of Cav1.2 α1C subunit channel was obtained on basis of previous work (Saponara S. et al, 2015). The structure of flavons were downloaded from Pubchem(Kim S. et al, 2015). Docking simulation was carried out through Autodock/Vina v.1.1.2 (O.Trott et al, 2010). PDBePISAwas used in order to evaluate buried surface area values (B.S.A). Protein-ligand interactions were obtained using protein–ligand interaction profiler (P.L.I.P)(Salentin S. et al, 2015). Pymol was used as molecular graphics system (The PyMOL Molecular Graphics System, Version 1.8 Schrödinger, LLC.).
Results and discussion
In vitro analysis on rat Cav1.2 L-type channel of 20 flavonoids have shown stimulatory and inhibitory activities (Saponara S. et al, 2015).The 11 inhibitors and 8 stimulators derivatives are positioned in their corresponding binding-sites with peculiar sensing-residues interactions (shown in figure 1). Analyzing the network of interactions among the two classes of flavonoids we have observed hydrogen bonds, hydrophobic interactions and π–π stacking bonds characterizing their activities that could differently promote pore open/closed conformation and decreasing voltage-sensitive calcium channel activity (Tikhonov D. et al, 2009). Furthermore, on the basis of the selectivity filters model, we have evaluated B.S.A residues values present in the binding-sites, we have observed that B.S.A of some residues dramatically decrease, showing that these residues play a key role in the pore stabilization. The different mechanism of action of these molecules can be attributed to their chemical-physical proprieties as steric hindrance and different positions of hydroxyl groups.</jats:p
Ca v 1.2 channel current block by the PKA inhibitor H-89 in rat tail artery myocytes via a PKA-independent mechanism: electrophysiological, functional, and molecular docking studies
No full textTo characterize the role of cAMP-dependent protein kinase (PKA) in regulating vascular Ca2+ current through Cav1.2 channels [ICa1.2], we have documented a marked capacity of the isoquinoline H-89, widely used as a PKA inhibitor, to reduce current intensity. We hypothesized that the ICa1.2 inhibitory activity of H-89 was mediated by mechanisms unrelated to PKA inhibition. To support this, an in-depth analysis of H-89 vascular effects on both ICa1.2 and contractility was undertaken by performing whole-cell patch-clamp recordings and functional experiments in rat tail main artery single myocytes and rings, respectively. H-89 inhibited ICa1.2 with a pIC50 (M) value of about 5.5, even under conditions where PKA activity was either abolished by both the PKA antagonists KT5720 and protein kinase inhibitor fragment 6–22 amide or enhanced by the PKA stimulators 6-Bnz-cAMP and 8-Br-cAMP. Inhibition of ICa1.2 by H-89 appeared almost irreversible upon washout, was charge carrier- and voltage-dependent, and antagonised by the Cav1.2 channel agonist (S)-(-)-Bay K 8644. H-89 did not alter both potency and efficacy of verapamil, did not affect current kinetics or voltage-dependent activation, while shifting to the left the 50% voltage of inactivation in a concentration-dependent manner. H-89 docked at the α1C subunit in a pocket region close to that of (S)-(-)-Bay K 8644 docking, forming a hydrogen bond with the same, key amino acid residue Tyr-1489. Finally, both high K+- and (S)-(-)-Bay K 8644-induced contractions of rings were fully reverted by H-89. In conclusion, these results indicate that H-89 inhibited vascular ICa1.2 and, consequently, the contractile function through a PKA-independent mechanism. Therefore, caution is recommended when interpreting experiments where H-89 is used to inhibit vascular smooth muscle PKA
Molecular and Evolution <i>In Silico</i> Studies Unlock the h4-HPPD C-Terminal Tail Gating Mechanism
Full text linkThe enzyme 4-hydroxyphenylpyruvate dioxygenase (4-HPPD) is involved in the catabolism of the amino acid tyrosine in organisms such as bacteria, plants, and animals. It catalyzes the conversion of 4-hydroxyphenylpyruvate to a homogenisate in the presence of molecular oxygen and Fe(II) as a cofactor. This enzyme represents a key step in the biosynthesis of important compounds, and its activity deficiency leads to severe, rare autosomal recessive disorders, like tyrosinemia type III and hawkinsinuria, for which no cure is currently available. The 4-HPPD C-terminal tail plays a crucial role in the enzyme catalysis/gating mechanism, ensuring the integrity of the active site for catalysis through fine regulation of the C-terminal tail conformation. However, despite growing interest in the 4-HPPD catalytic mechanism and structure, the gating mechanism remains unclear. Furthermore, the absence of the whole 3D structure makes the bioinformatic approach the only possible study to define the enzyme structure/molecular mechanism. Here, wild-type 4-HPPD and its mutants were deeply dissected by applying a comprehensive bioinformatics/evolution study, and we showed for the first time the entire molecular mechanism and regulation of the enzyme gating process, proposing the full-length 3D structure of human 4-HPPD and two novel key residues involved in the 4-HPPD C-terminal tail conformational change
In Silico Multi-Target Approach Revealed Potential Lead Compounds as Scaffold for the Synthesis of Chemical Analogues Targeting SARS-CoV-2
Full text linkSevere acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19), an infectious disease that spreads rapidly in humans. In March 2020, the World Health Organization (WHO) declared a COVID-19 pandemic. Identifying a multi-target-directed ligand approach would open up new opportunities for drug discovery to combat COVID-19. The aim of this work was to perform a virtual screening of an exclusive chemical library of about 1700 molecules containing both pharmacologically active compounds and synthetic intermediates to propose potential protein inhibitors for use against SARS-CoV-2. In silico analysis showed that our compounds triggered an interaction network with key residues of the SARS-CoV-2 spike protein (S-protein), blocking trimer formation and interaction with the human receptor hACE2, as well as with the main 3C-like protease (3CLpro), inhibiting their biological function. Our data may represent a step forward in the search for potential new chemotherapeutic agents for the treatment of COVID-19
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