Synthesis and Penicillin‐binding Protein Inhibitory Assessment of Dipeptidic 4‐Phenyl‐β‐lactams from α‐Amino Acid‐derived Imines

Monocyclic β‐lactams revive the research field on antibiotics, which are threatened by the emergence of resistant bacteria. A six‐step synthetic route was developed, providing easy access to new 3‐amino‐1‐carboxymethyl‐4‐phenyl‐β‐lactams, of which the penicillin‐binding protein (PBP) inhibitory potency was demonstrated biochemically.     

Dramatic Enhancement of Binding Affinities Between Foldamer‐Based Receptors and Anions by Intra‐Receptor π‐Stacking

As a synthetic model for intra‐protein interactions that reinforce binding affinities between proteins and ligands, the energetic interplay of binding and folding was investigated using foldamer‐based receptors capable of adopting helical structures. The receptors were designed to have identical hydrogen‐bonding sites for anion binding but different aryl appendages that simply provide additional π‐stacking within the helical backbones without direct interactions with the bound anions. In particular, the presence of electron‐deficient aryl appendages led to dramatic enhancements in the association constant between the receptor and chloride or nitrate ions, by up to three orders of magnitude. Extended stacking within the receptor contributes to the stabilization of the entire folding structure of complexes, thereby enhancing binding affinities.     

Chemical Synthesis of the 20 kDa Heme Protein Nitrophorin 4 by α‐Ketoacid‐Hydroxylamine (KAHA) Ligation

The chemical synthesis of the 184‐residue ferric heme‐binding protein nitrophorin 4 was accomplished by sequential couplings of five unprotected peptide segments using α‐ketoacid‐hydroxylamine (KAHA) ligation reactions. The fully assembled protein was folded to its native structure and coordinated to the ferric heme b cofactor. The synthetic holoprotein, despite four homoserine residues at the ligation sites, showed identical properties to the wild‐type protein in nitric oxide binding and nitrite dismutase reactivity. This work establishes the KAHA ligation as a valuable and viable approach for the chemical synthesis of proteins up to 20 kDa and demonstrates that it is well‐suited for the preparation of hydrophobic protein targets.     

New 3,6‐Disubstituted Pyrazolo[1,5‐a]quinazolines as Ligands to GABAA Receptor Subtype

A new series of 3,6‐disubstituted pyrazolo[1,5‐a]quinazolines (PQs) and their 4,5‐dihydro derivatives as isomer of the potent 3,8‐PQ previously reported by us as high affine GABA_A receptor subtype ligands, have been synthesized and evaluated. These new compounds have been obtained exploiting a different synthetic pathway with respect to the corresponding 3,8‐disubstituted isomers, proposing again the same groups present in the reference 3,8‐PQ. The movement of the substituents from position 8 to position 6 is detrimental for binding recognition, suggesting that the substituents at position 6 are not properly oriented to form adequate interaction with hydrogen bond point and lipophilic area in the receptor protein, as demonstrated in molecular modeling studies.     

Two‐Dimensional Crowding Uncovers a Hidden Conformation of α‐Synuclein

The intrinsically disordered protein (IDP), α‐synuclein (αS), is well‐known for phospholipid membrane binding‐coupled folding into tunable helical conformers. Here, using single‐molecule experiments in conjunction with ensemble assays and a theoretical model, we present a unique case demonstrating that the interaction–folding landscape of αS can be tuned by two‐dimensional (2D) crowding through simultaneous binding of a second protein on the bilayer surface. Unexpectedly, the experimental data show a clear deviation from a simple competitive inhibition model, but are consistent with a bimodal inhibition mechanism wherein membrane binding of a second protein (a membrane interacting chaperone, Hsp27, in this case) differentially inhibits two distinct modules of αS–membrane interaction. As a consequence, αS molecules are forced to access a hidden conformational state on the phospholipid bilayer in which only the higher‐affinity module remains membrane‐bound. Our results demonstrate that macromolecular crowding in two dimensions can play a significant role in shaping the conformational landscape of membrane‐binding IDPs with multiple binding modes.     

