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1.
Int J Nanomedicine ; 19: 9503-9547, 2024.
Article in English | MEDLINE | ID: mdl-39296940

ABSTRACT

Over the course of several decades, anticancer treatment with chemotherapy drugs for lung cancer has not changed significantly. Unfortunately, this treatment prolongs the patient's life only by a few months, causing many side effects in the human body. It has also been proven that drugs such as Cisplatin, Carboplatin, Oxaliplatin and others can react with other substances containing an aromatic ring in which the nitrogen atom has a free electron group in its structure. Thus, such structures may have a competitive effect on the nucleobases of DNA. Therefore, scientists are looking not only for new drugs, but also for new alternative ways of delivering the drug to the cancer site. Nanotechnology seems to be a great hope in this matter. Creating a new nanomedicine would reduce the dose of the drug to an absolute minimum, and thus limit the toxic effect of the drug; it would allow for the exclusion of interactions with competitive compounds with a structure similar to nucleobases; it would also permit using the so-called targeted treatment and bypassing healthy cells; it would allow for the introduction of other treatment options, such as radiotherapy directly to the cancer site; and it would provide diagnostic possibilities. This article is a review that aims to systematize the knowledge regarding the anticancer treatment of lung cancer, but not only. It shows the clear possibility of interactions of chemotherapeutics with compounds competitive to the nitrogenous bases of DNA. It also shows the possibilities of using nanostructures as potential Platinum drug carriers, and proves that nanomedicine can easily become a new medicinal product in personalized medicine.


Subject(s)
Antineoplastic Agents , Carcinoma, Non-Small-Cell Lung , Lung Neoplasms , Nanomedicine , Nanostructures , Humans , Lung Neoplasms/drug therapy , Antineoplastic Agents/chemistry , Antineoplastic Agents/pharmacology , Antineoplastic Agents/therapeutic use , Nanostructures/chemistry , Nanostructures/therapeutic use , Carcinoma, Non-Small-Cell Lung/drug therapy , Small Cell Lung Carcinoma/drug therapy , Drug Interactions
2.
Biomedicines ; 11(11)2023 Nov 10.
Article in English | MEDLINE | ID: mdl-38002019

ABSTRACT

The development of new substances with the ability to interact with a biological target is only the first stage in the process of the creation of new drugs. The 5-nitroisatin derivatives considered in this study are new inhibitors of cyclin-dependent kinase 2 (CDK2) intended for anticancer therapy. The research, carried out based on the ADMET (absorption, distribution, metabolism, excretion, toxicity) methods, allowed a basic assessment of the physicochemical parameters of the tested drugs to be made. The collected data clearly showed the good oral absorption, membrane permeability, and bioavailability of the tested substances. The analysis of the metabolite activity and toxicity of the tested drugs did not show any critical hazards in terms of the toxicity of the tested substances. The substances' low solubility in water meant that extended studies tested compounds were required, which helped to select solvents with a high dissolving capacity of the examined substances, such as DMSO or NMP. The use of aqueous binary mixtures based on these two solvents allowed a relatively high solubility with significantly reduced toxicity and environmental index compared to pure solvents to be maintained, which is important in the context of the search for green solvents for pharmaceutical use.

3.
Int J Mol Sci ; 24(2)2023 Jan 12.
Article in English | MEDLINE | ID: mdl-36675064

ABSTRACT

Pt (II) derivatives show anti-cancer activity by interacting with nucleobases of DNA, thus causing some spontaneous and non-spontaneous reactions. As a result, mono- and diaqua products are formed which further undergo complexation with guanine or adenine. Consequently, many processes are triggered, which lead to the death of the cancer cell. The theoretical and experimental studies confirm that such types of interactions can also occur with other chemical compounds. The vitamins from B group have a similar structure to the nucleobases of DNA and have aromatic rings with single-pair orbitals. Theoretical and experimental studies were performed to describe the interactions of B vitamins with Pt (II) derivatives such as cisplatin, oxaliplatin and carboplatin. The obtained results were compared with the values for guanine. Two levels of simulations were implemented at the theoretical level, namely, B3LYP/6-31G(d,p) with LANL2DZ bases set for platinum atoms and MN15/def2-TZVP. The polarizable continuum model (IEF-PCM preparation) and water as a solvent were used. UV-Vis spectroscopy was used to describe the drug-nucleobase and drug-B vitamin interactions. Values of the free energy (ΔGr) show spontaneous reactions with mono- and diaqua derivatives of cisplatin and oxaliplatin; however, interactions with diaqua derivatives are more preferable. The strength of these interactions was also compared. Carboplatin products have the weakest interaction with the studied structures. The presence of non-covalent interactions was demonstrated in the tested complexes. A good agreement between theory and experiment was also demonstrated.


