TY  - JOUR
AU  - Vlahović, Filip
AU  - Ivanović, Saša
AU  - Zlatar, Matija
AU  - Gruden, Maja
PY  - 2017
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/2107
AB  - Density functional method with continuum solvation model is used for the calculation of the partition coefficient log KOW and the determination of lipophilicity of 22 most frequently used organophosphate type pesticides. Excellent agreement with experimental data is obtained using three different density functional approximations (one local, one general gradient and one hybrid), and our results highlight DFT as a reliable and trustworthy method for the calculation of lipophilicity for this important class of molecules. Furthermore, the calculated lipophilicity results are associated with the experimentally determined LD50 and LC50 values, showing that the most toxic pesticides are those with transient characteristics (medium lipophilicity), although this conclusion must be taken with a caution, due to the many factors influencing the ingestion and action of a certain substance in the body besides lipophilicity.
PB  - Belgrade: Serbian Chemical Society
T2  - Journal of the Serbian Chemical Society
T1  - Density functional theory calculation of lipophilicity for organophosphate type pesticides
VL  - 82
IS  - 12
SP  - 1369
EP  - 1378
DO  - 10.2298/JSC170725104V
ER  - 

@article{
author = "Vlahović, Filip and Ivanović, Saša and Zlatar, Matija and Gruden, Maja",
year = "2017",
abstract = "Density functional method with continuum solvation model is used for the calculation of the partition coefficient log KOW and the determination of lipophilicity of 22 most frequently used organophosphate type pesticides. Excellent agreement with experimental data is obtained using three different density functional approximations (one local, one general gradient and one hybrid), and our results highlight DFT as a reliable and trustworthy method for the calculation of lipophilicity for this important class of molecules. Furthermore, the calculated lipophilicity results are associated with the experimentally determined LD50 and LC50 values, showing that the most toxic pesticides are those with transient characteristics (medium lipophilicity), although this conclusion must be taken with a caution, due to the many factors influencing the ingestion and action of a certain substance in the body besides lipophilicity.",
publisher = "Belgrade: Serbian Chemical Society",
journal = "Journal of the Serbian Chemical Society",
title = "Density functional theory calculation of lipophilicity for organophosphate type pesticides",
volume = "82",
number = "12",
pages = "1369-1378",
doi = "10.2298/JSC170725104V"
}

Vlahović, F., Ivanović, S., Zlatar, M.,& Gruden, M.. (2017). Density functional theory calculation of lipophilicity for organophosphate type pesticides. in Journal of the Serbian Chemical Society
Belgrade: Serbian Chemical Society., 82(12), 1369-1378.
https://doi.org/10.2298/JSC170725104V

Vlahović F, Ivanović S, Zlatar M, Gruden M. Density functional theory calculation of lipophilicity for organophosphate type pesticides. in Journal of the Serbian Chemical Society. 2017;82(12):1369-1378.
doi:10.2298/JSC170725104V .

Vlahović, Filip, Ivanović, Saša, Zlatar, Matija, Gruden, Maja, "Density functional theory calculation of lipophilicity for organophosphate type pesticides" in Journal of the Serbian Chemical Society, 82, no. 12 (2017):1369-1378,
https://doi.org/10.2298/JSC170725104V . .

