Design of proteins using rigid organic macrocycles as scaffolds

We have designed and synthesized new three-helix template-assembled synthetic proteins (TASPs) 1a-c. The template was the rigid cyclotribenzylene (CTB) macrocycle 2, which has C3 symmetry. Thiol moieties on the CTB template were used to link cysteine-containing peptide strands 3a-c via disulfide bonds. With designed peptide strands of 15 and 18 residues in length, the structure of TASPs 1a-c were determined to be helical in water according to circular dichroism (CD) spectroscopy. The helicities of TASPs 1a-c were unchanged over large ranges of pH (2-12) and salt concentrations (0-2 M KCl). TASPs 1a-c were also extremely resistant to chemical denaturants: it requires a guanidine hydrochloride (GnHCl) concentration of 7.4 M for TASPs 1a-c to lose 50% of their helicity. The major force for stabilization of TASPs 1a-c is the hydrophobic bundling of the helices.     

Fluorescence resonance energy transfer dye nucleotide terminators: a new synthetic approach for high-throughout DNA sequencing

Fluorescence resonance energy transfer (FRET) based dye-nucleotide terminators (10-13) were designed, synthesized, and formulated with Thermo Sequenase II DNA polymerase into a robust kit for high throughput DNA sequencing. The key energy transfer (ET) rigid and linear linker (2), required for the syntheses of energy transfer cassettes (6-9) was synthesized via Heck coupling reaction on t-Boc-L-4-iodo-phenylalanine (1) with N-TFA-propargylamine.     

A novel colorimetric fluoride sensor based on a semi‐rigid chromophore controlled by hydrogen bonding

A novel semi‐rigid latent chromophore E1, containing an amide subunit activated by an adjacent semi‐rigid intramolecular hydrogen‐bonding (IHB) unit, was designed for the detection of fluoride ion by the ‘naked‐eye’ in CH₃CN. Comparative studies on structural analogs (E2, E3, and E4) provided significant insight into the structural and functional role of the amide N–H and IHB segment in the selective recognition of fluoride ions. The deprotonation of the amide N–H followed by the enhancement of intramolecular charge transfer (ICT) induced the colorimetric detection of E1 for fluoride ion. Copyright © 2015 John Wiley & Sons, Ltd.     

Synthesis and pharmacological evaluation of pentacyclic 6a,7-dihydrodiindole and 2,3-dihydrodiindole derivatives as novel melatoninergic ligands

The synthesis of novel melatonin analogues 3a and 4a-c designed as melatonin receptor ligands is described. Among the newly synthesized ligands, 2-((S)-2-hydroxymethylindolin-1-ylmethyl)-melatonin 4b displayed the highest affinity for MT(1) receptors (K(i)=9.8 nM) and for MT(2) subtype (K(i)=7.8 nM), whereas the rigid pentacyclic ligand 3 showed the highest selectivity towards the MT(2) receptor subtype (K(i)=319.3 nM for MT(1) and K(i)=65.2 nM for MT(2)).     

Proline-glutamate chimeras in isopeptides. Synthesis and biological evaluation of conformationally restricted glutathione analogues

The two novel diastereoisomeric glutathione analogues 1 and 2 have been designed and synthesized by replacing the native gamma-glutamylic moiety with the conformational rigid skeleton of cis- or trans-4-carboxy-L-proline residue. Both analogues have been obtained by following the solution phase peptide chemistry methodologies and final reduction of the corresponding disulfide forms 13 and 14. The two analogues 1 and 2 have been tested towards gamma-glutamyltranspeptidase (gamma-GT) and human glutathione S-transferase (hGST P1-1). Both analogues 1 and 2 are completely resistant to enzymatic degradation by gamma-GT. The S-transferase utilizes the analogue 2 as a good substrate while is unable to bind the analogue 1.     

Guanylpiperidine peptidomimetics: potent and selective bis-cation inhibitors of factor Xa

A novel series of rigid P3-guanylpiperidine peptide mimics 3-14 was designed as potential factor Xa and prothrombinase inhibitors. Incorporation into a P2-gly-P1-argininal motif led to highly potent and selective inhibitors. The synthesis and biological activities of these derivatives are reported herein.     

Investigation of the S3 site of thrombin: design, synthesis and biological activity of 4-substituted 3-amino-2-pyridones incorporating P1-argininals

A novel scaffold for P4-P2 dipeptide mimics containing a rigid pyridone spacer was designed based on a virtual library strategy. Several selected nonpeptidic 4-aralkyl or 4-alkylpyridones incorporating a P1-argininal sequence were prepared. The modeling studies, synthesis and biological activities of these unique pyridone derivatives are reported herein.     

