Tag Archives: docking

Kinetic regularities of thiacalix[4]arene C-1087 inhibitory effect on the activity of Mg(2+)-dependent Ca(2+)-transporting ATP hydrolase in the plasma membrane of smooth muscle cells

Т. О. Veklich1, О. V. Bevza1, О. V. Maliuk1*, S. О. Kosterin1,
R. V. Rodik2, S. H. Vyshnevskyi2, V. І. Kalchenko2

1Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kyiv;
*e-mail: alexmaliukid@gmail.com;
2Institute of Organic Chemistry, National Academy of Sciences of Ukraine

Received: 05 November 2023; Revised: 04 January 2024;
Accepted: 01 February 2024; Available on-line: 26 February 2024

The experiments with the suspension of plasma membranes of myometrium cells, treated with 0.1% digitonin solution, were used to study kinetic regularities of the inhibitory effect of tetra-N-phenylsulfonyl trifluoroacetamidine-thiacalixarene (С-1087) on the activity of Са2+,Mg2+-ATPase. The studies demonstrated the impact of C-1087 on the cumulative effect and the maximal velocity of ATP hydrolysis. No effect of С-1087 on the affinity between Са2+,Mg2+-ATPase, and АТР, affinity and cumulative effect of Ca ions and activation coefficient for Mg ions was revealed. A considerable decrease in the maximal velocity of ATP hydrolysis evidenced a complete non-competitive mechanism of inhibiting Са2+,Mg2+-АТРase activity with thiacalix[4]arene С-1087. Computer simulation demonstrated that thiacalix[4]arene С-1087 inhibiting effect on Са2+,Mg2+-ATPase may be conditioned by the cumulative effect of four spatially oriented N-sulfonylamidine groups on the upper rim of its macrocyclic platform.

Computational investigation of honeybee venom proteins as potential Omicron SARS-CoV-2 inhibitors

H. A. Al-Madhagi1*, M. G. Saleh2

1Biochemical Technology Program, Faculty of Applied Sciences, Dhamar University, Yemen;
2Division of Microbiology, Biology Department, Faculty of Applied Sciences, Dhamar University, Yemen;
*e-mail: bio.haitham@gmail.com

Received: 01 October 2022; Revised: 07 November 2022;
Accepted: 17 February 2023; Available on-line:  27 February 2023

Because of the catastrophic consequences of COVID-19 on the world population, there should be novel­ interventions to handle ongoing infections and daily death cases. The aim of the current study is to examine the effectiveness of HBV (Honeybee venom) proteins on spike protein RBD by in silico tools. The sequences of 5 HBV proteins were used for homology modeling by Phyre 2. The generated protein models were employed for protein-protein docking against Omicron Spike glycoprotein receptor binding domain (RBD) (PDB ID# 7T9L) through HDock and ClusPro platforms followed by prediction of binding affinity using PRODIGY web portal and PDBsum for revealing interaction details. It was found that all of the examined HBV proteins exhibi­ted strong docking scores and binding affinity profiles toward RBD. The findings of the present study indicate the possible HBV as preventive as well as treatment options against Omicron SARS-CoV-2.

Calix[4]arene C-90 and its analogs activate ATPase of the myometrium myosin subfragment-1

R. D. Labyntseva1, O. V. Bevza1, K. V. Lytvyn1, M. O. Borovyk1,
R. V. Rodik2, V. I. Kalchenko2, S. O. Kosterin1

1Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kyiv;
e-mail: labyntseva@biochem.kiev.ua;
2Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Kyiv;
e-mail: vik@ioch.kiev.ua

