A New Approach to Predict the Biological Activity of Molecules Based on Similarity of Their Interaction Fields and the logP and logD Values: Application to Auxins.

Bertoša, Branimir; Kojić‐Prodić, Biserka; Wade, Rebecca C.; Ramek, Michael; Piperaki, Stavroula; Tsantili‐Kakoulidou, Anna; Tomić, Sanja

doi:10.1002/chin.200350241

Cited by 5 publications

(10 citation statements)

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“…For instance, auxin regulation of root development is also dependent on endogenous ethylene balance (Stepanova et al 2005). On the other hand, there are more than 50 diVerent compounds, which can express auxin activity (Bertosa et al 2003; and references therein). In the light of this, the signiWcance of HA-IAA groups in explaining the whole HA bioactivity should be regarded with caution, since this could be accounted for other bioactive molecules still unidentiWed in the HA endowed with such hormonal activity.…”

Section: Treatmentsmentioning

confidence: 98%

Indolacetic and humic acids induce lateral root development through a concerted plasmalemma and tonoplast H+ pumps activation

Zandonadi

Canellas

Façanha

2006

Planta

270

178

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Increasing evidences have indicated that humic substances can induce plant growth and productivity by functioning as an environmental source of auxinic activity. Here we comparatively evaluate the effects of indole-3-acetic acid (IAA) and humic acids (HA) isolated from two different soils (Inseptsol and Ultisol) and two different organic residues (vermicompost and sewage sludge) on root development and on activities of plasmalemma and tonoplast H(+ )pumps from maize roots. The data show that HA isolated from these different sources as well as low IAA concentrations (10(-10) and 10(-15) M) improve root growth through a markedly proliferation of lateral roots along with a differential activation not only of the plasmalemma but also of vacuolar H(+)-ATPases and H(+)-pyrophosphatase. Further, the vacuolar H(+)-ATPase had a peak of stimulation in a range from 10(-8) to 10(-10) M IAA, whereas the H(+)-pyrophosphatase was sensitive to a much broader range of IAA concentrations from 10(-3) to 10(-15) M. It is proposed a complementary view of the acid growth mechanism in which a concerted activation of the plasmalemma and tonoplast H(+ )pumps plays a key role in the root cell expansion process driven by environment-derived molecules endowed with auxinic activity, such as that of humic substances.

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Section: Treatmentsmentioning

confidence: 98%

Indolacetic and humic acids induce lateral root development through a concerted plasmalemma and tonoplast H+ pumps activation

Zandonadi

Canellas

Façanha

2006

Planta

270

178

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“…Complexes between ABP1 and the following auxin-related compounds were built: 1-naphtaleneacetic acid (NAA), indole-3-acetic acid (IAA), 4-chloro-indole-3-acetic acid (4-Cl-IAA), indole-3-isobutyric acid (IIBA), and benzoic acid (BA). The compounds were either manually docked into the ABP1 binding site, or the binding modes obtained from previous Monte Carlo searches (43) were used. Parameters for auxin-related compounds were derived using Antechamber in the AMBER 8.0 program package (56,57).…”

Section: System Preparationmentioning

confidence: 99%

“…Before the ABP1 crystal structure was solved, QSAR analysis based solely on the structures of auxin and auxinrelated molecules was possible. Different approaches were used to develop models (43)(44)(45)(46)(47)(48)(49) that related the biological activity of the compounds to their structural features. The models enabled identification of structural features important for auxin activity and classification of auxin-related com-pounds.…”

Section: Introductionmentioning

confidence: 99%

“…The models enabled identification of structural features important for auxin activity and classification of auxin-related com-pounds. The crystal structure of ABP1 (26) enables computational docking studies which can contribute to understanding of the ABP1 mechanism (43). Using different computational methods, the interactions of auxin-related molecules with ABP1 can be studied and hypotheses on the ABP1 function(s) proposed.…”

