Dan Mihailescu

Characteristics of ionic transport processes in fish intestinal epithelial cells

A general mathematical version of the cell model of a leaky epithelium for the NaCl absorption is presented, analysed and integrated numerically. The model consists in the adequate differential equations that describe the rate of change of the intracellular ion concentrations and are expressed in strict accordance with the law of mass conservation. The model includes many state variables representing ion concentrations, the cell volume, and membrane potentials. Ion movements are described by the Michaelis-Menten kinetics or by the constant field flux equation (Goldman-Hodgkin-Katz). In this paper, we model the intracellular ion concentrations, change in the cell volume, the transmembrane flux and membrane potentials of intestinal epithelium of both fresh water and sea water fish, and generate several simulations (in both the steady state and the transient state analysis) that appear to accord with prior experimental data in this area. For the ion movements of the sea water fish intestine, there were included a Na+/K+ pump, a K(+)-Cl- symport system, the K+ and Cl- channels in the basolateral membrane, whereas a Na(+)-K(+)-2Cl- cotransporter for NaCl absorption and K+ channels are located in the apical membrane. In the fresh water fish intestinal cells, the NaCl absorption is performed by two coupled antiporters Na+/H+ and Cl-/HCO3- presumably responsible for the intracellular pH regulation. In this type of cells, Na+ and K+ channels are located within the apical membrane, whereas Cl- channels are located within the basolateral membrane. The osmotically induced water transport across the apical and basolateral membranes has been taken into account as well. The simulations plot the steady state values for membrane potential difference, short-circuit current and intracellular ionic concentrations using the magnitude of the transmembrane flux through the Na+/K+ pump and Na(+)-K(+)-2Cl- cotransporter, or the basolateral Cl- permeability as dependent variables. The model behaves appropriately with regard to several experimental studies regarding the hyperpolarization (sea water fish intestine) and depolarization (fresh water fish intestine) of the apical membrane potential and inhibition of the short-circuit flux with reduced NaCl absorption. The model is also used to make several analytical predictions regarding the response of the membrane potential and ionic concentrations to variations in the basolateral Cl- flux. Furthermore, maintaining conservation of both mass and electroneutrality and taking into account the osmolar forces is an important advantage, because it allows a rigorous analysis of the relationship between membrane potential difference, volume and flux. The model can be used in the analysis and planning of the experiments and is capable of predicting the instantaneous values of ionic fluxes and intracellular concentrations and of cell volume.

Evaluation of Antimicrobial Activity of New Mastoparan Derivatives Using QSAR and Computational Mutagenesis

Antimicrobial peptides, also called body defense peptides, are used against a wide range of pathogens, such as negative- and positive-gram bacteria, mycobacteria, fungi, viruses, etc. Contrary to antibiotics, antimicrobial peptides do not develop resistance. Their wide antimicrobial spectrum situates them as important and attractive targets in research and pharmaceutical industry in order to obtain new structures using modern drug design techniques. We present here eleven QSAR models in which antimicrobial activity expressed as minimal inhibitory concentration values at Bacillus subtilis of 37 mastoparan analogs was correlated with different physicochemical parameters like: number of hydrophobic centers, molecular area and volume, internal dipole moment, refractivity, RPCG (relative positive charges) and number of donor and acceptor atoms generating by use of the computational software Sybyl. Significant R2 (0.68–0.72) correlation coefficients and standard error of prediction SEE (0.199–0.230) were obtained, indicating that the established equations can be used. Thus, these linear models allowed us to create a library of 19 derivatives of mastoparan analogs obtained through computational mutagenesis. We propose this library of compounds as a source of possible derivatives with a more potent antimicrobial activity.

Comparative study of some energetic and steric parameters of the wild type and mutants HIV-1 protease: a way to explain the viral resistance.

