Molecular Dynamics Approach to Probe the Allosteric Inhibition of PTP1B by Chlorogenic and Cichoric Acid

Protein tyrosine phosphatase 1B (PTP1B), a major negative regulator of the insulin and leptin signaling pathway, is a potential target for therapeutic intervention against diabetes and obesity. The recent discovery of an allosteric site in PTP1B has created an alternate strategy in the development of PTP1B targeted therapy. The current study investigates the molecular interactions between the allosteric site of PTP1B with two caffeoyl derivatives, chlorogenic acid (CGA) and cichoric acid (CHA), using computational strategies. Molecular docking analysis with CGA and CHA at the allosteric site of PTP1B were performed and the resulting protein-ligand complexes used for molecular dynamics simulation studies for a time scale of 10 ns. Results show stable binding of CGA and CHA at the allosteric site of PTP1B. The flexibility of the WPD loop was observed to be constrained by CGA and CHA in the open (inactive), providing molecular mechanism of allosteric inhibition. The allosteric inhibition of CGA and CHA of PTP1B was shown to be favorable due to no restriction by the α-7 helix in the binding of CGA and CHA at the allosteric binding site. In conclusion, our results exhibit an inhibitory pattern of CGA and CHA against PTP1B through potent binding at the allosteric site.     

Structural Bases for Hesperetin Derivatives: Inhibition of Protein Tyrosine Phosphatase 1B,Kinetics Mechanism and Molecular Docking Study

In the present study, we investigated the structure-activity relationship of naturally occurring hesperetin derivatives, as well as the effects of their glycosylation on the inhibition of diabetes-related enzyme systems, protein tyrosine phosphatase 1B (PTP1B) and α-glycosidase. Among the tested hesperetin derivatives, hesperetin 5-O-glucoside, a single-glucose-containing flavanone glycoside, significantly inhibited PTP1B with an IC₅₀ value of 37.14 ± 0.07 µM. Hesperetin, which lacks a sugar molecule, was the weakest inhibitor compared to the reference compound, ursolic acid (IC₅₀ = 9.65 ± 0.01 µM). The most active flavanone hesperetin 5-O-glucoside suggested that the position of a sugar moiety at the C-5-position influences the PTP1B inhibition. It was observed that the ability to inhibit PTP1B is dependent on the nature, position, and number of sugar moieties in the flavonoid structure, as well as conjugation. In the kinetic study of PTP1B enzyme inhibition, hesperetin 5-O-glucoside led to mixed-type inhibition. Molecular docking studies revealed that hesperetin 5-O-glucoside had a higher binding affinity with key amino residues, suggesting that this molecule best fits the PTP1B allosteric site cavity. The data reported here support hesperetin 5-O-glucoside as a hit for the design of more potent and selective inhibitors against PTP1B in the search for a new anti-diabetic treatment.     

On the Inhibitability of Natural Products Isolated from Tetradium ruticarpum towards Tyrosine Phosphatase 1B (PTP1B) and α-Glucosidase (3W37): An In Vitro and In Silico Study

Folk experiences suggest natural products in Tetradium ruticarpum can be effective inhibitors towards diabetes-related enzymes. The compounds were experimentally isolated, structurally elucidated, and tested in vitro for their inhibition effects on tyrosine phosphatase 1B (PTP1B) and α-glucosidase (3W37). Density functional theory and molecular docking techniques were utilized as computational methods to predict the stability of the ligands and simulate interaction between the studied inhibitory agents and the targeted proteins. Structural elucidation identifies two natural products: 2-heptyl-1-methylquinolin-4-one (1) and 3-[4-(4-methylhydroxy-2-butenyloxy)-phenyl]-2-propenol (2). In vitro study shows that the compounds (1 and 2) possess high potentiality for the inhibition of PTP1B (IC₅₀ values of 24.3 ± 0.8, and 47.7 ± 1.1 μM) and α-glucosidase (IC₅₀ values of 92.1 ± 0.8, and 167.4 ± 0.4 μM). DS values and the number of interactions obtained from docking simulation highly correlate with the experimental results yielded. Furthermore, in-depth analyses of the structure–activity relationship suggest significant contributions of amino acids Arg254 and Arg676 to the conformational distortion of PTP1B and 3W37 structures overall, thus leading to the deterioration of their enzymatic activity observed in assay-based experiments. This study encourages further investigations either to develop appropriate alternatives for diabetes treatment or to verify the role of amino acids Arg254 and Arg676.     