Subject(s)
Antineoplastic Agents , Neoplasms , Vitamin B Complex , Humans , Cisplatin/pharmacology , Cisplatin/therapeutic use , Cisplatin/chemistry , Carboplatin/pharmacology , Carboplatin/therapeutic use , Carboplatin/chemistry , Oxaliplatin/pharmacology , Oxaliplatin/therapeutic use , Platinum/chemistry , Vitamin B Complex/pharmacology , Vitamin B Complex/therapeutic use , Antineoplastic Agents/pharmacology , Antineoplastic Agents/therapeutic use , Antineoplastic Agents/chemistry , Organoplatinum Compounds/pharmacology , Organoplatinum Compounds/therapeutic use , Organoplatinum Compounds/chemistry , Neoplasms/drug therapy
4.
Int J Mol Sci ; 23(18)2022 Sep 12.
Article in English | MEDLINE | ID: mdl-36142479

ABSTRACT

Oxaliplatin, similar to Cisplatin, exhibits anticancer activity by interacting with DNA and inducing programmed cell death. It is biotransformed through a number of spontaneous and non-enzymatic processes. In this way, several transient reactive species are formed, including dichloro-, monochloro-, and diaqua-DACH platin, which can complex with DNA and other macromolecules. The molecular level suggests that such interactions can also take place with vitamins containing aromatic rings with lone pair orbitals. Theoretical and experimental studies were performed to investigate interactions of vitamins from the B group with Oxaliplatin, and the results were compared with values characterizing native purines. Quantum-chemical simulations were carried out at the B3LYP/6-31G(d,p) level, with the LANL2DZ basis set representing atomic orbitals of platinum atom, and at the MN15/def2-TZVP levels of theory with the use of Polarizable Continuum Model (IEF-PCM formulation) and water as a solvent. Additionally, time-dependent density functional theory (TD-DFT) was employed to study molecular properties in the electronic excited state. Interactions of vitamins and Oxaliplatin were investigated using UV-Vis spectroscopy. Values of the free energy (ΔGr) indicate spontaneous reactions with monoaqua [PtH2OClDACH]+ and diaqua [Pt(H2O)2DACH]2+ derivatives of Oxaliplatin. However, diaqua derivatives were found to be preferable. The free energy (ΔGr) values obtained for vitamins from the B group indicate lower affinity of Oxaliplatin compared with values characterizing complexes formed by guanine, adenine, and cytosine. The exception is the monoaqua form of vitamin B1 (thiamine) at the MN15/def2-TZVP levels of calculations. An application of atoms in molecules (AIM) theory revealed non-covalent interactions present in the complexes studied. The comparison of computed and experimental spectroscopic properties showed a good agreement.


Subject(s)
Cisplatin , Platinum , Adenine , Cisplatin/pharmacology , Cyclohexylamines , Cytosine , DNA , Guanine , Oxaliplatin , Quantum Theory , Solvents , Thiamine , Vitamin A , Vitamins , Water
5.
Int J Mol Sci ; 23(14)2022 Jul 21.
Article in English | MEDLINE | ID: mdl-35887396

ABSTRACT

Tumors are still one of the main causes of death; therefore, the search for new therapeutic agents that will enable the implementation of effective treatment is a significant challenge for modern pharmacy. One of the important factors contributing to the development of neoplastic diseases is the overexpression of enzymes responsible for the regulation of cell division processes such as cyclin-dependent kinases. Numerous studies and examples of already-developed drugs confirm that isatin is a convenient basis for the development of new groups of inhibitors for this class of enzyme. Therefore, in this work, a new group of potential inhibitors of the CDK2 enzyme, utilizing isatin derivatives and substituted benzoylhydrazines, has been designed based on the application of computational chemistry methods, such as docking and molecular dynamics, and their inhibiting ability was assessed. In the cases of the selected compounds, a synthesis method was developed, and the selected physicochemical properties of the newly synthesized derivatives were estimated. As part of the completed project, new compounds are developed which are potential inhibitors of the CDK2 enzyme.