Numerous female reproductive abnormalities are consequences of disorders in uterus smooth muscle (myometrium) contractile function. In this work, we described activators of ATPase, which could be used for development of effective treatments for correcting this dysfunction. Myosin ATPase localized in the catalytic domain of myosin subfragment-1 transforms a chemical energy deposited in macroergic bonds of ATP into mechanical movement. It was shown that сalix[4]arene C-90 and its structural analogs functionalized at the upper rim of macrocycle with four or at least two N-phenylsulfonуltrifluoroacetamidine groups, are able to activate ATP hydrolysis catalyzed by myometrium myosin subfragment-1. It was shown with the method of computer modeling that N-phenylsulfonуltrifluoroacetamidine groups of calix[4]arene C-90 interact with responsible for binding, coordination and the hydrolysis of ATP amino acid residues of myosin subfragment-1. The results can be used for further research aimed at using calix[4]arene C-90 and its analogs as pharmacological compounds that can effectively normalize myometrium contractile hypofunction.

Novel hybrid inhibitors of the phage T7 RNA polymerase: synthesis, docking and screening in vitro

V. G. Kostina, L. G. Palchykovska, M. O. Platonov,
О. V. Vasylchenko, N. A. Lysenko, I. V. Alexeeva

Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv,
e-mail: L. Palchykovska@ukr.net

A number of new hybrid heteroaromatic compounds, consisting of tricyclic fragments (acridone, thioxanthone and phenazine) and bicyclic fragments (benzimidazole, benzothiazole and benzoxa­zole) were synthesized using the method, developed by the authors. As a result of screening against the transcription model system of the phage T7 DNA-dependent RNA polymerase three effective inhibitors of the RNA syntheses with the IC50 value­ of 8.9, 5.7 and 19.8 µM were detected. To cast light on the mode of interaction between the synthesized compounds and the target, the molecular docking was applied to the model pocket of the phage Т7 RNA polymerase transcription complex. It was established that these ligands form networks of H-bonds with residues of the pocket conservative amino acids and π-interaction with the Mg2+ ion. A planar geometry of the hybrid molecules, realized due to the intramolecular H-bonds, proved to be an important structural feature, which correlates with an efficacious inhibitory activity.

Calixarene methylene bisphosphonic acids as promising effectors of biochemical processes

S. V. Komisarenko1, S. O. Kosterin1, E. V. Lugovskoy1, V. I. Kalchenko2

1Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kyiv;
e-mail: kinet@biochem.kiev.ua;
2Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Kyiv;
e-mail: vik@ioch.kiev.ua