FLUORESCENCE RESONANCE ENERGY TRANSFER DYE NUCLEOTIDE TERMINATORS: A NEW SYNTHETIC APPROACH FOR HIGH-THROUGHOUT DNA SEQUENCING

Fluorescence resonance energy transfer (FRET) based dye-nucleotide terminators (10–13) were designed, synthesized, and formulated with Thermo Sequenase? II DNA polymerase into a robust kit for high throughput DNA sequencing. The key energy transfer (ET) rigid and linear linker (2), required for the syntheses of energy transfer cassettes (6–9) was synthesized via Heck coupling reaction on t-Boc-L-4-iodo-phenylalanine (1) with N-TFA-propargylamine.     

Topical Delivery of Coumestrol from Lipid Nanoemulsions Thickened with Hydroxyethylcellulose for Antiherpes Treatment

We have recently shown that coumestrol, an isoflavonoid-like compound naturally occurring in soybeans, alfafa, and red clover, inhibited Herpes Simplex Virus types 1 (HSV-1) and 2 (HSV-2) replication. In this study, we designed coumestrol formulations in an attempt to enable its topical delivery to mucosa tissues. Physicochemical and microscopic examinations suggested that coumestrol was efficiently incorporated in positively-charged nanoemulsions dispersed in a hydroxyethylcellulose gel. The higher coumestrol flux through excised porcine esophageal mucosa was detected from nanoemulsions composed by a fluid phospholipid (dioleylphosphocholine, DOPC) in comparison with that of a rigid one (distearoylphosphocholine, DSPC) in two mucosa conditions (intact and injured). Such results were supported by confocal fluorescence images. Furthermore, the low IC₅₀ values demonstrated an increasement in the antiviral inhibition against HSV-1 and HSV-2 after incorporation of coumestrol into nanoemulsions containing DOPC. Overall, coumestrol-loaded nanoemulsions proved to be beneficial for herpes simplex treatment.     

Introducing a Rigid Loop Structure from Deer into Mouse Prion Protein Increases Its Propensity for Misfolding In Vitro

Prion diseases are fatal neurodegenerative disorders characterized by misfolding of the cellular prion protein (PrP^c) into the disease-associated isoform (PrP^Sc) that has increased β-sheet content and partial resistance to proteolytic digestion. Prion diseases from different mammalian species have varying propensities for transmission upon exposure of an uninfected host to the infectious agent. Chronic Wasting Disease (CWD) is a highly transmissible prion disease that affects free ranging and farmed populations of cervids including deer, elk and moose, as well as other mammals in experimental settings. The molecular mechanisms allowing CWD to maintain comparatively high transmission rates have not been determined. Previous work has identified a unique structural feature in cervid PrP, a rigid loop between β-sheet 2 and α-helix 2 on the surface of the protein. This study was designed to test the hypothesis that the rigid loop has a direct influence on the misfolding process. The rigid loop was introduced into murine PrP as the result of two amino acid substitutions: S170N and N174T. Wild-type and rigid loop murine PrP were expressed in E. coli and purified. Misfolding propensity was compared for the two proteins using biochemical techniques and cell free misfolding and conversion systems. Murine PrP with a rigid loop misfolded in cell free systems with greater propensity than wild type murine PrP. In a lipid-based conversion assay, rigid loop PrP converted to a PK resistant, aggregated isoform at lower concentrations than wild-type PrP. Using both proteins as substrates in real time quaking-induced conversion, rigid loop PrP adopted a misfolded isoform more readily than wild type PrP. Taken together, these findings may help explain the high transmission rates observed for CWD within cervids.     

Detection of triplet repeat sequences in the double-stranded DNA using pyrene-functionalized pyrrole-imidazole polyamides with rigid linkers

Methods for sequence-specific detection in double-stranded DNA (dsDNA) are becoming increasingly useful and important as diagnostic and imaging tools. Recently, we designed and synthesized pyrrole (Py)-imidazole (Im) polyamides possessing two pyrene moieties, 1, which showed an increased excimer emission in the presence of (CAG)(12)-containing oligodeoxynucleotides (ODN) 1 and 2. In this study, we synthesized bis-pyrenyl Py-Im polyamides with rigid linkers 2, 3, and 4 to improve their fluorescence properties. Among the conjugates, 2 showed a marked increase in excimer emission, which was dependent on the concentration of the target ODN and the number of CAG repeats in the dsDNA. Unlike conjugate 1, which has flexible linkers, the excimer emission intensity of 2 was retained at over 85%, even after 4h. Py-Im polyamides have the potential to be important diagnostic molecules for detecting genetic differences between individuals.     