Subject(s)
Antineoplastic Agents , Isatin , Antineoplastic Agents/chemistry , Cyclin-Dependent Kinase 2/metabolism , Cyclin-Dependent Kinases , Isatin/chemistry , Isatin/pharmacology , Molecular Docking Simulation , Molecular Dynamics Simulation , Molecular Structure , Structure-Activity Relationship
6.
J Mol Graph Model ; 113: 108144, 2022 06.
Article in English | MEDLINE | ID: mdl-35168146

ABSTRACT

The positively charged products of Cisplatin hydrolysis can form bonds with Guanine and Adenine, showing the ability to crosslink with nucleobases within the double helical DNA, and leading to apoptosis of the neoplastic cell. It has been proved that the presence of chemicals other than nucleobases, compound of aromatic rings with a nitrogen lone pair on the ring, such as B vitamins, may have a competitive character in relation to a chemotherapeutic drug. A theoretical study confirms the stability of bonds formed not only between Cisplatin and Guanine/Adenine but also Cisplatin and B vitamins, namely Thiamine (vit.B1), Niacin (vit.B3), Riboflavin (vit.B2) and Pyridoxal phosphate (vit.B6). That is why it seems to be justified to conduct the research on the physicochemical, thermochemical and optical properties of mono and diaqua complexes of Cisplatin with nucleobases and B vitamins. Equally important is carrying out such research as spectroscopic measurements, bond order analysis and vibrational analysis of the studied complexes. The complexation reaction is spontaneous and thermodynamically favored with the high electronegativity value, a shift of the electron density from the metal zone towards organic compounds, a reduction the value of gap parameter and a shift of the maximum absorbance ΔλABS towards longer wavelengths. Moreover, the performed density variation upon photoexcitation showed the contributions from HOMO→LUMO transition, where the maximum of the absorption band shifts towards shorter wavelengths compared to the cisPt derivatives, thereby lowering the photoexcitation energy. The formation of complexes causes the reduction of energy gap (ΔEgap) values and show higher kinetic stability with high values of gap. The bonding energies between Cisplatin and the target molecules were performed. Cisplatin forms the strongest bonds with Guanine and Pyridoxal phosphate (vit.B6). The vibrations of Pt-N7 bond in complexes occur in the low range of frequencies with low intensities. Only in case of nucleobases appeared vibrations of Pt-N7 in high frequencies. The highest intensity is shown by symmetry and asymmetry stretching vibrations of H-O(H2O) bonds in the high range of frequencies. The vibrations related with ammonium groups (NH3) of great importance appear in the medium and high range of frequencies. The complexes with Guanine show the highest intensities. A theoretical IR spectra were studied. The obtained calculated IR spectra for native nucleobases and vitamins from B group were compared with their experimental FT-IR. So the conducted research provides theoretical knowledge in practical terms regarding the physicochemical and spectral properties of the formed Cisplatin complexes with both nucleobases and B vitamins. Theoretical and partially experimental studies of the molecular and electronic structure or prediction of spectroscopic characteristics are quite useful for better understanding of the reactivity of this drug with physiological target molecules.


Subject(s)
Cisplatin , Vitamin B Complex , Cisplatin/chemistry , Guanine , Quantum Theory , Spectroscopy, Fourier Transform Infrared , Spectrum Analysis, Raman , Vibration , Vitamin B Complex/therapeutic use
7.
Materials (Basel) ; 14(12)2021 Jun 18.
Article in English | MEDLINE | ID: mdl-34207321

ABSTRACT

Novel fluorescent dyes such as difluoroborane complexes of 1-phenylazonaphthalen-2-ol derivatives were successfully synthesized and characterized with a focus on the influence of a substituent and a solvent on the basic photophysical properties. 1H, 11B, 13C, 15N, and 19F nuclear magnetic resonance (NMR) spectra of substituted 1-phenylazonaphthalen-2-ol difluoroboranes and their parent azo dyes were recorded and discussed. The absorption and emission properties of synthesized compounds were investigated in solvents of varying polarity. They were found to be fluorescent despite the presence of the azo group. The azo group rotation was blocked by complexing with -BF2 to get a red shift in absorption. Solvent-dependent spectral properties of compounds were investigated using Lipper-Mataga and Bakhshiev plot. The calculated DFT energies and Frontier Molecular Orbitals calculations of the studied compounds were proved to be consistent with the experimental observations.