TY  - JOUR
AU  - Borozan, Sunčica
AU  - Dimitrijević, Blagoje P.
AU  - Stojanović, Srđan
PY  - 2013
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/1247
AB  - In this work, we have analyzed the influence of cation-pi interactions to the stability of 59 high resolution protein-RNA complex crystal structures. The total number of Lys and Arg are similar in the dataset as well as the number of their interactions. On the other hand, the aromatic chains of purines are exhibiting more cation-pi interactions than pyrimidines. 35% of the total interactions in the dataset are involved in the formation of multiple cation-pi interactions. The multiple cation-pi interactions have been conserved more than the single interactions. The analysis of the geometry of the cation-pi interactions has revealed that the average distance (d) value falls into distinct ranges corresponding to the multiple (4.28 angstrom) and single (5.50 angstrom) cation-pi interactions. The G-Arg pair has the strongest interaction energy of -3.68 kcal mol(-1) among all the possible pairs of amino acids and bases. Further, we found that the cation-pi interactions due to five-membered rings of A and G are stronger than that with the atoms in six-membered rings. 8.7% stabilizing residues are involved in building cation-pi interactions with the nucleic bases. There are three types of structural motifs significantly over-represented in protein-RNA interfaces: beta-turn-ir, niche-4r and st-staple. Tetraloops and kink-turns are the most abundant RNA motifs in protein-RNA interfaces. Amino acids deployed in the protein-RNA interfaces are deposited in helices, sheets and coils. Arg and Lys, involved in cation-pi interactions, prefer to be in the solvent exposed surface. The results from this study might be used for structure-based prediction and as scaffolds for future protein-RNA complex design.
PB  - Elsevier Sci Ltd, Oxford
T2  - Computational Biology and Chemistry
T1  - Cation-pi interactions in high resolution protein-RNA complex crystal structures
VL  - 47
SP  - 105
EP  - 112
DO  - 10.1016/j.compbiolchem.2013.08.005
ER  - 

@article{
author = "Borozan, Sunčica and Dimitrijević, Blagoje P. and Stojanović, Srđan",
year = "2013",
abstract = "In this work, we have analyzed the influence of cation-pi interactions to the stability of 59 high resolution protein-RNA complex crystal structures. The total number of Lys and Arg are similar in the dataset as well as the number of their interactions. On the other hand, the aromatic chains of purines are exhibiting more cation-pi interactions than pyrimidines. 35% of the total interactions in the dataset are involved in the formation of multiple cation-pi interactions. The multiple cation-pi interactions have been conserved more than the single interactions. The analysis of the geometry of the cation-pi interactions has revealed that the average distance (d) value falls into distinct ranges corresponding to the multiple (4.28 angstrom) and single (5.50 angstrom) cation-pi interactions. The G-Arg pair has the strongest interaction energy of -3.68 kcal mol(-1) among all the possible pairs of amino acids and bases. Further, we found that the cation-pi interactions due to five-membered rings of A and G are stronger than that with the atoms in six-membered rings. 8.7% stabilizing residues are involved in building cation-pi interactions with the nucleic bases. There are three types of structural motifs significantly over-represented in protein-RNA interfaces: beta-turn-ir, niche-4r and st-staple. Tetraloops and kink-turns are the most abundant RNA motifs in protein-RNA interfaces. Amino acids deployed in the protein-RNA interfaces are deposited in helices, sheets and coils. Arg and Lys, involved in cation-pi interactions, prefer to be in the solvent exposed surface. The results from this study might be used for structure-based prediction and as scaffolds for future protein-RNA complex design.",
publisher = "Elsevier Sci Ltd, Oxford",
journal = "Computational Biology and Chemistry",
title = "Cation-pi interactions in high resolution protein-RNA complex crystal structures",
volume = "47",
pages = "105-112",
doi = "10.1016/j.compbiolchem.2013.08.005"
}

Borozan, S., Dimitrijević, B. P.,& Stojanović, S.. (2013). Cation-pi interactions in high resolution protein-RNA complex crystal structures. in Computational Biology and Chemistry
Elsevier Sci Ltd, Oxford., 47, 105-112.
https://doi.org/10.1016/j.compbiolchem.2013.08.005

Borozan S, Dimitrijević BP, Stojanović S. Cation-pi interactions in high resolution protein-RNA complex crystal structures. in Computational Biology and Chemistry. 2013;47:105-112.
doi:10.1016/j.compbiolchem.2013.08.005 .

Borozan, Sunčica, Dimitrijević, Blagoje P., Stojanović, Srđan, "Cation-pi interactions in high resolution protein-RNA complex crystal structures" in Computational Biology and Chemistry, 47 (2013):105-112,
https://doi.org/10.1016/j.compbiolchem.2013.08.005 . .