POLLINATION AND THE FUNCTION OF FLORAL PARTS IN CHAMAECRISTA FASCICULATA (FABACEAE)

Chamaecrista fasciculata has a rigid upper petal that curves over nine of the ten anthers. The single anther is deflexed, as is the style. An experimental pollination study was designed to test the hypotheses that: 1) the rigid petal acts as flight guide to ensure pollination; and 2) the nine grouped anthers serve as fodder anthers, whereas the single deflexed anther functions in pollination. The rigid petal was removed from 97 flowers. Only 5% of the manipulated flowers set fruit in comparison to a fruit set of 47% for the control group. The results of the study support the flight guide hypothesis. Pollen from both sets of anthers is viable and germinates on receptive stigmas. A pollen flow experiment using powdered metals, backscatter scanning electron microscopy, and X-ray microanalysis revealed that there is no difference in the frequency of pollen distribution from either set of anthers. Therefore, this study refutes the fodder/pollinating anther hypothesis.     

Design,synthesis and biological evaluation of cyclic angiotensin II analogues with 3,5 side-chain bridges. Role of C-terminal aromatic residue and ring cluster for activity and implications in the drug design of AT1 non-peptide antagonists

The novel amide linked angiotensin II (ANG II) cyclic analogues: gamma, epsilon -cyclo(3, 5)-[Sar(1)-Glu(3)-Lys(5)-Ile(8)] ANG II (I) and gamma, epsilon -cyclo(3, 5)-[Sar(1)-Glu(3)-Lys(5)-Phe(8)] ANG II (II) have been designed, synthesized and bioassayed in anesthetized rabbits in order to unravel structural ring cluster characteristics important for receptor activation. Analogue I with Ile at position 8 was an inhibitor of Angiotensin II while analogue II with Phe at position 8 was found to be an agonist. Similar results were reported for cyclic compounds that have reversed the linking between positions 3 and 5. The overall results show that positions 3 and 5 do not govern the biological activity of the synthetic analogues. It also appears that the aromatic ring cluster (Tyr-His-Phe) in agonist peptides is an essential stereo-electronic feature for Angiotensin II to exert its biological activity. A non-peptide mimetic of ANG II, 1-[2'-[(N-benzyl)tetrazol-5-yl]biphenyl-4-yl]methyl]-2-hydroxymethylbenzimidazole (BZI8) has been designed and synthesized. This molecule is more rigid and much less active than AT(1) non-peptide mimetic losartan probably because it lacks to mimic the orientation of tetrazole and the pharmacophore segments of butyl chain and imidazole ring.     

Tricyclic ureas: A new class of HIV-1 protease inhibitors

A new class of tricyclic ureas containing a conformationally constrained proline was designed with the aid of molecular modeling. Efficient stereoselective intermolecular pinacol coupling represented the highlight of the synthesis. These rigid cyclic ureas are active towards HIV-1 protease, with 9 being the most potent compound (Ki = 9 nM) despite interacting with only three side chain binding pockets of HIV protease.     

Exploring the Conformational Behavior of Rigid Porphyrin-Quinone Systems by High-Temperature MD Simulations and Temperature-Dependent 1H-NMR Experiments

Photoinduced electron transfer reactions play an important role in the primary step of the biological photosynthesis process. In an attempt to understand better the mechanism of the charge separation organic donor-acceptor molecules containing porphyrins and quinones were designed as photosynthesis models. In order to study the structure dependence of the photoinduced electron transfer twofold and fourfold bridged porphyrin-quinone systems with increasing donor-acceptor distance were synthesized (Figure 1) [1, 2, 3]. It was assumed that in these molecules the porphyrin and quinone should be linked in a rigid and well-defined orientation. To verify this assumption the conformational behavior of these systems was studied by high-temperature MD simulations in combination with conformational analysis of selected minimized structures [4, 5].     

