scholarly journals Study of interaction energies between residues of the active site of Hsp90 and geldanamycin analogues using quantum mechanics/molecular mechanics methods

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 2040
Author(s):  
Ricardo Vivas-Reyes ◽  
Alejando Morales-Bayuelo ◽  
Carlos Gueto ◽  
Juan C. Drosos ◽  
Johana Márquez Lázaro ◽  
...  
Keyword(s):  
Clinical Trials ◽  
Biological Activity ◽  
Active Site ◽  
Density Functional ◽  
Biological Response ◽  
Computational Techniques ◽  
Quantum Similarity ◽  
Interaction Energies ◽  
Atp Binding Site ◽  
Hsp90 Chaperone

Background: Heat shock protein (Hsp90KDa) is a molecular chaperone involved in the process of cellular oncogenesis, hence its importance as a therapeutic target in clinical trials. Geldanamycin is an inhibitor of Hsp90 chaperone activity, which binds to the ATP binding site in the N-terminal domain of Hsp90. However, geldanamycin has shown hepatotoxic damage in clinical trials; for this reason, its use is not recommended. Taking advantage that geldanamycin binds successfully to Hsp90, many efforts have focused on the search for similar analogues, which have the same or better biological response and reduce the side effects of its predecessor; 17-AAG and 17-DMAG are examples of these analogues. Methods: In order to know the chemical factors influencing the growth or decay of the biological activity of geldanamycin analogues, different computational techniques such as docking, 3DQSAR and quantum similarity were used.  Moreover, the study quantified the interaction energy between amino acids residues of active side and geldanamycin analogues, through hybrid methodologies and density functional theory (DFT) indexes. Results: The evaluation of interaction energies showed that the interaction with Lys58 residue is essential for the union of the analogues to the active site of Hsp90, and improves its biological activity. This union is formed through a substituent on C-11 of the geldanamycin macrocycle. A small and attractor group was found as the main steric and electrostatic characteristic that substituents on C11 need in order to interact with Lys 58; behavior was observed with hydroxy and methoxy series of geldanamycin analogues, under study. Conclusion: These outcomes were supported with quantum similarity and reactivity indices calculations using DFT in order to understand the non-covalent stabilization in the active site of these compounds.

scholarly journals Study of interaction energies between residues of the active site of Hsp90 and geldanamycin analogues using quantum mechanics/molecular mechanics methods

F1000Research ◽  
2020 ◽  
Vol 8 ◽  
pp. 2040
Author(s):  
Ricardo Vivas-Reyes ◽  
Alejando Morales-Bayuelo ◽  
Carlos Gueto ◽  
Juan C. Drosos ◽  
Johana Márquez Lázaro ◽  
...  
Keyword(s):  
Amino Acids ◽  
Biological Activity ◽  
Active Site ◽  
Biological Response ◽  
Computational Techniques ◽  
Quantum Similarity ◽  
Interaction Energies ◽  
Atp Binding Site ◽  
Hsp90 Chaperone ◽  
Hybrid Methodology

Background: Heat shock protein (Hsp90KDa) is a molecular chaperone involved in the process of cellular oncogenesis, hence its importance as a therapeutic target. Geldanamycin is an inhibitor of Hsp90 chaperone activity, which binds to the ATP binding site in the N-terminal domain of Hsp90. However, geldanamycin has shown hepatotoxic damage in clinical trials; for this reason, its use is not recommended. Taking advantage that geldanamycin binds successfully to Hsp90, many efforts have focused on the search for similar analogues, which have the same or better biological response and reduce the side effects of its predecessor; 17-AAG and 17-DMAG are examples of these analogues. Methods: In order to know the chemical factors influencing the growth or decay of the biological activity of geldanamycin analogues, different computational techniques such as docking, 3DQSAR and quantum similarity were used.  Moreover, the study quantified the interaction energy between amino acids residues of active side and geldanamycin analogues, through hybrid methodology (Autodock-PM6) and DFT indexes. Results: The evaluation of interaction energies showed that the interaction with Lys58 residue is essential for the union of the analogues to the active site of Hsp90, and improves its biological activity. This union is formed through a substituent on C-11 of the geldanamycin macrocycle. A small and attractor group was found as the main steric and electrostatic characteristic that substituents on C11 need in order to interact with Lys 58; behavior was observed with hydroxy and methoxy series of geldanamycin analogues, under study. Conclusion: This study contributes with new hybrid methodology (Autodock-PM6) for the generation of 3DQSAR models, which to consider the interactions between compounds and amino acids residues of Hsp90´s active site in the alignment generation. Additionally, quantum similarity and reactivity indices calculations using DFT were performed to know the non-covalent stabilization in the active site of these compounds.