Because, in vivo, the HIV‐1 PR (HIV‐1 protease) present a high mutation rate we performed a comparative study of the energetic behaviors of the wild type HIV‐1 PR and four type of mutants: Val82/Asn; Val82/Asp; Gln7/Lys, Leu33/Ile, Leu63/Ile; Ala71/Thr, Val82/Ala. We suggest that the energetic fluctuation (electrostatic, van der Waals and torsion energy) of the mutants and the solvent accessible surface (SAS) values can be useful to explain the viral resistance process developed by HIV‐1 PR. The number and localization of enzyme mutations induce important modifications of the van der Waals and torsional energy, while the electrostatic energy has an insignificant fluctuation. We showed that the viral resistance can be explored if the solvent accessible surfaces of the active site for the mutant structures are calculated. In this paper we have obtained the solvent accessible surface for a group of 15 mutants (11 mutants obtained by Protein Data Bank (PDB) file, 4 mutants modeled by CHARMM software) and for the wild type HIV‐1 PR). Our study try to show that the number and localization of the mutations are factors which induce the HIV‐1 PR viral resistance. The larger solvent accessible surface could be recorded for the point mutant Val 82/Phe.

Evaluation of the Pharmacological Descriptors Related to the Induction of Antidepressant Activity and its Prediction by QSAR/QRAR Methods

Antidepressants are psychiatric agents used for the treatment of different types of depression, being at present amongst the most commonly prescribed drugs, while their effectiveness and adverse effects are still the subject of many studies. To reduce the inefficiency of known antidepressants caused by their side-effects, many research efforts have recently focused on the development of improved strategies for new antidepressants drug design. For this reason it is necessary to apply very fast and precise techniques, such as QSAR (Quantitative Structure-Activity Relationships) and QRAR (Quantitative Retention-Activity Relationship), which are capable to analyze and predict the biological activity for these structures, taking in account the possible changes of the molecular structures and chromatographic parameters. We discuss the pharmaceutical descriptors (van der Waals, electrostatic, hydrophobicity, hydrogen donor/acceptor bond, Verloops parameters, polar area) involved in QSAR and also chromatographic parameters involved in QRAR studies of antidepressants. Antidepressant activities of alkanol piperazine, acetamides, arylpiperazines, thienopyrimidinone derivatives (as preclinical antidepressants) and also the antidepressants already used in clinical practice are mentioned.

Pharmacological descriptors related to the binding of Gp120 to CD4 corresponding to 60 representative HIV-1 strains

The standardization of HIV-1 strains for vaccine tests include the use of viral reference panels. We determined a series of pharmacological descriptors (molecular surfaces, volumes, electrostatic energies, solvation energies, number of atoms, number of hydrogen donors or acceptors and number of rigid bonds) for the gp120 CD4-binding sites structures in the unliganded state from a reference panel of 60 diverse strains of HIV-1. We identified the descriptors that varied significantly between the strains, the outliner strains for each descriptor set and the possible correlations between the descriptors. Our results improve the knowledge about gp120, its molecular and possible neutralization properties.

Recent Trends on QSAR in the Pharmaceutical Perceptions

Description: Quantitative Structure-Activity Relationship (QSAR) is a field where true multidisciplinary approaches are being used. This volume titled Recent Trends on QSAR in the Pharmaceutical Perceptions offers an overview on the latest advancements in the field. The e-book explains both basic approaches and new approaches and ideas in QSAR research, providing readers with an impression of recent inclinations and advances in different aspects of the QSAR strategies, such as descriptors, methods of modeling and validation. This e-book is a valuable reference for pharmacologists, medicinal chemists, drug designers, biotechnologists and industry (pharmaceutical and chemical) professionals. It should serve as an important reference material to stimulate interactions and bridge the gap between participants in academia and industries.

3D-QSAR Design of New Escitalopram Derivatives for the Treatment of Major Depressive Disorders

Antidepressants are psychiatric agents used for the treatment of different types of depression being at present amongst the most commonly prescribed drug, while their effectiveness and adverse effects are the subject of many studies and competing claims. Having studied five QSAR models predicting the biological activities of 18 antidepressants, already approved for clinical treatment, in interaction with the serotonin transporter (SERT), we attempted to establish the membrane ions’ contributions (sodium, potassium, chlorine and calcium) supplied by donor/acceptor hydrogen bond character and electrostatic field to the antidepressant activity. Significant cross-validated correlation q2 (0.5–0.6) and the fitted correlation r2 (0.7–0.82) coefficients were obtained indicating that the models can predict the antidepressant activity of compounds. Moreover, considering the contribution of membrane ions (sodium, potassium and calcium) and hydrogen bond donor character, we have proposed a library of 24 new escitalopram structures, some of them probably with significantly improved antidepressant activity in comparison with the parent compound.