TY  - JOUR
AU  - Dimitrijević, Blagoje P.
AU  - Borozan, Sunčica
AU  - Katic-Radivojevic, Sofija
AU  - Stojanović, Srđan
PY  - 2012
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/944
AB  - The objective of this study was to estimate and evaluate oxidative/nitrosative stress parameters in sheep infected with Strongyloides papillosus and after antihelminthic treatment with albendazole (ABZ). This parasite, especially during development stages can seriously damage parenchaematous organs during migration within the host. The presence of parasites leads to increased productions of reactive oxygen species (ROS) and reactive nitrogen species (RNS). It is also well known that certain drugs can be very harmful for the delicate oxidant-antioxidant equilibrium, provoking oxidative stress during their biotransformation. ABZ is a broad spectrum antihelminthic drug, frequently used in veterinary medicine for therapy of parasitic infections. The current research was performed on female Wurttemberg sheep (n = 48). The distribution of parasites in sheep was evaluated using the native smear coprological technique, by sedimentation and flotation methods, revealing the presence of S. papillosus. The degree of infection intensity per sheep was quantitatively established by the method of McMaster, the animals having been divided into three groups according to the intensity of infection; mild, moderate and high. The control group consisted of sheep negative to the parasites. After determining the type of parasite infection, the sheep were treated with ABZ, per orally, in single doses of 5 mg/kg per body weight. Sampling of feces for parasitological and blood for biochemical assaying was performed on the 0 and 21st day after treatment with ABZ. The oxidative stress parameters were measured for catalase activity (CAT), the red cell membrane damage by level of malondialdehyde (MDA), while carbonyl and thiol plasma protein group concentrations were used as indicators of the degree of protein oxidative modification. The activity of Cu,Zn-superoxide dismutase (SOD) and relative distribution of lactate dehydrogenase (LDH1-LDH5) activity were determined electrophoretically. The distribution of LDH isoenzymes in sheep moderately and highly infected with S. papillosus revealed that the parasite induced damage to the myocardial (LDH2), lung (LDH3) and liver cells (LDH5) in infected animals, while ABZ treatment only damaged liver cells (LDH5). The MDA concentration revealed that lipid peroxidation increased both in the presence of parasites and the antihelminthic formulation tested (p  LT  0.001) when compared to the control sheep, while the increase of carbonyl concentration (p  LT  0.001), as well as the observed decrease of thiol concentration (p  LT  0.001) indicated significant oxidative damage of plasma proteins in experimental sheep, when compared to the control animals. Our results indicate that S. papillosus induces oxidative/nitrosative stress in sheep. The antihelminthic treatment with ABZ further promotes the disbalance of oxidative-antioxidative equilibrium in all tested sheep.
PB  - Elsevier
T2  - Veterinary Parasitology
T1  - Effects of infection intensity with Strongyloides papillosus and albendazole treatment on development of oxidative/nitrosative stress in sheep
VL  - 186
IS  - 3-4
SP  - 364
EP  - 375
DO  - 10.1016/j.vetpar.2011.11.017
ER  - 