Study of interactions energies between residues of the active site of Hsp90 and the geldanamycin analogues using Quantum Mechanics/Molecular Mechanics (QM/MM) methods

2019 ◽  
Vol 15 ◽  
Author(s):  
Ricardo Vivas-Reyes ◽  
Alejandro Morales-Bayuelo ◽  
Carlos Gueto ◽  
Juan C. Droso ◽  
Johana Márquez ◽  
...  
Keyword(s):  
Molecular Chaperone ◽  
Active Site ◽  
Computational Techniques ◽  
Quantum Similarity ◽  
Interaction Energies ◽  
Reactivity Indices ◽  
Factors Influencing ◽  
Chemical Factors ◽  
Hsp90 Chaperone ◽  
Shock Proteins

Background: (Hsp90) 90KDa heat shock proteins are molecular chaperone involved in process of cellular oncogenesis, hence its marked importance as a therapeutic target. An inhibitor of Hsp90 chaperone activity is the geldanamycin, a thready compound that has the power to bind to the binding of ATP in the N-terminal of Hsp90 domain site, however this reported in clinical trials hepatotoxic damage, which I pitting to its disuse. On the other hand, taking advantage that the geldanamycin joins successfully Hsp90, efforts have focused on the search for similar that they have the same or better effect and both exhibited lower effects than its predecessor, as it has been the case with the similar 17-AAG and 17-DMAG. Methods: In order to know the chemical factors influencing the growth or decay of the biological activity of such compounds have been evaluated different computational techniques such as docking and 3DQSAR, however it has not been considered in a quantitative way what happens within the active site represented in terms of interaction energy, as it has been evaluated in this work. Results: To evaluate interaction energies found that the Lys58 is essential for the union of the analogs to the active site of Hsp90, and that the activity of these will depend on if these have on the C-11 position of the macrocycle a group of small and at the same time attractor of electrons, as it is reflected with the series C-11 hydroxy and methoxy C-11. Conclusion: Theses outcomes were supported with Quantum Similarity and reactivity indices using the Density Funtional Theory in order to understand the non-covalent stabilization in the active site for theses compounds.

Intrinsic Stacking Interactions of Natural and Artificial Nucleobases

2019 ◽  
Author(s):  
Drew P. Harding ◽  
Laura J. Kingsley ◽  
Glen Spraggon ◽  
Steven Wheeler
Keyword(s):  
Gas Phase ◽  
Electrostatic Interactions ◽  
Density Functional ◽  
Molecular Descriptors ◽  
Stacking Interactions ◽  
Interaction Energies ◽  
Functional Theory ◽  
Binding Partner ◽  
Heavy Atoms ◽  
Wide Range

The intrinsic (gas-phase) stacking energies of natural and artificial nucleobases were explored using density functional theory (DFT) and correlated ab initio methods. Ranking the stacking strength of natural nucleobase dimers revealed a preference in binding partner similar to that seen from experiments, namely G > C > A > T > U. Decomposition of these interaction energies using symmetry-adapted perturbation theory (SAPT) showed that these dispersion dominated interactions are modulated by electrostatics. Artificial nucleobases showed a similar stacking preference for natural nucleobases and were also modulated by electrostatic interactions. A robust predictive multivariate model was developed that quantitively predicts the maximum stacking interaction between natural and a wide range of artificial nucleobases using molecular descriptors based on computed electrostatic potentials (ESPs) and the number of heavy atoms. This model should find utility in designing artificial nucleobase analogs that exhibit stacking interactions comparable to those of natural nucleobases. Further analysis of the descriptors in this model unveil the origin of superior stacking abilities of certain nucleobases, including cytosine and guanine.