Copper‐Free Huisgen Cycloaddition for the 14‐3‐3‐Templated Synthesis of Fusicoccin‐Peptide Conjugates

Mid‐sized molecules have emerged as an attractive chemical space and potentially provide a robust basis for the development of synthetic agents to control intracellular protein interactions. However, the limited cell permeability and chemical tractability of such agents remain to be addressed. We envisioned that target‐templated synthesis of such mid‐sized molecules might provide a solution. Here, we exploited a copper‐free Huisgen cycloaddition for template synthesis using a peptide fragment containing a 4,8‐diazacyclononyne (DACN) moiety and an azide‐containing fusicoccin derivative in the presence or absence of recombinant 14‐3‐3ζ protein in vitro. Time‐course changes in the yield of products demonstrated that the reaction was accelerated in the presence of 14‐3‐3 and one of the regioisomers was generated predominantly, supporting the template effect.     

An Organometallic Inhibitor for the Human Repair Enzyme 7,8‐Dihydro‐8‐oxoguanosine Triphosphatase

The probe‐based discovery of the first small‐molecule inhibitor of the repair enzyme 8‐oxo‐dGTPase (MTH1) is presented, which is an unconventional cyclometalated ruthenium half‐sandwich complex. The organometallic inhibitor with low‐nanomolar activity displays astonishing specificity, as verified in tests with an extended panel of protein kinases and other ATP binding proteins. The binding of the organometallic inhibitor to MTH1 is investigated by protein crystallography.     

The Synthesis of 2‐(Chromon‐2/3‐yl)‐3‐(5‐thione‐4‐hydro‐1,3,4‐thiadiazol‐2‐yl)‐4‐oxo‐thiazolidine

2‐Formylchromones and 3‐formylchromones as the first materials singly reacted with 2‐amino‐5‐mercapto‐1,3,4‐thiadiazole to give the corresponding Schiff bases, which on cyclocondensation with mercapto‐acetic acid in 1,4‐dioxane yielded target compounds named 4‐oxo‐thiazolidines. The structures of all the synthetic compounds were confirmed by elemental analysis and IR, ¹H NMR, LC‐MS (ESI) spectral data.     

Two Histidines in an α‐Helix: A Rigid Co2+‐Binding Motif for PCS Measurements by NMR Spectroscopy

Pseudocontact shifts (PCS) generated by paramagnetic metal ions present valuable long‐range information in the study of protein structural biology by nuclear magnetic resonance (NMR) spectroscopy. Faithful interpretation of PCSs, however, requires complete immobilization of the metal ion relative to the protein, which is difficult to achieve with synthetic metal tags. We show that two histidine residues in sequential turns of an α‐helix provide a binding site for a Co²⁺ ion, which positions the metal ion in a uniquely well‐defined and predictable location. Exchange between the bound and free cobalt is slow on the timescale defined by chemical shifts, but the NMR resonance assignments are nonetheless readily transferred from the diamagnetic to the paramagnetic NMR spectrum by an I_zS_z‐exchange experiment. The double‐histidine‐Co²⁺ motif offers a straightforward, inexpensive, and convenient way of generating precision PCSs in proteins.     

Monitoring the Tanford transition in β‐lactoglobulin by 8‐anilino‐1‐naphthalene sulfonate and mass spectrometry

The fluorescent dye 8‐anilino‐1‐naphthalene sulfonate (ANS) is known to interact with proteins by conformation‐specific hydrophobic interactions and rather nonspecific electrostatic interactions. To which category the complexes detectable by mass spectrometry (MS) belong is still the subject of debate. Here, the Tanford transition in β‐lactoglobulin (BLG) is exploited as an experimental device to expose hydrophobic binding sites by an increase in pH, rather than, as usually done, by lowering the pH. Complex formation is monitored by electrospray ionization (ESI)‐MS and fluorescence spectroscopy. Both techniques reveal stronger ANS binding to BLG at pH 7.9 than at pH 5.9, suggesting that dye binding inside the calyx, which is known to be hydrophobically driven in solution, can contribute to the complexes detected by ESI‐MS. Electrostatic interactions between the protein and the ANS sulfonate group can only be weaker at pH 7.9 than at pH 5.9, supporting the interpretation of the results by the protein conformational change. Lysozyme is used as a negative control, which shows no variation in the interaction with ANS in the same range of pH, in the absence of conformational changes. However, comparison of MS and fluorescence data at variable pH for BLG and myoglobin (Mb) suggests that conformation‐specific ANS binding to proteins is detectable by ESI‐MS only inside well‐structured cavities of folded structures, like the BLG calyx and apoMb heme pocket. Indeed, ANS interactions with highly dynamic structures or molten globules, although detectable in solution, are easily lost in the gas phase. Copyright © 2008 John Wiley & Sons, Ltd.     