8.
Biology (Basel) ; 10(4)2021 Apr 15.
Article in English | MEDLINE | ID: mdl-33920768

ABSTRACT

The glycogen synthase kinase 3ß (GSK-3ß) is a protein kinase involved in regulating numerous physiological processes such as embryonic development, transcription, insulin action, cell division cycle and multiple neuronal functions. The overexpression of this enzyme is related to many diseases such as schizophrenia, Alzheimer's disease, diabetes and cancer. One of the basic methods of treatment in these cases is the usage of ATP-competitive inhibitors. A significant group of such compounds are indirubin and its analogs, e.g., oxindole derivatives. The compounds considered in this work are 112 newly designed oxindole derivatives. In the first stage, such molecular properties of considered compounds as toxicity and LogP were estimated. The preliminary analysis of the binding capabilities of considered compounds towards the GSK-3ß active site was conducted with the use of the docking procedure. Based on obtained molecular properties and docking simulations, a selected group of complexes that were analyzed in the molecular dynamics stage was nominated. The proposed procedure allowed for the identification of compounds such as Oxind_4_9 and Oxind_13_10, which create stable complexes with GSK-3ß enzyme and are characterized by the highest values of binding affinity. The key interactions responsible for stabilization of considered ligand-protein complexes were identified, and their dynamic stability was also determined. Comparative analysis including analyzed compounds and reference molecule 3a, which is also an oxindole derivative with a confirmed inhibitory potential towards GSK3B protein, clearly indicates that the proposed compounds exhibit an analogous binding mechanism, and the obtained binding enthalpy values indicate a slightly higher binding potential than the reference molecule.

9.
Int J Mol Sci ; 22(7)2021 Mar 31.
Article in English | MEDLINE | ID: mdl-33807309

ABSTRACT

Platinum compounds have found wide application in the treatment of various types of cancer and carboplatin is one of the main platinum-based drugs used as antitumor agents. The anticancer activity of carboplatin arises from interacting with DNA and inducing programmed cell death. However, such interactions may occur with other chemical compounds, such as vitamins containing aromatic rings with lone-pair orbitals, which reduces the anti-cancer effect of carboplatin. The most important aspect of the conducted research was related to the evaluation of carboplatin affinity to vitamins from the B group and the potential impact of such interactions on the reduction of therapeutic capabilities of carboplatin in anticancer therapy. Realized computations, including estimation of Gibbs Free Energies, allowed for the identification of the most reactive molecule, namely vitamin B6 (pyridoxal phosphate). In this case, the computational estimations indicating carboplatin reactivity were confirmed by spectrophotometric measurements.


Subject(s)
Carboplatin/chemistry , Nucleotides/chemistry , Vitamin B Complex/chemistry , Antineoplastic Agents/therapeutic use , Carboplatin/therapeutic use , Humans , Neoplasms/drug therapy , Nucleotides/metabolism , Pyridoxal Phosphate , Riboflavin , Thiamine , Vitamin A , Vitamin B 6/chemistry , Vitamin B Complex/therapeutic use
10.
Molecules ; 25(22)2020 Nov 19.
Article in English | MEDLINE | ID: mdl-33228150

ABSTRACT

Novel fluorescent dyes such as benzoxazole-boron complexes, bearing ß-ketoiminate ligands, have been synthesized and characterized with a focus on the influence of a substituent on the basic photophysical properties. 1H, 11B, 13C, 15N, and 19F nuclear magnetic resonance (NMR) spectra of substituted 2-phenacylbenzoxazole difluoroboranes have been recorded and discussed. It is worth mentioning that a high correlation coefficient was found between 15N-NMR parameters and substituent constants. The photophysical properties of these new dyes have been investigated by fluorescence and ultraviolet-visible (UV-Vis) absorption spectroscopy. The geometry optimization, vibrational spectra, and the HOMO and LUMO energies were calculated based on density functional theory with the use of the B3LYP functional and 6-311++G(d,p) basis set.