On the Nature of Halide-Water Interactions: Insights from Many-Body Representations and Density Functional Theory

2019 ◽  
Author(s):  
Brandon B. Bizzarro ◽  
Colin K. Egan ◽  
Francesco Paesani
Keyword(s):  
Density Functional Theory ◽  
Charge Transfer ◽  
Molecular Orbital ◽  
Density Functional ◽  
Decomposition Analysis ◽  
Orbital Energy ◽  
Energy Decomposition Analysis ◽  
Interaction Energies ◽  
Many Body ◽  
Functional Theory

<div> <div> <div> <p>Interaction energies of halide-water dimers, X<sup>-</sup>(H<sub>2</sub>O), and trimers, X<sup>-</sup>(H<sub>2</sub>O)<sub>2</sub>, with X = F, Cl, Br, and I, are investigated using various many-body models and exchange-correlation functionals selected across the hierarchy of density functional theory (DFT) approximations. Analysis of the results obtained with the many-body models demonstrates the need to capture important short-range interactions in the regime of large inter-molecular orbital overlap, such as charge transfer and charge penetration. Failure to reproduce these effects can lead to large deviations relative to reference data calculated at the coupled cluster level of theory. Decompositions of interaction energies carried out with the absolutely localized molecular orbital energy decomposition analysis (ALMO-EDA) method demonstrate that permanent and inductive electrostatic energies are accurately reproduced by all classes of XC functionals (from generalized gradient corrected (GGA) to hybrid and range-separated functionals), while significant variance is found for charge transfer energies predicted by different XC functionals. Since GGA and hybrid XC functionals predict the most and least attractive charge transfer energies, respectively, the large variance is likely due to the delocalization error. In this scenario, the hybrid XC functionals are then expected to provide the most accurate charge transfer energies. The sum of Pauli repulsion and dispersion energies are the most varied among the XC functionals, but it is found that a correspondence between the interaction energy and the ALMO EDA total frozen energy may be used to determine accurate estimates for these contributions. </p> </div> </div> </div>

Naphthoquinone Derivatives Isolated from Plants: Recent Advances in Biological Activity

2020 ◽  
Vol 20 (19) ◽  
pp. 2019-2035
Author(s):  
Esmaeil Sheikh Ahmadi ◽  
Amir Tajbakhsh ◽  
Milad Iranshahy ◽  
Javad Asili ◽  
Nadine Kretschmer ◽  
...  
Keyword(s):  
Clinical Trials ◽  
Biological Activity ◽  
Small Molecules ◽  
Anticancer Activity ◽  
Clinical Significance ◽  
Phase Ii ◽  
Biological Activities ◽  
Phase Ii Clinical Trials ◽  
Naturally Occurring ◽  
The Subject

Naturally occurring naphthoquinones (NQs) comprising highly reactive small molecules are the subject of increasing attention due to their promising biological activities such as antioxidant, antimicrobial, apoptosis-inducing activities, and especially anticancer activity. Lapachol, lapachone, and napabucasin belong to the NQs and are in phase II clinical trials for the treatment of many cancers. This review aims to provide a comprehensive and updated overview on the biological activities of several new NQs isolated from different species of plants reported from January 2013 to January 2020, their potential therapeutic applications and their clinical significance.