Pharmacophore generation,atom-based 3D-QSAR and molecular dynamics simulation analyses of pyridine-3-carboxamide-6-yl-urea analogues as potential gyrase B inhibitors

DNA gyrase subunit B (GyrB) is an attractive drug target for the development of antibacterial agents with therapeutic potential. In the present study, computational studies based on pharmacophore modelling, atom-based QSAR, molecular docking, free binding energy calculation and dynamics simulation were performed on a series of pyridine-3-carboxamide-6-yl-urea derivatives. A pharmacophore model using 49 molecules revealed structural and chemical features necessary for these molecules to inhibit GyrB. The best fitted model AADDR.13 was generated with a coefficient of determination (r²) of 0.918. This model was validated using test set molecules and had a good r² of 0.78. 3D contour maps generated by the 3D atom-based QSAR revealed the key structural features responsible for the GyrB inhibitory activity. Extra precision molecular docking showed hydrogen bond interactions with key amino acid residues of ATP-binding pocket, important for inhibitor binding. Further, binding free energy was calculated by the MM-GBSA rescoring approach to validate the binding affinity. A 10 ns MD simulation of inhibitor #47 showed the stability of the predicted binding conformations. We identified 10 virtual hits by in silico high-throughput screening. A few new molecules were also designed as potent GyrB inhibitors. The information obtained from these methodologies may be helpful to design novel inhibitors of GyrB.     

In Silico Strategy for Targeting the mTOR Kinase at Rapamycin Binding Site by Small Molecules

Computer aided drug-design methods proved to be powerful tools for the identification of new therapeutic agents. We employed a structure-based workflow to identify new inhibitors targeting mTOR kinase at rapamycin binding site. By combining molecular dynamics (MD) simulation and pharmacophore modelling, a simplified structure-based pharmacophore hypothesis was built starting from the FKBP12-rapamycin-FRB ternary complex retrieved from RCSB Protein Data Bank (PDB code 1FAP). Then, the obtained model was used as filter to screen the ZINC biogenic compounds library, containing molecules derived from natural sources or natural-inspired compounds. The resulting hits were clustered according to their similarity; moreover, compounds showing the highest pharmacophore fit-score were chosen from each cluster. The selected molecules were subjected to docking studies to clarify their putative binding mode. The binding free energy of the obtained complexes was calculated by MM/GBSA method and the hits characterized by the lowest ΔG_bind values were identified as potential mTOR inhibitors. Furthermore, the stability of the resulting complexes was studied by means of MD simulation which revealed that the selected compounds were able to form a stable ternary complex with FKBP12 and FRB domain, thus underlining their potential ability to inhibit mTOR with a rapamycin-like mechanism.     

Effects of B vitamins on the radiation-induced transformations of hydroxyl-containing organic compounds

In this work, the interaction of B vitamins with α-hydroxyl-containing carbon-centered radicals formed upon the irradiation of deaerated aqueous solutions of ethanol, ethylene glycol, α-methylglycoside, maltose, and α-glycerophosphate at pH 7 was studied by means of continuous radiolysis. Within the framework of the density functional theory, the homolytic bond dissociation enthalpies (BDEs) of -C-H, -O-H, and -N-H bonds and H-atom addition enthalpies (HAEs) at the -C=O and -C=N groups of the test compounds were calculated. The set of the experimental and theoretically calculated data suggests that vitamin B₂, nicotinamide and pyridoxal phosphate effectively oxidize α-hydroxyl-containing carbon-centered radicals, whereas vitamins B₁ and B₆ reduce these radicals to prevent their recombination and fragmentation reactions.     