Subject(s)
Benzoxazoles/chemistry , Benzoxazoles/chemical synthesis , Boranes/chemistry , Boranes/chemical synthesis , Chloroform/chemistry , Hardness , Magnetic Resonance Spectroscopy , Models, Molecular , Molecular Conformation , Solvents/chemistry , Spectrometry, Fluorescence , Spectrophotometry, Ultraviolet , Spectroscopy, Fourier Transform Infrared , Vibration
11.
Anticancer Agents Med Chem ; 19(14): 1775-1783, 2019.
Article in English | MEDLINE | ID: mdl-30914033

ABSTRACT

BACKGROUND: Cisplatin (CisPt) has a well-recognized anticancer activity by interacting with DNA and inducing programmed cell death. However, theoretical studies performed on the molecular level suggest that such nonspecific interactions can also take place with many competitive compounds, such as vitamins containing aromatic rings with lone-pair orbitals. OBJECTIVE: This work is a theoretical study on the initial Pt-N7(N1) bond formation with vitamins from B group and their comparison with values characterizing native purines. METHODS: Geometries of studied structures were optimized with an aid of Gaussian 09 using the B3LYP functional with the 6-31G** basis set. Atomic orbitals of platinum were represented by the lanl2dz basis. Solvation free energies were evaluated by a self-consistent reaction field (SCRF) approach. A dielectric constant of 78 for water was used in the PCM continuum model computations along with radii Bondii. RESULTS: The affinities of mono-aqua cis~[Pt(NH3)2Cl(H2O)]+ and di-aqua cis~ [Pt(NH3)2(H2O)2]2+ derivatives of Cisplatinum toward compounds belonging to the group of eight B vitamins were studied and compared to interactions with canonical purines. All the values of ΔGr unambiguously indicate that reactions with cisPt-diaqua are more preferable, but the comparison of ΔGr values obtained for compounds from vitamin B group and the ones characterizing complexes created by Guanine molecules indicates higher affinity of cisPt monomers toward purines. CONCLUSION: Based on the observations, the regular intake of vitamin-rich beetroot or carrot juices is strongly discouraged during anticancer therapy using CisPt drug. To confirm the results of the performed computational study, detailed clinical trials should be performed.


Subject(s)
Antineoplastic Agents/therapeutic use , Beta vulgaris/chemistry , Cisplatin/therapeutic use , Daucus carota/chemistry , Fruit and Vegetable Juices , Lung Neoplasms/drug therapy , Vitamin B Complex/therapeutic use , Antineoplastic Agents/administration & dosage , Cisplatin/administration & dosage , Density Functional Theory , Humans , Vitamin B Complex/administration & dosage
12.
Int J Biol Macromol ; 126: 1177-1185, 2019 Apr 01.
Article in English | MEDLINE | ID: mdl-30625357

ABSTRACT

The molecular interactions between two single-chain lysosomotropic surfactants DMM-11 (2-Dodecanoyloxyethyl)trimethylammonium bromide) and DMPM-11 (2-Dodecanoyloxypropyl)trimethylammonium bromide) with a small heme-protein (cytochrome c (cyt-c)) in Hepes buffer (pH = 7.4) were extensively investigated by surface tension, dynamic light scattering (DLS), circular dichroism (CD) and fluorescence spectroscopy in combination with molecular dynamic simulation techniques. The results demonstrated that surfactants can destroy the hydrophobic cavity of cyt-c, make the α-helical become loose and convert it into the ß-sheet structure. The interactions between surfactants and cyt-c are mainly hydrophobic. Molecular modelling approaches were also used to gather a deeper insight on the binding of lysosomotropic surfactants with cyt-c and the in silico results were found to be in good agreement with the experimental ones. This study provides a molecular basis for the applications of protein-surfactant complexes in biological, food, pharmaceutical, industrial and cosmetic systems.


