%0 Journal Article %J Bioorganic & Medicinal Chemistry %D 2011 %T 13,13-Dimethyl-des-C,D analogues of (20S)-1α,25-dihydroxy-2-methylene-19-norvitamin D₃ (2MD): total synthesis, docking to the VDR, and biological evaluation %A Katarzyna Plonska-Ocypa %A Izabela Sibilska %A Rafal R. Sicinski %A Wanda Sicinska %A Lori A. Plum %A Hector F. DeLuca %K Animals %K Calcitriol %K Cell Differentiation %K Crystallography, X-Ray %K HL-60 Cells %K Humans %K Male %K Models, Molecular %K Molecular Conformation %K Rats %K Receptors, Calcitriol %K Structure-Activity Relationship %X As a continuation of our studies focused on the vitamin D compounds lacking the C,D-hydrindane system, 13,13-dimethyl-des-C,D analogues of (20S)-1α,25-dihydroxy-2-methylene-19-norvitamin D(3) (2, 2MD) were prepared by total synthesis. The known cyclohexanone 30, a precursor of the desired A-ring phosphine oxide 11, was synthesized starting with the keto acetal 13, whereas the aldehyde 12, constituting an acyclic 'upper' building block, was obtained from the isomeric esters 34, prepared previously in our laboratory. The commercial 1,4-cyclohexanedione monoethylene ketal (13) was enantioselectively α-hydroxylated utilizing the α-aminoxylation process catalyzed by l-proline, and the introduced hydroxy group was protected as a TBS, TPDPS, and SEM ether. Then the keto group in the obtained compounds 15-17 was methylenated and the allylic hydroxylation was performed with selenium dioxide and pyridine N-oxide. After separation of the isomers, the newly introduced hydroxy group was protected and the ketal group hydrolyzed to yield the corresponding protected (3R,5R)-3,5-dihydroxycyclohexanones 30-32. The esters 34, starting compounds for the C,D-fragment 12, were first α-methylated, then reduced and the resulted primary alcohols 36 were deoxygenated using the Barton-McCombie protocol. Primary hydroxy group in the obtained diether 38 was deprotected and oxidized to furnish the aldehyde 12. The Wittig-Horner coupling of the latter with the anion of the phosphine oxide 11, followed by hydroxyl deprotection furnished two isomeric 13,13-dimethyl-des-C,D analogues of 2MD (compounds 10 and 42) differing in configuration of their 7,8-double bond. Pure vitamin D analogues were isolated by HPLC and their biological activity was examined. The in vitro tests indicated that, compared to the analogue 7, unsubstituted at C-13, the synthesized vitamin D analogue 10 showed markedly improved VDR binding ability, significantly enhanced HL-60 differentiation activity as well as increased transcriptional potency. Docking simulations provided a rational explanation for the observed binding affinity of these ligands to the VDR. Biological in vivo tests proved that des-C,D compound 10 retained some intestinal activity. Its geometrical isomer 42 was devoid of any biological activity. %B Bioorganic & Medicinal Chemistry %V 19 %P 7205-20 %8 2011 Dec 1 %G eng %N 23 %R 10.1016/j.bmc.2011.09.048 %0 Journal Article %J International Journal of Molecular Medicine %D 2011 %T Analysis and optimization of interactions between peptides mimicking the GD2 ganglioside and the monoclonal antibody 14G2a %A Irena Horwacik %A Mateusz Kurcinski %A Malgorzata Bzowska %A Aleksandra K. Kowalczyk %A Dominik Czaplicki %A Andrzej Koliński %A Hanna Rokita %K Amino Acid Sequence %K Antibodies %K Binding Sites %K Cell Line %K Gangliosides %K Gangliosides: immunology %K Humans %K Models %K Molecular %K Molecular Mimicry %K Molecular Sequence Data %K Monoclonal %K Monoclonal: chemistry %K Monoclonal: immunology %K Neuroblastoma %K Neuroblastoma: genetics %K Neuroblastoma: immunology %K Peptide Library %K Peptides %K Peptides: chemistry %K Peptides: immunology %K Structure-Activity Relationship %K Tumor %X