Triterpene glycosides fromTupidanthus calyptratus I. Structure of glycosides B1, B2, F1, and F2 from leaves of hooded tupidanthus

Chromatographically inseparable mixtures of oleanolic and ursolic 3-O-α-L-rhamnopyranosyl-(1→2)-O-α-L-arabinopyranosides (glycosides B₁ and B₂) and their 28-O-α-L-rhamnopyranosyl-(1→4)-O-β-D-glucopyranosyl-(1→6)-O-β-D-glucopyranosyl esters (glycosides F₁ and F₂) are isolated from the leaves ofTupidanthus calyptratus Hook f. (Araliaceae). The structures of the isolated glycosides are established from chemical methods and¹H and¹³C NMR spectra. Glycoside F₂ is a new triterpene glycoside. Simferopol' State University. Translated from Khimiya Prirodnykh Soedinenii, No. 5, pp. 627–633, September–October, 1999.     

Ensemble pharmacophore meets ensemble docking: a novel screening strategy for the identification of RIPK1 inhibitors

Programmed cell death has been a fascinating area of research since it throws new challenges and questions in spite of the tremendous ongoing research in this field. Recently, necroptosis, a programmed form of necrotic cell death, has been implicated in many diseases including neurological disorders. Receptor interacting serine/threonine protein kinase 1 (RIPK1) is an important regulatory protein involved in the necroptosis and inhibition of this protein is essential to stop necroptotic process and eventually cell death. Current structure-based virtual screening methods involve a wide range of strategies and recently, considering the multiple protein structures for pharmacophore extraction has been emphasized as a way to improve the outcome. However, using the pharmacophoric information completely during docking is very important. Further, in such methods, using the appropriate protein structures for docking is desirable. If not, potential compound hits, obtained through pharmacophore-based screening, may not have correct ranks and scores after docking. Therefore, a comprehensive integration of different ensemble methods is essential, which may provide better virtual screening results. In this study, dual ensemble screening, a novel computational strategy was used to identify diverse and potent inhibitors against RIPK1. All the pharmacophore features present in the binding site were captured using both the apo and holo protein structures and an ensemble pharmacophore was built by combining these features. This ensemble pharmacophore was employed in pharmacophore-based screening of ZINC database. The compound hits, thus obtained, were subjected to ensemble docking. The leads acquired through docking were further validated through feature evaluation and molecular dynamics simulation.     

Indole- and Pyrazole-Glycyrrhetinic Acid Derivatives as PTP1B Inhibitors: Synthesis,In Vitro and In Silico Studies

Regulating insulin and leptin levels using a protein tyrosine phosphatase 1B (PTP1B) inhibitor is an attractive strategy to treat diabetes and obesity. Glycyrrhetinic acid (GA), a triterpenoid, may weakly inhibit this enzyme. Nonetheless, semisynthetic derivatives of GA have not been developed as PTP1B inhibitors to date. Herein we describe the synthesis and evaluation of two series of indole- and N-phenylpyrazole-GA derivatives (4a–f and 5a–f). We measured their inhibitory activity and enzyme kinetics against PTP1B using p-nitrophenylphosphate (pNPP) assay. GA derivatives bearing substituted indoles or N-phenylpyrazoles fused to their A-ring showed a 50% inhibitory concentration for PTP1B in a range from 2.5 to 10.1 µM. The trifluoromethyl derivative of indole-GA (4f) exhibited non-competitive inhibition of PTP1B as well as higher potency (IC₅₀ = 2.5 µM) than that of positive controls ursolic acid (IC₅₀ = 5.6 µM), claramine (IC₅₀ = 13.7 µM) and suramin (IC₅₀ = 4.1 µM). Finally, docking and molecular dynamics simulations provided the theoretical basis for the favorable activity of the designed compounds.     

Vibrational spectra and stereochemistry of mono- and polysaccharides. IV. α-methyl-d-glucoside, α-methyl-d-galactopyranoside,and α-methyl-d-mannopyranoside