Subject(s)
Cytochromes c/chemistry , Cytochromes c/metabolism , Lysosomes/metabolism , Surface-Active Agents/metabolism , Biophysical Phenomena , Circular Dichroism , Dynamic Light Scattering , Hydrogen Bonding , Protein Conformation , Spectrometry, Fluorescence , Spectrophotometry, Ultraviolet , Surface Tension , Time Factors
13.
Org Biomol Chem ; 16(20): 3788-3800, 2018 05 23.
Article in English | MEDLINE | ID: mdl-29737356

ABSTRACT

The presented research focuses on the theoretical design and procedures for preparing protein conjugates with markers. For this purpose a series of phenanthroimidazole (PhI) analogous compounds was designed and investigated by means of first principle methods. Through the judicious choice of cross-linking reagents and the selection of reactive groups, five target fluorescent probes were selected, one of which was previously described using in vitro tests. For the best cognitive purpose and understanding of the nature of the protein conjugation, the studies describe the impact of the reactive group on the solvatochromism, the polarity of the charge transfer of the excited states, the Stokes' shift, ECD spectra and two-photon cross sections. The research is also extended to an analysis of PhI-Concanavalin A biocomplexes and changes in photophysical properties after conjugation. In order to identify valuable alternatives to commercial probes designed for cellular labelling in biological and biomedical imaging, biological properties were described such as ecotoxicity, log P and log BCF, and dye-protein binding was quantified by means of AutoDock and molecular dynamics simulations. The study showed that for phenanthroimidazole derivatives the factor which limits the possibility of their use in medical imaging is the presence of a pyridyl disulfide group, while the introduction of an N-hydroxysuccinimide ester may be used to create stable and valuable fluorescent probes with a wide spectrum for applications in biomedical imaging.


Subject(s)
Fluorescent Dyes/chemistry , Imidazoles/chemistry , Concanavalin A/chemistry , Concanavalin A/metabolism , Fluorescent Dyes/metabolism , Imidazoles/metabolism , Molecular Conformation , Molecular Docking Simulation , Protein Conformation , Spectrometry, Fluorescence
14.
J Mol Model ; 23(8): 230, 2017 Aug.
Article in English | MEDLINE | ID: mdl-28726150

ABSTRACT

A good understanding of the inhibition mechanism of enzymes exhibiting high levels of similarity is the first step to the discovery of new drugs with selective potential. Examples of such proteins include glycogen synthase kinase-3 (GSK-3ß) and cyclin-dependent kinase 2 (CDK-2). This article reports the mechanism of such enzyme inhibition as analyzed by an indoline sulfamylophenyl derivative (CHEMBL410072). Previous work has shown that such compounds exhibit selective properties towards their biological targets. This study used a combined procedure involving docking and molecular dynamics simulations, which allowed identification of interactions responsible for stabilization of complexes, and analysis of the dynamic stability of the systems obtained. The initial data obtained during the molecular docking stage show that the ligand molecule exhibits a similar affinity towards both active sites, which was confirmed by quantification of identified interactions and energy values. However, the data do not cover dynamic aspects of the considered systems. Molecular dynamics simulations realized for both complexes indicate significant dissimilarities in dynamics properties of both side chains of the considered ligands, especially in the case of the part containing the sulfamide group. Such increased mobility of the analyzed systems disrupts the stability of binding in the stabilized complex with GSK-3ß protein, which finally affects also the binding affinity of the ligand molecule towards this enzyme.

15.
J Mol Model ; 23(7): 208, 2017 Jul.
Article in English | MEDLINE | ID: mdl-28634829

ABSTRACT

Nicotinamide phosphoribosyl-transferases (NAMPT) are enzymes that play a role in targeting cancer metabolism, while beta lactamases are involved in bacterial resistance to beta-lactam antibiotics. Many protein inhibitors exhibit such property which is often correlated with their cellular potency. In order to understand such a phenomenon, the present article conducts an analysis of the dynamic behavior of complexes formed by the inhibitors, that is indolizine derivatives, with the studied enzymes. Both docking and molecular dynamics led to identification of their interactions and showed the mechanism of inhibition of the two studied enzymes. The differences in the behavior of ligand at the active sites of beta lactamases and nicotinamide phosphoribosyl-transferases are indicated by structural and enthalpy values.