@article{
author = "Dimitrijević, Blagoje P. and Borozan, Sunčica and Katic-Radivojevic, Sofija and Stojanović, Srđan",
year = "2012",
abstract = "The objective of this study was to estimate and evaluate oxidative/nitrosative stress parameters in sheep infected with Strongyloides papillosus and after antihelminthic treatment with albendazole (ABZ). This parasite, especially during development stages can seriously damage parenchaematous organs during migration within the host. The presence of parasites leads to increased productions of reactive oxygen species (ROS) and reactive nitrogen species (RNS). It is also well known that certain drugs can be very harmful for the delicate oxidant-antioxidant equilibrium, provoking oxidative stress during their biotransformation. ABZ is a broad spectrum antihelminthic drug, frequently used in veterinary medicine for therapy of parasitic infections. The current research was performed on female Wurttemberg sheep (n = 48). The distribution of parasites in sheep was evaluated using the native smear coprological technique, by sedimentation and flotation methods, revealing the presence of S. papillosus. The degree of infection intensity per sheep was quantitatively established by the method of McMaster, the animals having been divided into three groups according to the intensity of infection; mild, moderate and high. The control group consisted of sheep negative to the parasites. After determining the type of parasite infection, the sheep were treated with ABZ, per orally, in single doses of 5 mg/kg per body weight. Sampling of feces for parasitological and blood for biochemical assaying was performed on the 0 and 21st day after treatment with ABZ. The oxidative stress parameters were measured for catalase activity (CAT), the red cell membrane damage by level of malondialdehyde (MDA), while carbonyl and thiol plasma protein group concentrations were used as indicators of the degree of protein oxidative modification. The activity of Cu,Zn-superoxide dismutase (SOD) and relative distribution of lactate dehydrogenase (LDH1-LDH5) activity were determined electrophoretically. The distribution of LDH isoenzymes in sheep moderately and highly infected with S. papillosus revealed that the parasite induced damage to the myocardial (LDH2), lung (LDH3) and liver cells (LDH5) in infected animals, while ABZ treatment only damaged liver cells (LDH5). The MDA concentration revealed that lipid peroxidation increased both in the presence of parasites and the antihelminthic formulation tested (p  LT  0.001) when compared to the control sheep, while the increase of carbonyl concentration (p  LT  0.001), as well as the observed decrease of thiol concentration (p  LT  0.001) indicated significant oxidative damage of plasma proteins in experimental sheep, when compared to the control animals. Our results indicate that S. papillosus induces oxidative/nitrosative stress in sheep. The antihelminthic treatment with ABZ further promotes the disbalance of oxidative-antioxidative equilibrium in all tested sheep.",
publisher = "Elsevier",
journal = "Veterinary Parasitology",
title = "Effects of infection intensity with Strongyloides papillosus and albendazole treatment on development of oxidative/nitrosative stress in sheep",
volume = "186",
number = "3-4",
pages = "364-375",
doi = "10.1016/j.vetpar.2011.11.017"
}

Dimitrijević, B. P., Borozan, S., Katic-Radivojevic, S.,& Stojanović, S.. (2012). Effects of infection intensity with Strongyloides papillosus and albendazole treatment on development of oxidative/nitrosative stress in sheep. in Veterinary Parasitology
Elsevier., 186(3-4), 364-375.
https://doi.org/10.1016/j.vetpar.2011.11.017

Dimitrijević BP, Borozan S, Katic-Radivojevic S, Stojanović S. Effects of infection intensity with Strongyloides papillosus and albendazole treatment on development of oxidative/nitrosative stress in sheep. in Veterinary Parasitology. 2012;186(3-4):364-375.
doi:10.1016/j.vetpar.2011.11.017 .

Dimitrijević, Blagoje P., Borozan, Sunčica, Katic-Radivojevic, Sofija, Stojanović, Srđan, "Effects of infection intensity with Strongyloides papillosus and albendazole treatment on development of oxidative/nitrosative stress in sheep" in Veterinary Parasitology, 186, no. 3-4 (2012):364-375,
https://doi.org/10.1016/j.vetpar.2011.11.017 . .