Overexpression of the GD2 ganglioside (GD2) is a hallmark of neuroblastoma. The antigen is used in neuroblastoma diagnosis and to target newly developed therapies to cancer cells. Peptide mimetics are novel approaches in the design of antigens for vaccine development. We previously reported the isolation of five GD2-mimicking peptides from the LX-8 phage display library with the monoclonal antibody (mAb) 14G2a. The goal of our current study was to analyze and optimize the binding of the peptide mimetics to the mAb 14G2a. Therefore, we performed further experiments and supported them with molecular modeling to investigate structure-activity relationships that are the basis for the observed mimicry of GD2 by our peptides. Here, we show that the peptides have overlapping binding sites on the mAb, 14G2a and restricted specificity, as they did not crossreact with other ganglioside-specific antibodies tested. In addition we demonstrate that the phage environment was involved in the process of selection of our peptides. The AAEGD sequence taken from the viral major coat protein, p8, and added to the C-termini of the peptides \#65, \#85 and \#94 significantly improved their binding to the mAb, 14G2a. By application of analogs with amino acid substitutions and sequence truncations, we elucidated the structure-activity relationships necessary for the interactions between the 14G2a mAb and the peptide \#94 (RCNPNMEPPRCF). We identified amino acids indispensable for the observed GD2-mimicry by \#94 and confirmed a pivotal role of the disulphide bridge between the cysteine residues of \#94 for binding to the mAb 14G2a. More importantly, we report five new peptides demonstrating a significant improvement of mAb 14G2a binding. The experimental data were supported and expanded with molecular modeling tools. Taken together, the experimental results and the in silico data allowed us to probe in detail the mechanism of the molecular mimicry of GD2 by the peptides. Additionally, we significantly optimized binding of the leading peptide sequence \#94 to the mAb 14G2a. We can conclude that our findings add to the knowledge on factors governing selections of peptide mimetics from phage-display libraries.

%B International Journal of Molecular Medicine %V 28 %P 47–57 %8 jul %G eng %U http://www.ncbi.nlm.nih.gov/pubmed/21455557 %R 10.3892/ijmm.2011.655 %0 Journal Article %J Biophys J %D 2008 %T Stretching to understand proteins - a survey of the protein data bank. %A Joanna I. Sulkowska %A Cieplak, Marek %K Computer Simulation %K Databases, Protein %K elasticity %K Models, Chemical %K Models, Molecular %K Proteins %K Sequence Analysis, Protein %K Stress, Mechanical %K Structure-Activity Relationship %X We make a survey of resistance of 7510 proteins to mechanical stretching at constant speed as studied within a coarse-grained molecular dynamics model. We correlate the maximum force of resistance with the native structure, predict proteins which should be especially strong, and identify the nature of their force clamps. %B Biophys J %V 94 %P 6-13 %8 2008 Jan 1 %G eng %N 1 %R 10.1529/biophysj.107.105973 %0 Journal Article %J Bioinformatics (Oxford, England) %D 2005 %T A new approach to prediction of short-range conformational propensities in proteins %A Dominik Gront %A Andrzej Koliński %K Algorithms %K Amino Acid %K Artificial Intelligence %K Chemical %K Computer Simulation %K Databases %K Gas Chromatography-Mass Spectrometry %K Gas Chromatography-Mass Spectrometry: methods %K Models %K Protein %K Protein Conformation %K Protein: methods %K Proteins %K Proteins: analysis %K Proteins: chemistry %K Sequence Alignment %K Sequence Alignment: methods %K Sequence Analysis %K Sequence Homology %K Structure-Activity Relationship %X

MOTIVATION: Knowledge-based potentials are valuable tools for protein structure modeling and evaluation of the quality of the structure prediction obtained by a variety of methods. Potentials of such type could be significantly enhanced by a proper exploitation of the evolutionary information encoded in related protein sequences. The new potentials could be valuable components of threading algorithms, ab-initio protein structure prediction, comparative modeling and structure modeling based on fragmentary experimental data. RESULTS: A new potential for scoring local protein geometry is designed and evaluated. The approach is based on the similarity of short protein fragments measured by an alignment of their sequence profiles. Sequence specificity of the resulting energy function has been compared with the specificity of simpler potentials using gapless threading and the ability to predict specific geometry of protein fragments. Significant improvement in threading sensitivity and in the ability to generate sequence-specific protein-like conformations has been achieved.