Structure-based design,synthesis, and evaluation of structurally rigid donepezil analogues as dual AChE and BACE-1 inhibitors

A new series of structurally rigid donepezil analogues was designed, synthesized and evaluated as potential multi-target-directed ligands (MTDLs) against neurodegenerative diseases. The investigated compounds 10–13 displayed dual AChE and BACE-1 inhibitory activities in comparison to donepezil, the FDA-approved drug. The hybrid compound 13 bearing 2-aminoquinoline scaffold exhibited potent AChE inhibition (IC₅₀ value of 14.7?nM) and BACE-1 inhibition (IC₅₀ value of 13.1?nM). Molecular modeling studies were employed to reveal potential dual binding mode of 13 to AChE and BACE-1. The effect of the investigated compounds on the viability of SH-SY5Y neuroblastoma cells and their ability to cross the blood-brain barrier (BBB) in PAMPA-BBB assay were further studied.     

Molecular modeling in the design of phospholipase A2 inhibitors

The X-ray structures of pancreatic bovine and porcine phospholipases A2 have been used along with interactive computer graphics to design conformationally rigid, novel compounds (1-meta-hydroxybenzyl-2-substituted acenaphthenes) directed at the active sites of these enzymes. In vitro testing confirmed that the designed compounds are potent inhibitors of the porcine pancreatic phospholipase A2 and exhibit both stereoselectivity and structure-activity relationships that are consistent with the proposed mode of binding. These compounds take advantage of a hydrophobic "slot" positioned between residues Leu-2 and Tyr-69 while positioning hydrogen-bonding functionality directed at the nd1-N of His-48. Experimental evidence shows a regioselective preference for this H-bond acceptor. A second part of the strategy used a tethered amine to displace the essential calcium providing a bisubstrate analog.     

FeFe]-Hydrogenase active site models with relatively low reduction potentials: Diiron dithiolate complexes containing rigid bridges

Three diiron dithiolate complexes containing rigid and conjugated bridges, [mu-SC(6)H(4)-2-(CO)S-mu]Fe(2)(CO)(6) (1), [2-mu-SC(5)H(3)N-3-(CO)S-mu]Fe(2)(CO)(6) (2), and the PPh(3)-monosubstituted complex [mu-SC(6)H(4)-2-(CO)S-mu]Fe(2)(CO)(5)(PPh(3)) (1-P), were prepared as biomimetic models for the [FeFe]-hydrogenase active site. The structures of complexes 1 and 2 were determined by single crystal X-ray analysis, which shows that each complex features a rigid coplanar dithiolate bridge with a 2-3 degrees deviation from the bisect plane of the molecule. The influence of the rigid bridge on the reduction potentials of complexes 1, 2 and 1-P was investigated by electrochemistry. The cyclic voltammograms of complexes 1 and 2 display large positive shifts for the primary reduction potentials, that is, 380-480mV in comparison to that of the pdt-bridged (pdt=propane-1,3-dithiolato) complex (mu-pdt)Fe(2)(CO)(6) and 160-260mV to that of the bdt-bridged (bdt=benzene-1,2-dithiolato) analogue (mu-bdt)Fe(2)(CO)(6).     

Drug design, synthesis, and evaluation of a non-sugar-based selectin antagonist

We have designed a series of simple rigid compounds (2) having a phenyl ring attached to three essential groups necessary for selectin binding, i.e., a fucose unit, a carboxylic acid, and the hydrophobic part. In this series of compound 2, 2a exhibited strong inhibitory activity in in vitro P-selectin mediated cell adhesion assay. The novel type of compound 2a would be a potential lead compound for selectin antagonist.     

Error in the description of foot kinematics due to violation of rigid body assumptions

Kinematic data from rigid segment foot models inevitably includes errors because the bones within each segment move relative to each other. This study sought to define error in foot kinematic data due to violation of the rigid segment assumption. The research compared kinematic data from 17 different mid and forefoot rigid segment models to kinematic data of the individual bones comprising these segments. Kinematic data from a previous dynamic cadaver model study was used to derive individual bone as well as foot segment kinematics.Mean and maximum errors due to violation of the rigid body assumption varied greatly between models. The model with least error was the combination of navicular and cuboid (mean errors <=1.3°, average maximum error <=2.4°). Greatest error was seen for the model combining all the ten bones (mean errors <=4.4°, average maximum errors <=6.9°). Based on the errors reported a three segment mid and forefoot model is proposed: (1) Navicular and cuboid, (2) cuneiforms and metatarsals 1, 2 and 3, and (3) metatarsals 4 and 5. However the utility of this model will depend on the precise purpose of the in vivo foot kinematics research study being undertaken.