TY  - JOUR
AU  - Dimitrijević, Blagoje P.
AU  - Borozan, Sunčica
AU  - Stojanović, Srđan
PY  - 2012
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/1119
AB  - In this study we have described the pi-pi and cation-pi interactions between the porphyrin ring and the protein part of porphyrin-containing proteins to better understand their stabilizing role. The number of pi-pi interactions was higher than that of cation-pi interactions in the same set of proteins studied. The pyrrole groups of one porphyrin can be involved in pi-pi interactions with pi systems of another porphyrin in the protein. We have found 5.1% cation-pi interactions between porphyrin Fe2+ metal cations and pi systems of surrounding amino acids as well as the pyrrole rings of other porphyrins. We observed that most of the pi-pi interactions have an energy in the range -0.5 to -2.0 kcal mol(-1), while the cation-pi interactions showed an energy in the range 22 to -4 kcal mol(-1). Further, an appreciable number of metal/cation-pi interaction pairs have an energy in the range -6 to -13 kcal mol(-1). The preferred parallel-stacked orientation is found to be more stable than a T-shaped structure for the full set of pi-pi interaction pairs. In the case of cation-pi interactions, it was found that 44% of the cation-pi interactions involved planar stacking, 37% of the interactions belonged to the oblique category, and the remaining 19% of the interactions were of the orthogonal type. The separation distance between the cation group and the aromatic ring decreases as the interplanar angle decreases. Furthermore, in the present study we have found that 10.4% of pi residues and 3.9% of cationic residues were found to have one or more stabilization centers. Amino acids deployed in the environment of porphyrin rings are deposited in helices and coils. The results from this study might be used for structure-based porphyrin protein prediction and as scaffolds for future porphyrin-containing protein design.
PB  - The Royal Society of Chemistry
T2  - RSC Advances
T1  - pi-pi and cation-pi interactions in protein-porphyrin complex crystal structures
VL  - 2
IS  - 33
SP  - 12963
EP  - 12972
DO  - 10.1039/c2ra21937a
ER  - 

@article{
author = "Dimitrijević, Blagoje P. and Borozan, Sunčica and Stojanović, Srđan",
year = "2012",
abstract = "In this study we have described the pi-pi and cation-pi interactions between the porphyrin ring and the protein part of porphyrin-containing proteins to better understand their stabilizing role. The number of pi-pi interactions was higher than that of cation-pi interactions in the same set of proteins studied. The pyrrole groups of one porphyrin can be involved in pi-pi interactions with pi systems of another porphyrin in the protein. We have found 5.1% cation-pi interactions between porphyrin Fe2+ metal cations and pi systems of surrounding amino acids as well as the pyrrole rings of other porphyrins. We observed that most of the pi-pi interactions have an energy in the range -0.5 to -2.0 kcal mol(-1), while the cation-pi interactions showed an energy in the range 22 to -4 kcal mol(-1). Further, an appreciable number of metal/cation-pi interaction pairs have an energy in the range -6 to -13 kcal mol(-1). The preferred parallel-stacked orientation is found to be more stable than a T-shaped structure for the full set of pi-pi interaction pairs. In the case of cation-pi interactions, it was found that 44% of the cation-pi interactions involved planar stacking, 37% of the interactions belonged to the oblique category, and the remaining 19% of the interactions were of the orthogonal type. The separation distance between the cation group and the aromatic ring decreases as the interplanar angle decreases. Furthermore, in the present study we have found that 10.4% of pi residues and 3.9% of cationic residues were found to have one or more stabilization centers. Amino acids deployed in the environment of porphyrin rings are deposited in helices and coils. The results from this study might be used for structure-based porphyrin protein prediction and as scaffolds for future porphyrin-containing protein design.",
publisher = "The Royal Society of Chemistry",
journal = "RSC Advances",
title = "pi-pi and cation-pi interactions in protein-porphyrin complex crystal structures",
volume = "2",
number = "33",
pages = "12963-12972",
doi = "10.1039/c2ra21937a"
}

Dimitrijević, B. P., Borozan, S.,& Stojanović, S.. (2012). pi-pi and cation-pi interactions in protein-porphyrin complex crystal structures. in RSC Advances
The Royal Society of Chemistry., 2(33), 12963-12972.
https://doi.org/10.1039/c2ra21937a

Dimitrijević BP, Borozan S, Stojanović S. pi-pi and cation-pi interactions in protein-porphyrin complex crystal structures. in RSC Advances. 2012;2(33):12963-12972.
doi:10.1039/c2ra21937a .

Dimitrijević, Blagoje P., Borozan, Sunčica, Stojanović, Srđan, "pi-pi and cation-pi interactions in protein-porphyrin complex crystal structures" in RSC Advances, 2, no. 33 (2012):12963-12972,
https://doi.org/10.1039/c2ra21937a . .