The IR and Raman spectra of α-methyl-D-glucoside (αMDG), α-methyl-D-galactoside (αMDGal), and α-methyl-D-mannoside (αMDM) are compared. The main distinctions between these spectra have been interpreted using experimental and theoretical data on the frequencies and modes of normal vibrations and on the potential energy distributions over particular bonds and atomic groups of the substances under investigation. Spectral characteristics that are determined by different configurations of C−O (CH) groups attached to C2 and C4 atoms and different conformations of C6H₂O6H fragments have been revealed. It has been established that replacement of hydroxyls at C1 with methoxy groups significantly increases the number of frequencies of normal vibrations that are localized mostly in the C1C2 bonds (particularly in αMDGal). For the αMDGal molecules with axial C4O4 groups, the number of frequencies of normal vibrations that show predominant contributions of these groups of PED is smaller. For the αMDM molecules, in which the conformation of CH₂OH groups (with respect to rotation around the C5C6 bonds) differs from that in αMDG and αMDGal molecules, most vibrations are localized in the C6O6 bonds rather than in the C5O5 bonds. This fact is very important in correlating the vibrational spectra and structural properties of mono- and polysaccharides. B.I. Stepanov Institute of Physics, Belarus Academy of Sciences. V. Tshebyatoski Institute of Low Temperatures and Structural Studies, Polish Academy of Sciences. Translated fromZhurmal Struktumoi Khimii, Vol. 36, No. 3, pp. 456–466, May–June, 1995. Translated by I. Izvekova     

Structural investigation of cellulose Iα and Iβ by 2D RFDR NMR spectroscopy: determination of sequence of magnetically inequivalent d-glucose units along cellulose chain

In our previous studies of the crystal structure of native cellulose (cellulose I) by solid-state two-dimensional (2D) ¹³C–¹³C INADEQUATE, it was revealed that cellulose I_α contains two kinds of β-d-glucose residues (A and A′) in the unit cell and that cellulose I_β contains another two kinds of residues (B and B′). In the present study, the sequence of residues A and A′ along the same chains in cellulose I_α and that of residues B and B′ in I_β were investigated by 2D ¹³C–¹³C rotor-synchronized radiofrequency-driven recoupling (RFDR) experiments using, respectively, uniformly ¹³C₆-labeled (U−¹³C₆) bacterial cellulose and the same [U−¹³C₆] cellulose sample after thermal treatment at 260 °C. The RFDR spectra recorded with a short mixing time (1.0 ms) showed dipolar-coupled ¹³C spin pairs of only the neighboring carbon of the both phases, while those recorded with a longer mixing time (3.0–15 ms) provided correlations between weakly coupled ¹³C spin pairs as well as strongly coupled ¹³C spin pairs such as neighboring carbon nuclei. In the RFDR spectrum of the [U−¹³C₆] cellulose recorded with a mixing time of 15 ms, the inter-residue ¹³C–¹³C correlation between C4 of residue A and C2 of residue A′ and that between C3 of residue A and C4 of residue A′ were clearly observed. In the case of cellulose I_β, however, inter-residue ¹³C–¹³C correlations between residues B and B′ could not be detected in the series of RFDR spectra recorded with different mixing times of annealed [U−¹³C₆] cellulose. From these findings, that cellulose I_α was revealed to have the –A–A′– repeating units along the cellulose chain. For cellulose I_β, it was revealed that the respective residues B and B′ are composed of independent chains (–B–B– and –B′–B′– repeating units) and that there are no –B–B′– repeating units in the chain.     

Pharmacophore model-aided virtual screening combined with comparative molecular docking and molecular dynamics for identification of marine natural products as SARS-CoV-2 papain-like protease inhibitors

Targeting SARS-CoV-2 papain-like protease using inhibitors is a suitable approach for inhibition of virus replication and dysregulation of host anti-viral immunity. Engaging all five binding sites far from the catalytic site of PLpro is essential for developing a potent inhibitor. We developed and validated a structure-based pharmacophore model with 9 features of a potent PLpro inhibitor. The pharmacophore model-aided virtual screening of the comprehensive marine natural product database predicted 66 initial hits. This hit library was downsized by filtration through a molecular weight filter of ≤ 500 g/mol. The 50 resultant hits were screened by comparative molecular docking using AutoDock and AutoDock Vina. Comparative molecular docking enables benchmarking docking and relieves the disparities in the search and scoring functions of docking engines. Both docking engines retrieved 3 same compounds at different positions in the top 1 % rank, hence consensus scoring was applied, through which CMNPD28766, aspergillipeptide F emerged as the best PLpro inhibitor. Aspergillipeptide F topped the 50-hit library with a pharmacophore-fit score of 75.916. Favorable binding interactions were predicted between aspergillipeptide F and PLpro similar to the native ligand XR8-24. Aspergillipeptide F was able to engage all the 5 binding sites including the newly discovered BL2 groove, site V. Molecular dynamics for quantification of Cα-atom movements of PLpro after ligand binding indicated that it exhibits highly correlated domain movements contributing to the low free energy of binding and a stable conformation. Thus, aspergillipeptide F is a promising candidate for pharmaceutical and clinical development as a potent SARS-CoV-2 PLpro inhibitor.     

