Tom Solmajer

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Papers by Tom Solmajer

In Silico Discovery of a Substituted 6-Methoxy-quinalidine with Leishmanicidal Activity in Leishmania infantum

Molecules, Mar 27, 2018

There is an urgent need for the discovery of new antileishmanial drugs with a new mechanism of ac... more There is an urgent need for the discovery of new antileishmanial drugs with a new mechanism of action. Type 2 NADH dehydrogenase from Leishmania infantum (LiNDH2) is an enzyme of the parasite’s respiratory system, which catalyzes the electron transfer from NADH to ubiquinone without coupled proton pumping. In previous studies of the related NADH: ubiquinone oxidoreductase crystal structure from Saccharomyces cerevisiae, two ubiquinone-binding sites (UQI and UQII) were identified and shown to play an important role in the NDH-2-catalyzed oxidoreduction reaction. Based on the available structural data, we developed a three-dimensional structural model of LiNDH2 using homology detection methods and performed an in silico virtual screening campaign to search for potential inhibitors targeting the LiNDH2 ubiquinone-binding site 1—UQI. Selected compounds displaying favorable properties in the computational screening experiments were assayed for inhibitory activity in the structurally simi...

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Quantitative structure–activity relationship study of antitubercular fluoroquinolones

Molecular Diversity, Mar 14, 2010

Quantitative structure-activity relationship study on three diverse sets of structurally similar ... more Quantitative structure-activity relationship study on three diverse sets of structurally similar fluoroquinolones was performed using a comprehensive set of molecular descriptors. Multiple linear regression technique was applied as a preprocessing tool to find the set of relevant descriptors (10) which are subsequently used in the artificial neural networks approach (non-linear procedure). The biological activity in the series (minimal inhibitory concentration (µg/mL) was treated as negative decade logarithm, pMIC). Using the non-linear technique counter propagation artificial neural networks, we obtained good predictive models. All models were validated using cross validation leave-one-out procedure. The results (the best models: Assay1, R = 0.8108; Assay2, R = 0.8454, and Assay3, R = 0.9212) obtained on external, previously excluded test datasets show the ability of these models in providing structure-activity relationship of fluoroquinolones. Thus, we demonstrated the advantage of non-linear approach in prediction of biological activity in these series. Furthermore, these validated models could be proficiently used for the design of novel structurally similar fluoroquinolone analogues with potentially higher activity.

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QSAR of flavonoids: 4. Differential inhibition of aldose reductase and p561ck protein tyrosine kinase

Croatica Chemica Acta, 2002

Flavonoids are a group of low molecular weight plant products, based on the parent compound, flav... more Flavonoids are a group of low molecular weight plant products, based on the parent compound, flavone (2-phenylchromone) and have shown potential for application in a variety of pharmacological targets. By using random screening techniques flavones have been proposed as inhibitors of aldose reductase, an enzyme crucial in the treatment of diabetic complications such as cataract formation. On the other hand, a large number of natural and synthetic flavonoids are being tested as specific inhibitors of protein tyrosine kinase (PTK). Kinetic analyses of the PTK inhibition indicate that flavonoids are competitive inhibitors with respect to the nucleotide ATP. A thorough investigation of the available experimental data base by using both classical and quantum chemical descriptors has been performed in order to develop quantitative structure-activity relationships for these enzyme systems. Relevance of the descriptors to binding properties of both enzyme receptors active site is proposed an...

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Conformational Study of Catecholamines in Solution

Zeitschrift für Naturforschung C, 1983

Conformations of noradrenaline, dopamine and ephedrine have been studied in aqueous solutions usi... more Conformations of noradrenaline, dopamine and ephedrine have been studied in aqueous solutions using high resolution PMR spectroscopy. We found that for dopamine the mole fraction of trans rotamer is increased if pH is changed from acidic to basic while for noradrenaline and ephedrine the opposite trend is observed: gauche rotamer forms of the side chain become more populated. These changes are discussed in relation to the role of the benzylic hydroxyl group for conformation and/or binding to a receptor site in the biophase.