The flexibility of hydrated bovine serum albumin investigated by THz spectroscopy and molecular modeling

The native cellular environment represents a crowded system comprising high concentrations of soluble molecules that interact mostly in a nonspecific manner. Some of the macromolecular crowding effects occurring in biological media are conformational changes and macromolecular associations. Most of our knowledge on protein folding and protein-protein interactions was acquired from experiments on proteins in dilute solutions or from theoretical models of isolated proteins in either explicit or implicit solvent. Here we present a 50% w/w bovine serum albumin (BSA) solution model that comprises two solute molecules included in a single water box. We determined the vibration spectrum of the 50% w/w BSA solution using THz spectroscopy and we calculated the theoretical THz spectrum. We observed a good correlation between the experimental and theoretical spectra for the frequency range of 0.3 - 1.5 THz. We also investigated the contribution of each BSA molecule to the solution THz spectrum by simulating THz spectra of the two BSA molecules from the solution model and water, each accounting for a 50% w/w BSA solution. The spectra appear to be similar. As the two molecules in our solution model have different conformations, we investigated the importance of the apparently insignificant differences between simulated THz spectra of the two proteins. We found that the differences should be considered significant, as they reflect differences between the flexibility of the two BSA molecules.

Structure–Biological Function Relationship Extended to Mitotic Arrest-Deficient 2-Like Protein Mad2 Native and Mutants-New Opportunity for Genetic Disorder Control

Overexpression of mitotic arrest-deficient proteins Mad1 and Mad2, two components of spindle assembly checkpoint, is a risk factor for chromosomal instability (CIN) and a trigger of many genetic disorders. Mad2 transition from inactive open (O-Mad2) to active closed (C-Mad2) conformations or Mad2 binding to specific partners (cell-division cycle protein 20 (Cdc20) or Mad1) were targets of previous pharmacogenomics studies. Here, Mad2 binding to Cdc20 and the interconversion rate from open to closed Mad2 were predicted and the molecular features with a critical contribution to these processes were determined by extending the quantitative structure-activity relationship (QSAR) method to large-size proteins such as Mad2. QSAR models were built based on available published data on 23 Mad2 mutants inducing CIN-related functional changes. The most relevant descriptors identified for predicting Mad2 native and mutants action mechanism and their involvement in genetic disorders are the steric (van der Waals area and solvent accessible area and their subdivided) and energetic van der Waals energy descriptors. The reliability of our QSAR models is indicated by significant values of statistical coefficients: Cross-validated correlation q2 (0.53–0.65) and fitted correlation r2 (0.82–0.90). Moreover, based on established QSAR equations, we rationally design and analyze nine de novo Mad2 mutants as possible promoters of CIN.

Prediction of improved antimicrobial mastoparan derivatives by 3D-QSAR-CoMSIA/CoMFA and computational mutagenesis

Antimicrobial peptides are an important class of therapeutic agents used against a wide range of pathogens such as gram-negative and -positive bacteria, fungi, and viruses. The minimal inhibitory concentration at the level of the pathogen membrane is a major determinant of the pharmacokinetic behavior and, consequently, it can affect their antimicrobial activity. Here we generated quantitative structure-activity relationship models (3D-QSAR—comparative molecular field analysis/comparative molecular similarity indices analysis) using a database of 33 mastoparan analogs, antimicrobial peptides with known experimental activity, and further used these models to predict the minimal inhibitory concentration for 18 new mastoparan analogs, obtained by computational mutagenesis. We discuss two options for structural alignment of mastoparan analogs: superposition of Cα trace atoms or superposition of all backbone atoms. Significant values of the cross-validated correlation q2 (higher than 0.60) and the fitted correlation r2 (higher than 0.90) of our models indicate that they are reliable enough for activity prediction in the case of new derivatives. This allows us to identify compounds with possibly enhanced antimicrobial activity against Bacillus subtilis, which are suggested for further experimental studies.Graphical Abstract