Synthesis of New α-Amino Phosphonates Containing 3-Amino-4(3H) Quinazolinone Moiety as Anticancer and Antimicrobial Agents: DFT, NBO, and Vibrational Studies

2018 ◽  
Vol 15 (2) ◽  
pp. 286-296 ◽  
Author(s):  
Mohamed K. Awad ◽  
Mahmoud F. Abdel-Aal ◽  
Faten M. Atlam ◽  
Hend A. Hekal
Keyword(s):  
Biological Activity ◽  
Cell Line ◽  
Quantum Chemical ◽  
Density Functional ◽  
Carcinoma Cell ◽  
Liver Carcinoma ◽  
Anticancer Activities ◽  
Functional Theory ◽  
Ft Ir ◽  
Good Agreement

Aim and Objective: Synthesis of new .-aminophosphonates containing quinazoline moiety through Kabachnik-Fields reaction in the presence of copper triflate catalyst [32], followed by studying their antimicrobial activities and in vitro anticancer activities against liver carcinoma cell line (HepG2) with the hope that new anticancer agents could be developed. Also, the quantum chemical calculations are performed using density functional theory (DFT) to study the effect of the changes of molecular and electronic structures on the biological activity of the investigated compounds. Materials and Method: The structures of the synthesized compounds are confirmed by FT-IR, 1H NMR, 13C NMR, 31P NMR and MS spectral data. The synthesized compounds show significant antimicrobial and also remarkable cytotoxicity anticancer activities against liver carcinoma cell line (HepG2). Density functional theory (DFT) was performed to study the effect of the molecular and electronic structure changes on the biological activity. Results: It was found that the electronic structure of the substituents affects on the reaction yield. The electron withdrawing substituent, NO2 group 3b, on the aromatic aldehydes gave a good yield more than the electron donating substituent, OH group 3c. The electron deficient on the carbon atom of the aldehydic group may increase the interaction of the Lewis acid (Cu(OTf)2) and the Lewis base (imine nitrogen), and accordingly, facilitate the formation of imine easily, which is attacked by the nucleophilic phosphite species to give the α- aminophosphonates. Conclusion: The newly synthesized compounds exhibit a remarkable inhibition of the growth of Grampositive, Gram-negative bacteria and fungi at low concentrations. The cytotoxicity of the synthesized compounds showed a significant cytotoxicity against the liver cancer cell line (HepG 2). Also, it was shown from the quantum chemical calculations that the electron-withdrawing substituent increases the biological activity of the α-aminophosphonates more than the electron donating group which was in a good agreement with the experimental results. Also, a good agreement between the experimental FT-IR and the calculated one was found.

The melanocyte stimulating activity of N-nitroso-2-chloroethyl-carbamoyl derivatives of α-melanotropin fragments

1988 ◽  
Vol 53 (11) ◽  
pp. 2574-2582 ◽  
Author(s):  
Hedvig Medzihradszky-Schweiger ◽  
Helga Süli-Vargha ◽  
József Bódi ◽  
Kálmán Medzihradszky
Keyword(s):  
Biological Activity ◽  
Active Site ◽  
Frog Skin ◽  
Terminal Sequence ◽  
Subsequent Reaction ◽  
Affinity Labels ◽  
Derivatives Of

A number of N-nitroso-2-chloroethyl-carbamoyl (Q(NO)) derivatives of α-melanotropin fragments have been synthesized and their effect on the frog skin melanocytes studied. Peptides substituted in this way possess the biological activity of the parent compounds, indicating that they preserved their receptor recognizing ability. These compounds can therefore serve as affinity labels. Some of these derivatives, related to the C-terminal sequence of α-melanotropin show prolonged darkening reaction, which does not influence the subsequent reaction of melanocytes with α-melanotropin. The Q(NO)-derivative of a fragment derived from the classical active site of the hormone shows, however, inhibition of the effect of α-melanotropin. It can be concluded that the latter peptide acts through the melanotropin receptor, while others, related to the C-terminal sequence of the hormone through another mechanism.

scholarly journals Extracts of Emmer Wheatgrass Grown with Distilled Water, Salinity or Selenium Differently Affect Germination and Cytosolic Ca2+ of Maize Pollen