This interdisciplinary study, performed with participation of research workers of Palladin Institute of Biochemistry and Institute of Organic Chemist­ry of NAS of Ukraine, is devoted to analysis of biochemical effects of some calixarene methylene bisphosphonic acids (cyclic phenol oligomers) on two well-known biological phenomenons – Mg2+-dependent ATP hydrolysis (myosin subfragment-1 of myometrium smooth muscle was used as an example) and fibrin polymerization.
Calix[4]arene С-97 (calix[4]arene methylene bisphosphonic acids) is a macrocyclic substance, which contains intramolecular highly ordered lipophilic cavity formed by four aromatic rings, one of which is functionalized at the upper rim with methylene bisphosphonic group. At concentration of 100 µM, this substance was shown to effectively inhibit ATPase activity of pig myometrium myosin subfragment-1 (inhibition coefficient І0.5 = 83 ± 7 µM). At the same time, this calix[4]arene causes significant (vs. control) increase of myosin subfragment-1 hydrodynamic diameter, which may indicate formation of an intermolecular complex between calixa­rene and myosin head. Computer simulation methods (docking and molecular dynamics with addition of grid technologies) enabled to elucidate the grounds of intermolecular interactions between calix[4]arene С-97 and myometrium myosin subfragment-1, that involve hydrophobic, electrostatic and π-π-stacking interactions, some of which are close to the ATPase active centre. In view of the ability of calixarenes to penetrate into the cell and their low toxicity, the results obtained may be used as a basis for further development of a new generation of supramolecular effectors (starting from the above mentioned substances, in particular calix[4]arene С-97) for regulation of smooth muscle contractile activity at the level of ATP dependent actin-myosin interaction.
Calix[4]arenes bearing two or four methylenebisphosphonic acid groups at the macrocyclic upper rim have been studied with respect to their effects on fibrin polymerization. The most potent inhibitor proved to be calix[4]arene tetrakis-methylene-bis-phosphonic acid (C-192), in which case the maximum rate of fibrin polymerization in the fibrinogen + thrombin reaction decreased by 50% at concentrations of 0.52·10-6 M (IC50). At this concentration, the molar ratio of the compound to fibrinogen was 1.7 : 1. For the case of desAB fibrin polymerization, the IC50 was 1.26·10-6 M at a molar ratio of C-192 to fibrin monomer of 4 : 1. Dipropoxycalix[4]-arene bis-methylene-bis-phosphonic acid (C-98) inhibited fibrin desAB polymerization with an IC50 = 1.31·10-4 M. We hypothesized that C-192 blocks fibrin formation by combining with polymerization site ‘A’ (Aa17–19), which ordinarily initiates protofibril formation in a ‘knob-hole’ manner. This suggestion was confirmed by an HPLC assay, which showed a host–guest inclusion complex of C-192 with the synthetic peptide Gly-Pro-Arg-Pro, an analogue of site ‘A’. Further confirmation that the inhibitor was acting at the initial step of the reaction was obtained by electron microscopy, with no evidence of protofibril formation being evident. Calixarene C-192 also doubled both the prothrombin time and the activated partial thromboplastin time in normal human blood plasma at concentrations of 7.13·10-5 and 1.10·10-5 M, respectively. These experiments demonstrate that C-192 is a specific inhibitor of fibrin polymerization and blood coagulation and can be used for the design of a new class of antithrombotic agents.

Analysis of conformational flexibility of loop 110-120 of protein tyrosine phosphatase 1B

V. Yu. Tanchuk, V. O. Tanin, A. I. Vovk

Institute of Bioorganic Chemistry and Petrochemistry,
National Academy of Sciences of Ukraine, Kyiv;
e-mail: v_tanchuk@yahoo.com; vovk@bpci.kiev.ua

Conformations of the catalytic center of protein tyrosine phosphatase 1B (PTP1B) and surrounding loops are known to be important in catalysis and inhibition of the enzyme. There were 98 conformations from 88 PDB files representing PTP1B with different ligands which were analyzed to investigate the details of loop 110-120 movement and mobility of separate residues. The differences were identified by a special software tool which performs multiple comparisons of selected parts of PDB files. The conformations were divided into 6 clusters. It was found that the loop formed by residues 110-120 can be characterized by four main conformations. Predominantly, the loop 110-120 adopts the main conformation and keeps it during WPD loop movement. Three other conformations appear to be stabilized in case of closed WPD loop and seem to be favorable for PTP1B with subunit structure.

The сalix[4]arene C-107 is highly effective supramolecular inhibitor of the Na+,K+-АТРase of plasmatic membrane

O. V. Bevza1, T. O. Veklich1, O. A. Shkrabak1, R. V. Rodik2, V. I. Kalchenko2, S. O. Kosterin1

 1Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kyiv;
e-mail: kinet@biochem.kiev.ua;
2Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Kyiv;
e-mail: vik@bpci.kiev.ua