%B Bioinformatics (Oxford, England) %V 21 %P 981–987 %G eng %U http://www.ncbi.nlm.nih.gov/pubmed/15509604 %R 10.1093/bioinformatics/bti080 %0 Journal Article %J Journal of Medicinal Chemistry %D 2002 %T 2-Ethyl and 2-ethylidene analogues of 1alpha,25-dihydroxy-19-norvitamin D(3): synthesis, conformational analysis, biological activities, and docking to the modeled rVDR ligand binding domain. %A Rafal R. Sicinski %A Piotr Rotkiewicz %A Andrzej Koliński %A Wanda Sicinska %A Jean M. Prahl %A Connie M. Smith %A Hector F. DeLuca %K Animals %K Binding Sites %K Biological Transport %K Calcitriol %K Calcium %K Cell Differentiation %K Chromatography, High Pressure Liquid %K HL-60 Cells %K Humans %K Intestinal Mucosa %K Ligands %K Magnetic Resonance Spectroscopy %K Male %K Models, Molecular %K Molecular Conformation %K Rats %K Receptors, Calcitriol %K Spectrophotometry, Ultraviolet %K Structure-Activity Relationship %K Swine %X Novel 19-nor analogues of 1alpha,25-dihydroxyvitamin D(3) were prepared and substituted at C-2 with an ethylidene group. The synthetic pathway was via Wittig-Horner coupling of the corresponding A-ring phosphine oxides with the protected 25-hydroxy Grundmann's ketones. Selective catalytic hydrogenation of 2-ethylidene analogues provided the 2alpha- and 2beta-ethyl compounds. The 2-ethylidene-19-nor compounds with a methyl group from the ethylidene moiety in a trans relationship to the C(6)-C(7) bond (E-isomers) were more potent than the corresponding Z-isomers and the natural hormone in binding to the vitamin D receptor. Both geometrical isomers (E and Z) of (20S)-2-ethylidene-19-norvitamin D(3) and both 2alpha-ethyl-19-norvitamins (in the 20R- and 20S-series) have much higher HL-60 differentiation activity than does 1alpha,25-(OH)(2)D(3). Both E-isomers (20R and 20S) of 2-ethylidene vitamins are characterized by very high calcemic activity in rats. The three-dimensional structure model of the rat vitamin D receptor and the computational docking of four synthesized (20R)-19-norvitamin D(3) analogues into its binding pocket are also reported. %B Journal of Medicinal Chemistry %V 45 %P 3366-80 %8 2002 Aug 1 %G eng %N 16 %0 Journal Article %J Nature Biotechnology %D 2000 %T Structural genomics and its importance for gene function analysis %A Jeffrey Skolnick %A Jacquelyn S. Fetrow %A Andrzej Koliński %K Animals %K Computer Simulation %K Databases %K Evolution %K Factual %K Genome %K Humans %K Internet %K Molecular %K Molecular Biology %K Molecular Biology: methods %K Protein Folding %K Structure-Activity Relationship %X Structural genomics projects aim to solve the experimental structures of all possible protein folds. Such projects entail a conceptual shift from traditional structural biology in which structural information is obtained on known proteins to one in which the structure of a protein is determined first and the function assigned only later. Whereas the goal of converting protein structure into function can be accomplished by traditional sequence motif-based approaches, recent studies have shown that assignment of a protein's biochemical function can also be achieved by scanning its structure for a match to the geometry and chemical identity of a known active site. Importantly, this approach can use low-resolution structures provided by contemporary structure prediction methods. When applied to genomes, structural information (either experimental or predicted) is likely to play an important role in high-throughput function assignment. %B Nature Biotechnology %V 18 %P 283–287 %8 mar %G eng %U http://www.ncbi.nlm.nih.gov/pubmed/10700142 %R 10.1038/73723 %0 Journal Article %J Proceedings of the National Academy of Sciences of the United States of America %D 1986 %T Monte Carlo simulations on an equilibrium globular protein folding model %A Andrzej Koliński %A Jeffrey Skolnick %A Robert Yaris %K Models %K Protein Conformation %K Statistics as Topic %K Structural %K Structure-Activity Relationship %K Temperature %K Thermodynamics %X

Monte Carlo simulations were performed on a diamond lattice, globular protein model in which the trans conformational state is energetically favored over the gauche states (thereby perhaps favoring a beta-sheet secondary structure) and in which nonspecific nonbonded nearest-neighbor attractive interactions are allowed. If the attractive interactions are sufficiently weak that the molecule possesses a relatively high fraction of trans states in the denatured state, then on collapse, a beta-barrel tertiary structure, highly reminiscent of the "native" structure seen in beta-proteins, spontaneously forms. If, however, the attractive interactions are dominant, a coil-to-random globule collapse transition is observed. The roles of short-, medium-, and long-range interactions and topological constraints in determining the observed tertiary structure are addressed, and the implications and limitations of the simulations for the equilibrium folding process in renal globular proteins are explored.

%B Proceedings of the National Academy of Sciences of the United States of America %V 83 %P 7267–71 %8 oct %G eng %U http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=386697&tool=pmcentrez&rendertype=abstract