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In Silico Discovery of a Substituted 6-Methoxy-quinalidine with Leishmanicidal Activity in Leishmania infantum

Molecules (Basel, Switzerland), Jan 27, 2018

There is an urgent need for the discovery of new antileishmanial drugs with a new mechanism of ac... more There is an urgent need for the discovery of new antileishmanial drugs with a new mechanism of action. Type 2 NADH dehydrogenase from (NDH2) is an enzyme of the parasite's respiratory system, which catalyzes the electron transfer from NADH to ubiquinone without coupled proton pumping. In previous studies of the related NADH: ubiquinone oxidoreductase crystal structure from , two ubiquinone-binding sites (UQ and UQ) were identified and shown to play an important role in the NDH-2-catalyzed oxidoreduction reaction. Based on the available structural data, we developed a three-dimensional structural model of NDH2 using homology detection methods and performed an in silico virtual screening campaign to search for potential inhibitors targeting the NDH2 ubiquinone-binding site 1-UQ. Selected compounds displaying favorable properties in the computational screening experiments were assayed for inhibitory activity in the structurally similar recombinant NDH-2 from and leishmanicidal acti...

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Chemometrical Exploration of Combinatorially Generated Drug-like Space of 6-fluoroquinolone Analogs: A QSAR Study

A classical virtual combinatorial chemistry approach (CombiChem) was applied for combinatorial ge... more A classical virtual combinatorial chemistry approach (CombiChem) was applied for combinatorial generation of 5590 novel structurally-similar 6-fluoroquinolone analogs by using a virtual synthetic pathway with selected primary (43) and secondary amines (130). The obtained virtual combinatorial library was filtered using an in-house developed set of cheminformatics drug-likeness filters with pre-integrated Boolean options (TRUE/FALSE) for compounds reduction/selection. The retained number (304) of fluoroquinolone analogs (with TRUE outcome) defines the drug-like chemical space (CombiData). Quantitative structure-activity relationships (QSAR) study on these 304 virtually generated 6-fluoroquinolone analogs with unknown activity values was performed using a pre-built five-parameter multiple linear regression (MLR) model developed on a set of compounds with experimentally determined activity values (R tr = 0.8417, R tr-cv = 0.7884). The obtained activity values for the unknown compounds together with the model results were used to define the applicability domain (AD). The obtained AD offers a good graphical representation and establishment of structure-activity relationships (SAR) which could be used for design of new 6-fluoroquinolones with possible better activity.

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Precursor of a β-lactamase inhibitor: allyl (4S,8S,9R)-10-[(E)-ethylidene]-4-methoxy-11-oxo-1-azatricyclo[7.2.0.03,8]undec-2-ene-2-carboxylate

Acta Crystallographica Section C Crystal Structure Communications, 2002

ABSTRACT The molecular structure of the title tricyclic compound, C(17)H(21)NO(4), which is the i... more ABSTRACT The molecular structure of the title tricyclic compound, C(17)H(21)NO(4), which is the immediate precursor of a potent synthetic inhibitor [Lek157: sodium (8S,9R)-10-[(E)-ethylidene]-4-methoxy-11-oxo-1-azatricyclo[7.2.0.0(3,8)]undec-2-ene-2-carboxylate] with remarkable potency, provides experimental evidence for the previously modelled relative position of the fused cyclohexyl ring and the carbonyl group of the beta-lactam ring, which takes part in the formation of the initial tetrahedral acyl-enzyme complex. In this hydrophobic molecule, the overall geometry is influenced by C[bond]H...O intramolecular hydrogen bonds [3.046 (4) and 3.538 (6) A, with corresponding normalized H.O distances of 2.30 and 2.46 A], whereas the molecules are interconnected through intermolecular C[bond]H...O hydrogen bonds [3.335 (4)-3.575 (5) A].

Benzene-1,3-dicarboxylic acid 2,5-dimethylpyrrole derivatives as multiple inhibitors of bacterial Mur ligases (MurC–MurF)

