Browsing by Subject "binding affinity"

Article

Adsorption of hexavalent chromium on dunite

Demetriou, Antri; Pashalidis, Ioannis (2011)

The paper presents and discusses the effect of various physicochemical parameters (e.g. pH, ionic strength, Cr(VI) initial concentration, amount of the adsorbent, temperature and contact time between metal ion and adsorbent) ...

Article

Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase

Archontis, Georgios Z.; Simonson, T.; Karplus, M. (2001)

Specific amino acid binding by aminoacyl-tRNA synthetases (aaRS) is necessary for correct translation of the genetic code. Engineering a modified specificity into aminoacyl-tRNA synthetases has been proposed as a means to ...

Article

Competition studies of L1-deferiprone with copper and iron. Possible implications on efficacy, toxicity and new therapeutic applications

Pashalidis, Ioannis; Kontoghiorghes, G. J. (2000)

Article

Computational design of novel fullerene analogues as potential HIV-1 PR inhibitors: Analysis of the binding interactions between fullerene inhibitors and HIV-1 PR residues using 3D QSAR, molecular docking and molecular dynamics simulations

Durdagi, S.; Mavromoustakos, Thomas M.; Chronakis, Nikos; Papadopoulos, Manthos G. (2008)

A series of experimentally reported as well as computationally designed monoadducts and bisadducts of [60]fullerene analogues have been used in order to analyze the binding interactions between fullerene based inhibitors ...

Article

Computational protein design with a generalized born solvent model: Application to asparaginyl-tRNA synthetase

Polydorides, Savvas; Amara, Najette; Aubard, C.; Plateau, P.; Simonson, T.; Archontis, Georgios Z. (2011)

Computational Protein Design (CPD) is a promising method for high throughput protein and ligand mutagenesis. Recently, we developed a CPD method that used a polar-hydrogen energy function for protein interactions and a ...

Article

Design considerations for nanotherapeutics in oncology

Stylianopoulos, T.; Jain, R. K. (2015)

Nanotherapeutics have improved the quality of life of cancer patients, primarily by reducing the adverse effects of chemotherapeutic agents, but improvements in overall survival are modest. This is in large part due to the ...

Article

Design of a modified mouse protein with ligand binding properties of its human analog by molecular dynamics simulations: The case of C3 inhibition by compstatin

Tamamis, Phanourios; Pierou, P.; Mytidou, C.; Floudas, C. A.; Morikis, D.; Archontis, Georgios Z. (2011)

The peptide compstatin and its derivatives inhibit the complement-component protein C3 in primate mammals and are potential therapeutic agents against the unregulated activation of complement in humans, but are inactive ...

Article

Detection of the His-heme Fe2+-NO species in the reduction of NO to N2O by ba3-oxidase from thermus thermophilus

Pinakoulaki, Eftychia; Ohta, T.; Soulimane, T.; Kitagawa, T.; Varotsis, Constantinos (2005)

Reaction pathways in the enzymatic formation and cleavage of the N-N and N-O bonds, respectively, are difficult to verify without the structure of the intermediates, but we now have such information on the heme a3 2+-NO ...

Article

Glycogen phosphorylase inhibitors: A free energy perturbation analysis of glucopyranose spirohydantoin analogues

Archontis, Georgios Z.; Watson, K. A.; Xie, Q.; Andreou, Georgia; Chrysina, Evangelia D.; Zographos, Spyros E.; Oikonomakos, Nikos G.; Karplus, M. (2005)

GP catalyzes the phosphorylation of glycogen to Glc-1-P. Because of its fundamental role in the metabolism of glycogen, GP has been the target for a systematic structure-assisted design of inhibitory compounds, which could ...

Article

ICPBCZin: A red emitting ratiometric fluorescent indicator with nanomolar affinity for Zn2+ ions

Roussakis, E.; Voutsadaki, S.; Pinakoulaki, Eftychia; Sideris, D. P.; Tokatlidis, K.; Katerinopoulos, H. E. (2008)

A new fluorescent Zn2+ indicator, namely, ICPBCZin was synthesized and the spectral profile of its free and Zn2+ bound forms was studied. The newly synthesized zinc indicator incorporates as chromophore the chromeno ...

Article

Interactions of hydroxycarbamide (Hydroxyurea) with Iron and copper: Implications on toxicity and therapeutic strategies

Konstantinou, E.; Pashalidis, Ioannis; Kolnagou, A.; Kontoghiorghes, G. J. (2011)

Presented at the 19th International Conference on Chelation, London, UK, 13-16 November 2009Preliminary spectrophotometric and potentiometric studies have shown that hydroxycarbamide or hydroxyurea (HU) can interact with ...