The inhibition of the Na+,K+-АТРase activity of the myometrium cell plasma membranes with calixarene С-107 (5,17-diamino(2-pyridyl)methylphosphono-11,23-di-tret-butyl-26,28-dihydroxy-25,27-dipropoxycalix[4]arene) was investigated. It has been shown that calixarene С-107 reduced the Na+,K+-АТРase activity more efficiently than ouabain did, while it did not practically influence the “basal” Mg2+-АТРase activity of the same membrane. The magnitude of the cofficient of inhibition I0.5 was 33 ± 4 nМ, Hill coefficient was 0.38 ± 0.06. The model calixa­rene C-150 – the calixarene “scaffold” (26,28-dihydroxy-25,27-dipropoxycalix[4]arene), and the model compound М-3 (4-hydroxyaniline(2-pyridine)methylphosphonic acid) – a fragment of the calixarene С-107, had practically no influence on the enzymatic activity of Na+,K+-АТРase and Mg2+-АТРаse.  We carried out the computer simulation of interaction of calixarenes C-107 and the mentioned model compound with ligand binding sites of the Na+,K+-АТРase of plasma membrane and structure foundation of their intermolecular interaction was found out. The participation of hydrogen, hydrophobic, electrostatic and π-π (stacking) interaction between calixarene and enzyme aminoacid residues, some of which are located near the active center of Na+,K+-АТРase, was discussed.

Protective effect of tiacalix[4]arene-tetrasulphonate on heavy metal inhibition of myometrium myosin subfragment-1 ATP-hydrolase activity

R. D. Labyntsevа1, O. V. Bevza1, A. A. Bevza1, A. M. Lulko1,
S. Kharchenko2, V. I. Kalchenko2, S. O. Kosterin1

1Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kyiv;
е-mail: labyntseva@biochem.kiev.ua;  kinet@biochem.kiev.ua;
2Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Kyiv;
е-mail: vik@ioch.kiev.ua

Heavy metals have a negative effect on the contractility of uterine smooth muscles (myometrium), these effects can lead to various pathologies of a women reproductive system. To overcome these effects the methods for correcting the myometrium contractile activity are  to be developed. Catalyzed by myosin ATPase ATP hydrolysis is the most important reaction in the molecular mechanism of myo­metrium contraction. We have found an inhibitory effect of 0.03-0.3 mM Ni2+, Pb2+ and Cd2+ on enzymatic hydrolysis of ATP by myosin subfragment-1 obtained from swine uterine smooth muscles. We have demonstrated that 100 µM thiacalix[4]arene-tetrasulphonate (C-798) recovered to the control level of ATPase activity of myosin subfragment-1 in the presence of heavy metal cations. One of the most probable mechanisms of C-798 corrective activity is based on its ability to chelate heavy metals, thus cations Pb, Cd and Ni can be removed from the incubation medium. Computer simulation has demonstrated that the protective effect of C-798 may also be the result of weakening the interaction of heavy metal ions with amino acid residues of the myosin molecule near the active site of ATP hydrolase. The obtained results can be used for further research aimed at assessing the prospects of thiacalix[4]arene-tetrasulfonate as pharmacological compounds.

Synthesis, biological evaluation and docking of novel bisamidinohydrazones as NON-peptide inhibitors of furin

V. K. Kibirev1, T. V. Osadchuk2, O. P. Kozachenko2, V. Kholodovych3, O. D. Fedoryak2, V. S. Brovarets2

1Palladin Institute of Biochemistry,
National Academy of Sciences of Ukraine, Kyiv;
e-mail: kibirev@biochem.kiev.ua;
2Institute of Bioorganic Chemistry and Petrochemistry,
National Academy of Sciences of Ukraine, Kyiv;
3Rutgers University, Newark, USA

A series of novel non-peptidic furin inhibitors with values of inhibitory constants (Ki) in the range of 0.74-1.54 μM was obtained by interactions of aminoguanidine hydrocarbonate with three diaryldicarbaldehydes. Correspondingly p-hydroquinone, piperazine and adipic acid were used as linkers between their benzene moieties. Docking studies of these new inhibitors into recently published 3D-structure of human furin (PDB code 4OMC) showed that they were able to interact with subsites S1 and S4 of the enzyme. The overall arrangement of bisamidinohydrazones into furin active site was similar to the position of the ligand co-crystallized with a protease. Observations obtained with molecular modeling allowed further guidance into chemical modifications of the synthesized inhibitors which improve their inhibitory activity.