Bioorganic & Medicinal Chemistry, 2014

Enzymes catalyzing the biosynthesis of bacterial peptidoglycan represent traditionally a collecti... more Enzymes catalyzing the biosynthesis of bacterial peptidoglycan represent traditionally a collection of highly selective targets for novel antibacterial drug design. Four members of the bacterial Mur ligase family-MurC, MurD, MurE and MurF-are involved in the intracellular steps of peptidoglycan biosynthesis, catalyzing the synthesis of the peptide moiety of the Park&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;s nucleotide. In our previous virtual screening campaign, a chemical class of benzene-1,3-dicarboxylic acid 2,5-dimethylpyrrole derivatives exhibiting dual MurD/MurE inhibition properties was discovered. In the present study we further investigated this class of compounds by performing inhibition assays on all four Mur ligases (MurC-MurF). Furthermore, molecular dynamics (MD) simulation studies of one of the initially discovered compound 1 were performed to explore its geometry as well as its energetic behavior based on the Linear Interaction Energy (LIE) method. Further in silico virtual screening (VS) experiments based on the parent active compound 1 were conducted to optimize the discovered series. Selected hits were assayed against all Escherichia coli MurC-MurF enzymes in biochemical inhibition assays and molecules 10-14 containing benzene-1,3-dicarboxylic acid 2,5-dimethylpyrrole coupled with five member-ring rhodanine moiety were found to be multiple inhibitors of the whole MurC-MurF cascade of bacterial enzymes in the micromolar range. Steady-state kinetics studies suggested this class to act as competitive inhibitors of the MurD enzyme towards d-Glu. These compounds represent novel valuable starting point in the development of novel antibacterial agents.

Thiol-reactive Clenbuterol Analogues Conjugated to Bovine Serum Albumin

Zeitschrift für Naturforschung C, 2004

Several novel thiol-reactive clenbuterol analogues were coupled in high yield with bovine serum a... more Several novel thiol-reactive clenbuterol analogues were coupled in high yield with bovine serum albumin (BSA). After labelling of unreacted cysteines with maleimide spin label (MiSL), the yield of the coupling reaction was determined by electron paramagnetic resonance (EPR) spectroscopy and spectral analysis. Two spin-probe populations with different mobility states were quantitatively determined. Molecular dynamics was used to model the structure of clenbuterol analogues and spin label conjugated to BSA and recognition of conjugates by anti-clenbuterol antibodies was demonstrated. The recognition of BSA-A, BSA-C and BSAS conjugates with monoclonal and polyclonal anti-clenbuterol (mCLB-Ab and rCLB-Ab) antibodies was an indication, that chlorine substituents on the aromatic ring of clenbuterol derivatives are not necessary for the binding of antibodies to the conjugates. These results confirmed the importance of the tert-butylamino group as a part of the epitope and contribute to the...

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Structural analysis of a Peptide fragment of transmembrane transporter protein bilitranslocase

PloS one, 2012

Using a combination of genomic and post-genomic approaches is rapidly altering the number of iden... more Using a combination of genomic and post-genomic approaches is rapidly altering the number of identified human influx carriers. A transmembrane protein bilitranslocase (TCDB 2.A.65) has long attracted attention because of its function as an organic anion carrier. It has also been identified as a potential membrane transporter for cellular uptake of several drugs and due to its implication in drug uptake, it is extremely important to advance the knowledge about its structure. However, at present, only the primary structure of bilitranslocase is known. In our work, transmembrane subunits of bilitranslocase were predicted by a previously developed chemometrics model and the stability of these polypeptide chains were studied by molecular dynamics (MD) simulation. Furthermore, sodium dodecyl sulfate (SDS) micelles were used as a model of cell membrane and herein we present a high-resolution 3D structure of an 18 amino acid residues long peptide corresponding to the third transmembrane par...

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Spin-Labeled Alkylphospholipids in a Dipalmitoylphosphatidylcholine Bilayer: Molecular Dynamics Simulations

The Journal of Physical Chemistry B, 2006

Molecular dynamics simulation has been performed to investigate the structural properties of peri... more Molecular dynamics simulation has been performed to investigate the structural properties of perifosine and its synthetic spin-labeled alkylphospholipid analogues. The conformations adopted by these compounds in water and in a dipalmitoylphosphatidylcholine bilayer as a function of the presence and position of the N-oxyl-4&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;,4&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;-dimethyloxazolidine ring (doxyl group) have been investigated by all-atom molecular dynamics. No predominant conformation was observed in water, but the molecules adopt specific orientations and conformations in the lipid bilayer. As is expected, alkyl chains tend to insert into the hydrophobic core, while charged groups stay at the lipid-water interface. A doxyl group in the middle of the alkyl chain moves up to the interface region, thus preventing adoption of the extended conformation. Compounds with a doxyl group close to the polar head group adopt conformations similar to that of unlabeled perifosine within the first nanoseconds of simulation. When the doxyl group is at the end of alkyl chain, the spin-labeled molecule needs more time to reach equilibrium. These results indicate a considerable effect of the doxyl position within the alkyl chain on its localization in the lipid bilayer and can be extended further to other similar spin probes used in the electron paramagnetic resonance spectroscopy of biological membranes.