Article

Kinetic and crystallographic studies of glucopyranose spirohydantoin and glucopyranosylamine analogs inhibitors of glycogen phosphorylase

Watson, K. A.; Chrysina, Evangelia D.; Tsitsanou, K. E.; Zographos, Spyros E.; Archontis, Georgios Z.; Fleet, G. W. J.; Oikonomakos, Nikos G. (2005)

Glycogen phosphorylase (GP) is currently exploited as a target for inhibition of hepatic glycogenolysis under high glucose conditions. Spirohydantoin of glucopyranose and N-acetyl-β-D-glucopyranosylamine have been identified ...

Article

Mathematical modeling of herpes simplex virus distribution in solid tumors: Implications for cancer gene therapy

Mok, W.; Stylianopoulos, T.; Boucher, Y.; Jain, R. K. (2009)

Purpose: Although oncolytic viral vectors show promise for the treatment of various cancers, ineffective initial distribution and propagation throughout the tumor mass often limit the therapeutic response. A mathematical ...

Article

Molecular Dynamics in Drug Design: New Generations of Compstatin Analogs

Tamamis, Phanourios; López de Victoria, A.; Gorham, R. D.; Bellows-Peterson, M. L.; Pierou, P.; Floudas, C. A.; Morikis, D.; Archontis, Georgios Z. (2012)

We report the computational and rational design of new generations of potential peptide-based inhibitors of the complement protein C3 from the compstatin family. The binding efficacy of the peptides is tested by extensive ...

Article

Molecular factors affecting the complex formation between deferiprone (L1) and Cu(II): Possible implications on efficacy and toxicity

Pashalidis, Ioannis; Kontoghiorghes, G. J. (2001)

Deferiprone (1,2-dimethyl-3-hydroxypyrid-4-one, L1, CAS 30652-11-0) is a new chelating drug used worldwide for the treatment of iron overloading conditions. Spectrophotometric and potentiometric measurements were carried ...

Article

Novel mixed metal Ag(I)-Sb(III)-metallotherapeutics of the NSAIDs, aspirin and salicylic acid: Enhancement of their solubility and bioactivity by using the surfactant CTAB

Gkaniatsou, E. I.; Banti, Christina N.; Kourkoumelis, Nikolaos; Skoulika, S.; Manoli, Maria; Tasiopoulos, Anastasios J.; Hadjikakou, Sotiris K. (2015)

The already known Ag(I)-Sb(III) compound of the formula {Ag(Ph3Sb)3(NO3)} (1) and two novel mixed metal Ag(I)-Sb(III) metallotherapeutics of the formulae {Ag(Ph3Sb)3(SalH)}(2) and {Ag(Ph3Sb)3(Asp)}(3) (SalH2 = salicylic ...

Article

Optimization of biaryl piperidine and 4-amino-2-biarylurea MCH1 receptor antagonists using QSAR modeling, classification techniques and virtual screening

Melagraki, G.; Afantitis, Antreas; Sarimveis, H.; Koutentis, Panayiotis Andreas; Markopoulos, J.; Igglessi-Markopoulou, O. (2007)

This paper presents the results of an optimization study on biaryl piperidine and 4-amino-2-biarylurea MCH1 receptor antagonists, which was accomplished by using quantitative-structure activity relationships (QSARs), ...

Article

Probing nitrite coordination in horseradish peroxidase by resonance Raman spectroscopy: Detection of two binding sites

Ioannou, Androulla; Pinakoulaki, Eftychia (2017)

Nitrite is a powerful oxidant that affects the activity of peroxidases towards various substrates and leads to heme macrocycle modifications in members of the peroxidase family, such as the horseradish peroxidase (HRP). ...

Article

Proteus and the design of ligand binding sites

Polydorides, Savvas; Michael, E.; Mignon, D.; Druart, Karen; Archontis, Georgios Z.; Simonson, T. (2016)

This chapter describes the organization and use of Proteus, a multitool computational suite for the optimization of protein and ligand conformations and sequences, and the calculation of pKα shifts and relative binding ...

Article

Recognition of ribonuclease A by 3′-5′-pyrophosphate-linked dinucleotide inhibitors: A molecular dynamics/continuum electrostatics analysis

Polydoridis, Savvas; Leonidas, Demetres D.; Oikonomakos, Nikos G.; Archontis, Georgios Z. (2007)

The proteins of the pancreatic ribonuclease A (RNase A) family catalyze the cleavage of the RNA polymer chain. The development of RNase inhibitors is of significant interest, as some of these compounds may have a therapeutic ...