Standard molar enthalpies and entropies of vaporization for twolow-melting trichlorophenoxy herbicides

The standard sublimation enthalpies of (2,4,5-trichlorophenoxy)acetonitrile and (2,4,5-trichlorophenoxy)aniline were determined by isothermal thermogravimetry using the Langmuir equation and by non-isothermal differential scanning calorimetry for comparison. The used procedure was previously tested using three reference compounds: benzoic acid, succinic acid and salicylic acid. The results compared to those reported in literature show an excellent agreement for two of the three compounds while the third agrees quite well. For (2,4,5-trichlorophenoxy)acetonitrile and (2,4,5-trichlorophenoxy)aniline, the extrapolation of data at 298.15 K were obtained, respectively: Δ_subH°(298 K)={(106±4) and (101±4)} kJ mol^–1. From Clausius Clapeyron equation obtained after the determination of the vaporization constant α′, the following standard sublimation entropies for (2,4,5-trichlorophenoxy)acetonitrile and (2,4,5-trichlorophenoxy)aniline equal to Δ_subS°(298 K)=(251 and 237) J K^–1 mol^–1, respectively, were derived, with an error of ±4 J K^–1 mol^–1 equal for the studied herbicides.     

Pharmacophore modeling,virtual screening and molecular docking of ATPase inhibitors of HSP70

Heat shock protein 70 is an effective anticancer target as it influences many signaling pathways. Hence the study investigated the important pharmacophore feature required for ATPase inhibitors of HSP70 by generating a ligand based pharmacophore model followed by virtual based screening and subsequent validation by molecular docking in Discovery studio V4.0. The most extrapolative pharmacophore model (hypotheses 8) consisted of four hydrogen bond acceptors. Further validation by external test set prediction identified 200 hits from Mini Maybridge, Drug Diverse, SCPDB compounds and Phytochemicals. Consequently, the screened compounds were refined by rule of five, ADMET and molecular docking to retain the best competitive hits. Finally Phytochemical compounds Muricatetrocin B, Diacetylphiladelphicalactone C, Eleutheroside B and 5-(3-{[1-(benzylsulfonyl)piperidin-4-yl]amino}phenyl)- 4-bromo-3-(carboxymethoxy)thiophene-2-carboxylic acid were obtained as leads to inhibit the ATPase activity of HSP70 in our findings and thus can be proposed for further in vitro and in vivo evaluation.     

Comparative virtual screening and novelty detection for NMDA-GlycineB antagonists

Identification of novel compound classes for a drug target is a challenging task for cheminformatics and drug design when considerable research has already been undertaken and many potent lead structures have been identified, which leaves limited unclaimed chemical space for innovation. We validated and successfully applied different state-of-the-art techniques for virtual screening (Bayesian machine learning, automated molecular docking, pharmacophore search, pharmacophore QSAR and shape analysis) of 4.6 million unique and readily available chemical structures to identify promising new and competitive antagonists of the strychnine-insensitive Glycine binding site (Glycine_B site) of the NMDA receptor. The novelty of the identified virtual hits was assessed by scaffold analysis, putting a strong emphasis on novelty detection. The resulting hits were tested in vitro and several novel, active compounds were identified. While the majority of the computational methods tested were able to partially discriminate actives from structurally similar decoy molecules, the methods differed substantially in their prospective applicability in terms of novelty detection. The results demonstrate that although there is no single best computational method, it is most worthwhile to follow this concept of focused compound library design and screening, as there still can new bioactive compounds be found that possess hitherto unexplored scaffolds and interesting variations of known chemotypes.     