Electrostatic screening in molecular dynamics simulations

"Protein Engineering, Design and Selection", 1991

The screened Coulombic potential has been shown to describe satisfactorily equilibrium properties... more The screened Coulombic potential has been shown to describe satisfactorily equilibrium properties like pA" shifts, the effects of charged groups on redox potentials and binding constants of metal ions. To test how well the screening of the electrostatic potential describes the dynamical trajectory of a macromolecular system, a series of comparative simulations have been carried out on a protein system which explicitly included water molecules and a system in vacuo. For the system without solvent the results of using (i) the standard potential form were compared with results of (ii) the potential where the Coulomb term was modified by the inclusion of a distance dependent dielectric, e(r), to model the screening effect of bulk water, and (iii) standard potential modified by reducing the charge on ionized residue side chains. All molecular dynamics simulations have been carried out on bovine pancreatic trypsin inhibitor. Comparisons between the resulting trajectories, averaged structures, hydrogen bonding patterns and properties such as solvent accessible surface area and radius of gyration are described. The results show that the dynamical behaviour of the protein calculated with a screened electrostatic term compares more favourably with the time-dependent structural changes of the full system with explicitly included water than the standard vacuum simulation.

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Reply to ‘Comment on models for electrostatic effects in proteins’ by J.Âqvist

"Protein Engineering, Design and Selection", 1992

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Electrostatic effects in proteins: comparison of dielectric and charge models

"Protein Engineering, Design and Selection", 1991

Two approaches for calculating electrostatic effects in proteins are compared and an analysis is ... more Two approaches for calculating electrostatic effects in proteins are compared and an analysis is presented of the dependence of calculated properties on the model used to define the charge distribution. Changes in electrostatic free energy have been calculated using a screened Coulomb potential (SCP) with a distance-dependent effective dielectric permittivity to model bulk solvent effects and a finite difference approach to solve the Poisson-Boltzmann (FDPB) equation. The properties calculated include shifts in dissociation constants of ionizable groups, the effect of annihilating surface charges on the binding of metals, and shifts in redox potentials due to changes in the charge of ionizable groups. In the proteins considered the charged sites are separated by 3.5-12 A. It is shown that for the systems studied in this distance range the SCP yields calculated values which are at least as accurate as those obtained from solution of the FDPB equation. In addition, in the distance range 3-5 A the SCP gives substantially better results than the FDPB equation. Possible sources of this difference between the two methods are discussed. Shifts in binding constants and redox potentials were calculated with several standard charge sets, and the resulting values show a variation of 20-40% between the 'best' and 'worst' cases. From this study it is concluded that in most applications, changes in electrostatic free energies can be calculated economically and reliably using an SCP approach with a single functional form of the screening function.

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Combinatorially-generated library of 6-fluoroquinolone analogs as potential novel antitubercular agents: a chemometric and molecular modeling assessment

Journal of Molecular Modeling, 2011

The virtual combinatorial chemistry approach as a methodology for generating chemical libraries o... more The virtual combinatorial chemistry approach as a methodology for generating chemical libraries of structurally-similar analogs in a virtual environment was employed for building a general mixed virtual combinatorial library with a total of 53.871 6-FQ structural analogs, introducing the real synthetic pathways of three well known 6-FQ inhibitors. The druggability properties of the generated combinatorial 6-FQs were assessed using an in-house developed druglikeness filter integrating the Lipinski/Veber rule-sets. The compounds recognized as drug-like were used as an external set for prediction of the biological activity values using a neural-networks (NN) model based on an experimentally-determined set of active 6-FQs. Furthermore, a subset of compounds was extracted from the pool of drug-like 6-FQs, with predicted biological activity, and subsequently used in virtual screening (VS) campaign combining pharmacophore modeling and molecular docking studies. This complex scheme, a powerful combination of chemometric and molecular modeling approaches provided novel QSAR guidelines that could aid in the further lead development of 6-FQs agents.