Subject(s)
Databases, Protein , Indolizines/chemistry , Molecular Dynamics Simulation , Nicotinamide Phosphoribosyltransferase , beta-Lactamase Inhibitors/chemistry , beta-Lactamases/chemistry , Nicotinamide Phosphoribosyltransferase/antagonists & inhibitors , Nicotinamide Phosphoribosyltransferase/chemistry
16.
Curr Comput Aided Drug Des ; 13(1): 22-29, 2017.
Article in English | MEDLINE | ID: mdl-27719631

ABSTRACT

BACKGROUND: Indolizines represent a class of heteroaromatic compounds, of pharmacological importance, containing two condensed 5- and 6-memebered rings bridged by a nitrogen atom. Despite indolizine is an important medicinal moiety, a detailed view on the mechanism of action of biologically active indolizines is unavailable. OBJECTIVE: The study of ligand-enzyme affinity is of high interest; description of characteristics (energetic and geometric ones) of ligand binding to the active sites of an enzyme could be useful in understanding the action mechanism of a given ligand on the concerned enzyme. METHOD: After conducting a QSAR study, to predict IC50 (on 15-LO protein from soybeans) of indolizine derivatives and a docking study of indolizines on Beta lactamase and Nicotinamide phosphoribosyltransferase proteins [1], a molecular dynamics analysis was performed on one of the indolizine derivatives, complexed to the above proteins. RESULTS: The performed molecular dynamics study led to the identification of interactions responsible for the stabilization of complexes of the chosen ligand (i.e., indolizine derivative) with the considered enzymes and the specificity of the ligand interaction as well. The structural data and enthalpy values clearly indicate the differences in the behavior of ligand at the active sites of the three investigated enzymes. Among the studied proteins, the hydrophobicity of the active site of Nicotinamide phosphoribosyltransferase seems to be the main factor in promoting the interaction enzyme-ligand, much more manifested in this case, in comparison to the other two proteins Beta lactamase and Nicotinamide phosphoribosyltransferase. CONCLUSION: The present paper discusses a possible mechanism of interaction of an indolizine derivative with three enzyme proteins, providing information for future work in this topic.


Subject(s)
Catalytic Domain/drug effects , Indolizines/chemistry , Indolizines/pharmacology , Molecular Dynamics Simulation , Nicotinamide Phosphoribosyltransferase/chemistry , beta-Lactamases/chemistry , Molecular Docking Simulation , Protein Binding , Quantitative Structure-Activity Relationship
17.
J Mol Model ; 22(6): 120, 2016 06.
Article in English | MEDLINE | ID: mdl-27154340

ABSTRACT

In the present study, we analyze the interactions of NAD+-dependent deacetylase (Sir2 homolog yeast Hst2) with carba-nicotinamide-adenine-dinucleotide (ADP-HPD). For the Sir2 homolog, a yeast Hst2 docking procedure was applied. The structure of the protein-ADP-HPD complex obtained during the docking procedure was used as a starting point for molecular dynamics simulation. The intermolecular interaction energy partitioning was performed for protein-ADP-HPD complex resulting from molecular dynamics simulation. The analysis was performed for ADP-HPD and 15 amino acids forming a deacetylase binding pocket. Although the results indicate that the first-order electrostatic interaction energy is substantial, the presence of multiple hydrogen bonds in investigated complexes can lead to significant value of induction component.

18.
J Mol Model ; 21(4): 74, 2015 Apr.
Article in English | MEDLINE | ID: mdl-25754137

ABSTRACT

Indirubin derivatives and analogs comprise a significant group of ATP-competitive inhibitors. The inhibitory effects of ChEMBL474807 (1-(4-amino-1,2,5-oxadiazol-3-yl)-5-(piperidin-1-ylmethyl)-N'-(pyridin-4-ylmethylene)-1H-1,2,3-triazole-4-carbohydrazide) on two enzymes, namely glycogen synthase kinase-3ß (GSK-3ß) and cyclin-dependent kinase-2 (CDK-2), were analyzed. The close resemblance of the amino acid sequences of these two enzymes (with 25% identity and 41% similarity) explains why indirubin derivatives are inhibitors of both of the enzymes studied. The docking and molecular dynamics investigation performed here led to the identification of the interactions responsible for stabilizing the ligand ChEMBL474807 at the active sites of the enzymes considered. The structural and energetic data collected during our investigations clearly indicate that there are important differences in the behavior of the ligand at the two active sites investigated here.