Section: Introductionmentioning

confidence: 99%

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Mechanism of Auxin Interaction with Auxin Binding Protein (ABP1): A Molecular Dynamics Simulation Study

Bertoša

Kojić‐Prodić

Wade

et al. 2008

Biophysical Journal

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Auxin Binding Protein 1 (ABP1) is ubiquitous in green plants. It binds the phytohormone auxin with high specificity and affinity, but its role in auxin-induced processes is unknown. To understand the proposed receptor function of ABP1 we carried out a detailed molecular modeling study. Molecular dynamics simulations showed that ABP1 can adopt two conformations differing primarily in the position of the C-terminus and that one of them is stabilized by auxin binding. This is in agreement with experimental evidence that auxin induces changes at the ABP1 C-terminus. Simulations of ligand egress from ABP1 revealed three main routes by which an auxin molecule can enter or leave the ABP1 binding site. Assuming the previously proposed orientation of ABP1 to plant cell membranes, one of the routes leads to the membrane and the other two to ABP1's aqueous surroundings. A network of hydrogen-bonded water molecules leading from the bulk water to the zinc-coordinated ligands in the ABP1 binding site was formed in all simulations. Water entrance into the zinc coordination sphere occurred simultaneously with auxin egress. These results suggest that the hydrogen-bonded water molecules may assist in protonation and deprotonation of auxin molecules and their egress from the ABP1 binding site.

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“…Besides structural properties, VolSurf+ descriptors describe the ADME (absorption, distribution, metabolism, and excretion) properties of the molecule as well. Similar approaches for building 3D-derived QSAR models have already been proven to be successful and useful in investigation of different classes of the potentially biologically active compounds. − …”

Section: Introductionmentioning

confidence: 99%

Novel Substituted Benzothiophene and Thienothiophene Carboxanilides and Quinolones: Synthesis, Photochemical Synthesis, DNA-Binding Properties, Antitumor Evaluation and 3D-Derived QSAR Analysis

Aleksić

Bertoša²,

Nhili

et al. 2012

J. Med. Chem.

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A series of new N,N-dimethylaminopropyl- and 2-imidazolinyl-substituted derivatives of benzo[b]thienyl- and thieno[2,3-b]thienylcarboxanilides and benzo[b]thieno[2,3-c]- and thieno[3',2':4,5]thieno[2,3-c]quinolones were prepared. Quinolones were prepared by the reaction of photochemical dehydrohalogenation of corresponding anilides. Carboxanilides and quinolones were tested for the antiproliferative activity. 2-Imidazolinyl-substituted derivatives showed very prominent activity. By use of the experimentally obtained antitumor measurements, 3D-derived QSAR analysis was performed for the set of compounds. Highly predictive 3D-derived QSAR models were obtained, and molecular properties that have the highest impact on antitumor activity were identified. Carboxanilides 6a-c and quinolones 9a-c and 11a were evaluated for DNA binding propensities and topoisomerases I and II inhibition as part of their mechanism of action assessment. The evaluated differences in the mode of action nicely correlate with the results of the 3D-QSAR analysis. Taken together, the results indicate which modifications of the compounds from the series should further improve their anticancer properties.

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A New Approach to Predict the Biological Activity of Molecules Based on Similarity of Their Interaction Fields and the logP and logD Values: Application to Auxins.

Cited by 5 publications

References 1 publication

Indolacetic and humic acids induce lateral root development through a concerted plasmalemma and tonoplast H+ pumps activation

Indolacetic and humic acids induce lateral root development through a concerted plasmalemma and tonoplast H+ pumps activation

Mechanism of Auxin Interaction with Auxin Binding Protein (ABP1): A Molecular Dynamics Simulation Study

Novel Substituted Benzothiophene and Thienothiophene Carboxanilides and Quinolones: Synthesis, Photochemical Synthesis, DNA-Binding Properties, Antitumor Evaluation and 3D-Derived QSAR Analysis

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