Synthesis of Novel 3‐Aryl‐5‐dichloromethyl‐Δ2‐1,2,4‐oxadiazolines

The first synthetic approach to hitherto unknown 3‐aryl‐5‐dichloromethyl‐Δ²‐1,2,4‐oxadiazolines, of synthetic and biological interest, has been developed involving high‐yield reactions between N‐(2,2‐dichlorovinyl)benzimidoyl chlorides and hydroxylamine. The molecular structure of one member of this new family of compounds—5‐dichloromethyl‐3‐(4‐fluorophenyl)‐1,2,4‐oxadiazoline—has been determined by X‐ray crystallography. Density functional theory calculations supporting the proposed reaction pathway for the formation of these products have been carried out.     

The Double‐Histidine Cu2+‐Binding Motif: A Highly Rigid,Site‐Specific Spin Probe for Electron Spin Resonance Distance Measurements

The development of ESR methods that measure long‐range distance distributions has advanced biophysical research. However, the spin labels commonly employed are highly flexible, which leads to ambiguity in relating ESR measurements to protein‐backbone structure. Herein we present the double‐histidine (dHis) Cu²⁺‐binding motif as a rigid spin probe for double electron–electron resonance (DEER) distance measurements. The spin label is assembled in situ from natural amino acid residues and a metal salt, requires no postexpression synthetic modification, and provides distance distributions that are dramatically narrower than those found with the commonly used protein spin label. Simple molecular modeling based on an X‐ray crystal structure of an unlabeled protein led to a predicted most probable distance within 0.5 Å of the experimental value. Cu²⁺ DEER with the dHis motif shows great promise for the resolution of precise, unambiguous distance constraints that relate directly to protein‐backbone structure and flexibility.     

Diphenylacetylene‐Linked Peptide Strands Induce Bidirectional β‐Sheet Formation

In the search for synthetic mimics of protein secondary structures relevant to the mediation of protein–protein interactions, we have synthesized a series of tetrasubstituted diphenylacetylenes that display β‐sheet structures in two directions. Extensive X‐ray crystallographic and NMR solution phase studies are consistent with these proteomimetics adopting sheet structures, displaying both hydrophobic and hydrophilic amino acid side chains.     

The Double‐Histidine Cu2+‐Binding Motif: A Highly Rigid,Site‐Specific Spin Probe for Electron Spin Resonance Distance Measurements

The development of ESR methods that measure long‐range distance distributions has advanced biophysical research. However, the spin labels commonly employed are highly flexible, which leads to ambiguity in relating ESR measurements to protein‐backbone structure. Herein we present the double‐histidine (dHis) Cu²⁺‐binding motif as a rigid spin probe for double electron–electron resonance (DEER) distance measurements. The spin label is assembled in situ from natural amino acid residues and a metal salt, requires no postexpression synthetic modification, and provides distance distributions that are dramatically narrower than those found with the commonly used protein spin label. Simple molecular modeling based on an X‐ray crystal structure of an unlabeled protein led to a predicted most probable distance within 0.5 Å of the experimental value. Cu²⁺ DEER with the dHis motif shows great promise for the resolution of precise, unambiguous distance constraints that relate directly to protein‐backbone structure and flexibility.     