Synthesis of mangiferin derivatives as protein tyrosine phosphatase 1B inhibitors

Protein tyrosine phosphatase 1B (PTP1B) has received much attention due to its pivotal role in type 2 diabetes and obesity as a negative regulator of the insulin signaling pathway. Mangiferin, a xanthone glucoside, has been reported to possess significant antidiabetic activity. In the present study, a series of mangiferin derivatives was synthesized and evaluated for their PTP1B inhibitory activity. Some of the screened compounds displayed good PTP1B inhibitory activity. Published in Khimiya Prirodnykh Soedinenii, No. 6, pp. 549–551, November–December, 2007.     

A new “hydrophobic template” method detects segments forming transmembrane α-helical bundles in ion channels

We present a “hydrophobic template” method enabling recognition of α-helix bundles in membrane channels from sequence analysis. Inspection of hydrophobic properties of pore-forming helices in proteins with known structure (A-B₅ toxins) permits delineation of a common polarity motif: two hydrophobic surface stretches separated by polar areas. The bundles are stabilized by nonpolar interhelical contacts. A number of transmembrane segments were checked for presence of this motif, and it was detected for pore-forming helices of several ion transporters (segments M2 of acetylcholine and GABA_A receptors, α5 peptide of δ-endotoxin), which reveal five α-helix bundle architecture. Applications of the method to modeling of membrane channels are discussed. Received: 24 April 1998 / Accepted: 3 September 1998 / Published online: 7 December 1998     

Triterpene and steroidal glycosides from the genus <Emphasis Type="Italic">Melilotus</Emphasis> and their genins.

Three new triterpene oleanane glycosides, melilotosides A₁, B₁, and C₁, and non-glycosylated soyasapogenol B were isolated from Melilotus officinalis (L.) Pall. (Fabaceae) roots. The structures of the glycosides were proved using chemical transformations and spectral data. Melilotoside A₁ is soyasapogenol B 3-O-β-Dxylopyranoside; melilotoside B₁, soyasapogenol B 3-O-[β-D-galactopyranosyl-(1-2)-f-D-xylopyranoside]; melilotoside C₁, soyasapogenol B 3-O-[α-L-rhamnopyranosyl-(1-2)-β-D-galactopyranosyl(1-2)-β-Dxylopyranoside].     

Theoretical analysis of the dependence of the vibration spectra of a monosaccharide on the conformation of the hexapyranose ring

Using the molecular mechanics method, we calculated the vibration spectra of methyl-2,6-di-O-acetyl-3,4-anhydro-α-DL-(6,6-²H₂) derivatives of galactopyranoside (G) and talopyranoside (T) molecules, the former in three conformations of the hexapyranose ring (half-chair¹H₀ and⁰H_1dis and also distorted boat^2.5B_dis), and the latter in the E₀+¹H₀ conformation. The sensitivity of vibration frequencies to variations of the hexapyranose ring conformation and to the configuration of the C(2) substituent is analyzed within spectral domains containing specific vibrations. Institute of Physics, Byelorussian Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 35, No. 6, pp. 35–45, November–December, 1994. Translated by A. Arbuznikov     

Computational insights into allosteric interaction between benzoazepin-2-ones and lung cancer-associated PDK1: Implications for activator design

3-Phosphoinositide-dependent kinase-1 (PDK1) plays a key role in the regulation of physiological processes and its catalytic activity is tightly regulated by allosteric modulators which bind to the PDK1 Interacting Fragment (PIF) pocket. However, details on the allosteric modulators regulation of the PDK1 catalytic activity remain elusive. Here, molecular docking and molecular dynamics (MD) simulations were performed to investigate the allosteric regulation of PDK1 induced by one of the benzoazepin-2-ones, the most potent compound 17 (BAZ2O). Molecular docking and MD simulation revealed that BAZ2O was located in the PIF pocket formed by residues from β4 and β5 sheets and helices αB and αC. BAZ2O formed a hydrogen bond with Arg131 and participated in hydrophobic interactions with Ile119, Thr148, Gln150, Leu155 and Phe157. Further comparative analyses of PDK1 in its apo and BAZ2O-bound states unveiled that BAZ2O promoted the structural coupling between the important catalytic domains of PDK1, including the activation loop and the helices αB and αC, thereby stabilizing the PDK1 conformation for catalysis. Understanding the allosteric interaction of PDK1 with small molecules provides a potentially valuable possibility of designing more potent allosteric modulators with therapeutic implications for lung cancer.