Agronomy ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 633
Author(s):  
Alberto Marco Del Pino ◽  
Beatrice Falcinelli ◽  
Roberto D’Amato ◽  
Daniela Businelli ◽  
Paolo Benincasa ◽  
...  
Keyword(s):  
Biological Activity ◽  
Phenolic Acids ◽  
Triticum Turgidum ◽  
Germination Rate ◽  
Biological Response ◽  
Pollen Grains ◽  
Water Salinity ◽  
Distilled Water ◽  
Agonist Activity ◽  
Maize Pollen

In this work, the biological activity of emmer (Triticum turgidum L. spp. dicoccum (Schrank ex Shubler) Thell.) wheatgrass extracts obtained from grains sprouted with distilled water, or salinity (50 mM) or selenium (45 mg L−1 of Na2SeO3), was tested through an experimental biological model based on the germination and cytosolic Ca2+ homeostasis of maize pollen grains. The effects of thapsigargin (TG) and of four phenolic acids (PAs: ferulic, coumaric, salicylic and 3-HO benzoic) on maize pollen were also tested as controls. Wheatgrass extracts influenced both pollen cytosolic Ca2+ and germination. The Ca2+ agonist activity of emmer wheatgrass was transient, different from that of TG, which caused a depletion of the stored Ca2+ and a permanent alteration of Ca2+ homeostasis. The results obtained with extracts compared to those obtained with pure PAs suggest that PAs in unconjugated forms, which are known to be well represent in emmer wheatgrass, contribute to the biological activity of extracts. The extent of the biological response of emmer wheatgrass extracts was influenced by emmer sprouting conditions (i.e., distilled water, or salinity or selenium). Maize pollen treated with Se-enriched wheatgrass extracts showed a less perturbed cytosolic Ca2+ and a higher germination rate.

scholarly journals Mechanism of selective benzene hydroxylation catalyzed by iron-containing zeolites

2018 ◽  
Vol 115 (48) ◽  
pp. 12124-12129 ◽  
Author(s):  
Benjamin E. R. Snyder ◽  
Max L. Bols ◽  
Hannah M. Rhoda ◽  
Pieter Vanelderen ◽  
Lars H. Böttger ◽  
...  
Keyword(s):  
High Activity ◽  
Active Site ◽  
Active Sites ◽  
High Performance ◽  
Density Functional ◽  
Catalyst Deactivation ◽  
Density Functional Theory Calculations ◽  
Oxidation Catalysis ◽  
Spectroscopic Techniques ◽  
Benzene Hydroxylation

A direct, catalytic conversion of benzene to phenol would have wide-reaching economic impacts. Fe zeolites exhibit a remarkable combination of high activity and selectivity in this conversion, leading to their past implementation at the pilot plant level. There were, however, issues related to catalyst deactivation for this process. Mechanistic insight could resolve these issues, and also provide a blueprint for achieving high performance in selective oxidation catalysis. Recently, we demonstrated that the active site of selective hydrocarbon oxidation in Fe zeolites, named α-O, is an unusually reactive Fe(IV)=O species. Here, we apply advanced spectroscopic techniques to determine that the reaction of this Fe(IV)=O intermediate with benzene in fact regenerates the reduced Fe(II) active site, enabling catalytic turnover. At the same time, a small fraction of Fe(III)-phenolate poisoned active sites form, defining a mechanism for catalyst deactivation. Density-functional theory calculations provide further insight into the experimentally defined mechanism. The extreme reactivity of α-O significantly tunes down (eliminates) the rate-limiting barrier for aromatic hydroxylation, leading to a diffusion-limited reaction coordinate. This favors hydroxylation of the rapidly diffusing benzene substrate over the slowly diffusing (but more reactive) oxygenated product, thereby enhancing selectivity. This defines a mechanism to simultaneously attain high activity (conversion) and selectivity, enabling the efficient oxidative upgrading of inert hydrocarbon substrates.

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