Identification and X‐ray Co‐crystal Structure of a Small‐Molecule Activator of LFA‐1‐ICAM‐1 Binding

Stabilization of protein–protein interactions by small molecules is a concept with few examples reported to date. Herein we describe the identification and X‐ray co‐crystal structure determination of IBE‐667, an ICAM‐1 binding enhancer for LFA‐1. IBE‐667 was designed based on the SAR information obtained from an on‐bead screen of tagged one‐bead one‐compound combinatorial libraries by confocal nanoscanning and bead picking (CONA). Cellular assays demonstrate the activity of IBE‐667 in promoting the binding of LFA‐1 on activated immune cells to ICAM‐1.     

Synthesis and biological properties of 4‐substituted quinolin‐2(1H)‐one analogues

A variety of 4‐substituted quinolin‐2(1H)‐ones were prepared and evaluated for N‐methyl‐D‐aspar‐tate (NMDA) receptor binding site activity and their abilities to inhibit neurotoxicity. The 4‐(2‐car‐bethoxyethanamino)‐7‐chloro‐3‐nitroquinolin‐2(1H)‐one ( 9b ) exhibited favorable NMDA receptor binding site activity and 7‐chloro‐4‐(benzylamino)‐3‐nitroquinolin‐2(1H)‐one ( 9c ) showed the most potent neurotoxicity among them. The synthetic strategies involve the use of well known keto ester condensation and reductive ring cyclization of intermediates ( 2a‐d ) to afford 4‐substituted quinolin‐2(1H)‐ones.     

The N Terminus of α‐Synuclein Forms CuII‐Bridged Oligomers

The oligomerization of α‐synuclein (αSyn) is one of the defining features of Parkinson’s disease. Binding of divalent copper to the N terminus of αSyn has been implicated in both its function and dysfunction. Herein, the molecular details of the Cu^II/αSyn binding interface have been revealed using a library of synthetic 56‐residue αSyn peptides containing site‐specific isotopic labels. Using electron paramagnetic resonance spectroscopy, αSyn is shown to coordinate Cu^II with high affinity via two pH‐dependent coordination modes between pH 6.5–8.5. Most remarkably, the data demonstrate that the dominant mode is associated with binding to oligomers (antiparallel dimers and/or cyclic trimers) in which Cu^II ions occupy intermolecular bridging sites. The findings provide a molecular link between Cu^II‐bound αSyn and its associated quaternary oligomeric structure.     

A New Solution—phase Parallel Synthesis of 2—Alkyamino—3—aryl—5—phenylmethylene—3,5—dihydro—4H—imidazol—4—ones

Thirteen new 2-alkylaminoimidazolones(4) wre rapidly synthesized by a new solution-phase parallel synthetic method,which includes aza-Wittig reaction of iminophosphorane(1) with aromatic isocyanate to give carbodi-imide(2) and subsequent reaction of 2 with various aliphatic primary amine in a parallel fashion.The products were confirmed by ^1H NMR,MS,IR and X-ray crystallographic analysis.The unusual selectivity of the cyclization was probably due to the deometry of the guanidine intermediate.     

A Mild Approach to the Synthesis of sn‐Glycerol 1,2‐Di‐γ‐linolenate 3‐Palmitate

A synthetic approach comprising several studied modifications was applied to the preparation of sn‐glycerol 1,2‐di‐γ‐linolenate 3‐palmitate ( 4 ). Thereby, a convenient and mild synthetic method was elaborated, affording 4 from 1,2‐O‐isopropylidene‐sn‐glycerol ( 1 ) in an average yield of 65 – 75% and analytically acceptable purity.     

Synthesis of β‐1,4‐Linked Galactan Side‐Chains of Rhamnogalacturonan I

The synthesis of linear‐ and (1→6)‐branched β‐(1→4)‐d ‐galactans, side‐chains of the pectic polysaccharide rhamnogalacturonan I is described. The strategy relies on iterative couplings of n‐pentenyl disaccharides followed by a late stage glycosylation of a common hexasaccharide core. Reaction with a covalent linker and immobilization on N‐hydroxysuccinimide (NHS)‐modified glass surfaces allows the generation of carbohydrate microarrays. The glycan arrays enable the study of protein–carbohydrate interactions in a high‐throughput fashion, demonstrated herein with binding studies of mAbs and a CBM.