Subject(s)
Cyclin-Dependent Kinase 2/chemistry , Glycogen Synthase Kinase 3/chemistry , Molecular Dynamics Simulation , Catalytic Domain , Cyclin-Dependent Kinase 2/antagonists & inhibitors , Cyclin-Dependent Kinase 2/metabolism , Glycogen Synthase Kinase 3/antagonists & inhibitors , Glycogen Synthase Kinase 3/metabolism , Glycogen Synthase Kinase 3 beta , Humans , Indoles/pharmacology , Ligands , Molecular Docking Simulation , Protein Conformation , Protein Kinase Inhibitors/pharmacology
19.
J Mol Model ; 19(8): 3339-49, 2013 Aug.
Article in English | MEDLINE | ID: mdl-23674370

ABSTRACT

The structural and energetic properties of native and oxidized telomeric complexes were defined by means of molecular dynamic (MD) simulations. As a starting point, the experimental conformation of B-DNA d(GpTpTpApGpGpGpTpTpApGpGpG) oligomer bound to human protein telomeric repeat binding factor 1 (TRF1) was used. The influence on the stability of the telomeric complex of the presence of 8-oxoguanine (8oxoG) in the central telomeric triad (CTT) was estimated based on trajectories collected during 130 ns MD runs. The data obtained indicate that the system analyzed is highly sensitive to the presence of oxidative damage in the CTT of the B-DNA telomeric sequence. The most important changes were observed in the immediate vicinity of the 8-oxoguanine molecule. The significantly higher mobility of arginine 425 interacting directly with the oxidized guanine molecule has a large influence on the structural, dynamic and energetic properties of neighboring amino acids. Local changes observed for individual hydrogen bonded interactions localized in the major groove of B-DNA also have significant impact on the properties of hydrophobic clusters, which are the second type of force responsible for stability of the studied bio-system. All the changes reported in detail here unambiguously indicate a significant decrease in telomer binding affinity after oxidation.


Subject(s)
Aptamers, Nucleotide/chemistry , DNA, B-Form/chemistry , Guanine/analogs & derivatives , Molecular Dynamics Simulation , Telomere/chemistry , Telomeric Repeat Binding Protein 1/chemistry , Arginine/chemistry , Guanine/chemistry , Humans , Hydrogen Bonding , Hydrophobic and Hydrophilic Interactions , Oxidation-Reduction , Protein Binding , Telomere/genetics , Thermodynamics
20.
Int J Mol Sci ; 14(3): 4444-60, 2013 Feb 25.
Article in English | MEDLINE | ID: mdl-23439552

ABSTRACT

1H and 13C NMR spectra of eleven 2-phenacylbenzoxazoles (ketimine form) show that their CDCl(3)-solutions contains also (Z)-2-(benzo[d]oxazol-2-yl)-1-phenylethenols (enolimine form). Intramolecular hydrogen bonding in the latter tautomer was found to be significantly weaker than that one in respective (Z)-2-(2-hydroxy-2-phenylvinyl)pyridines. Integrals of the 1H NMR signals were used to evaluate the molar ratio of the tautomers. Strong electron-donating substituents were found to stabilize the ketimine tautomer. pK(T) (negative logarithm of the equilibrium constant, K(T) = [ketimine]/[enolimine]) was found to be linearly dependent on the Hammett substituent constant σ. The results of the MP2 ab initio calculations reveal enolimine including an intramolecular OH…N hydrogen bond to be the most stable form both with electron-donor and electron-acceptor substituents. The stability of ketimines is an intermediate of those found for enolimines and enaminones i.e., (E)-2-(benzo[d]oxazol-2(3H)-ylidene)-1-phenylethanones. 13C CPMAS NMR spectral data reveal that in the crystalline state the ketimine tautomer is predominant in p-NMe(2) substituted congener. On the other hand, enolimine forms were detected there when the substituent has less electron-donating character or when it is an electron-acceptor by character.

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