Short-chain reactive probes as tools to unravel the Pseudomonas aeruginosa quorum sensing regulon

In recent years, the world has seen a troubling increase in antibiotic resistance among bacterial pathogens. In order to provide alternative strategies to combat bacterial infections, it is crucial deepen our understanding into the mechanisms that pathogens use to thrive in complex environments. Most bacteria use sophisticated chemical communication systems to sense their population density and coordinate gene expression in a collective manner, a process that is termed “quorum sensing” (QS). The human pathogen Pseudomonas aeruginosa uses several small molecules to regulate QS, and one of them is N-butyryl-l-homoserine lactone (C₄-HSL). Using an activity-based protein profiling (ABPP) strategy, we designed biomimetic probes with a photoreactive group and a ‘click’ tag as an analytical handle. Using these probes, we have identified previously uncharacterized proteins that are part of the P. aeruginosa QS network, and we uncovered an additional role for this natural autoinducer in the virulence regulon of P. aeruginosa, through its interaction with PhzB1/2 that results in inhibition of pyocyanin production.

Short-chain reactive probes can be used as tools to shed new light on virulence mechanisms in bacterial pathogens.     

The Coordinate Reaction Model: An Obstacle to Interpreting the Emergence of Chemical Complexity

The way chemical transformations are described by models based on microscopic reversibility does not take into account the irreversibility of natural processes, and therefore, in complex chemical networks working in open systems, misunderstandings may arise about the origin and causes of the stability of non-equilibrium stationary states, and general constraints on evolution in systems that are far from equilibrium. In order to be correctly simulated and understood, the chemical behavior of complex systems requires time-dependent models, otherwise the irreversibility of natural phenomena is overlooked. Micro reversible models based on the reaction-coordinate model are time invariant and are therefore unable to explain the evolution of open dissipative systems. The important points necessary for improving the modeling and simulations of complex chemical systems are: a) understanding the physical potential related to the entropy production rate, which is in general an inexact differential of a state function, and b) the interpretation and application of the so-called general evolution criterion (GEC), which is the general thermodynamic constraint for the evolution of dissipative chemical systems.     

A reduced-restricted-quasi-Newton–Raphson method for locating and optimizing energy crossing points between two potential energy surfaces

We present a method for the location and optimization of an intersection energy point between two potential energy surfaces. The procedure directly optimizes the excited state energy using a quasi-Newton–Raphson method coupled with a restricted step algorithm. A linear transformation is also used for the solution of the quasi-Newton–Raphson equations. The efficiency of the algorithm is analyzed and demonstrated in some examples. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 :992–1003, 1997     

Protein secondary structure and stability determined by combining exoproteolysis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

In the post-genomic era, several projects focused on the massive experimental resolution of the three-dimensional structures of all the proteins of different organisms have been initiated. Simultaneously, significant progress has been made in the ab initio prediction of protein three-dimensional structure. One of the keys to the success of such a prediction is the use of local information (i.e. secondary structure). Here we describe a new limited proteolysis methodology, based on the use of unspecific exoproteases coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), to map quickly secondary structure elements of a protein from both ends, the N- and C-termini. We show that the proteolytic patterns (mass spectra series) obtained can be interpreted in the light of the conformation and local stability of the analyzed proteins, a direct correlation being observed between the predicted and the experimentally derived protein secondary structure. Further, this methodology can be easily applied to check rapidly the folding state of a protein and characterize mutational effects on protein conformation and stability. Moreover, given global stability information, this methodology allows one to locate the protein regions of increased or decreased conformational stability. All of this can be done with a small fraction of the amount of protein required by most of the other methods for conformational analysis. Thus limited exoproteolysis, together with MALDI-TOF MS, can be a useful tool to achieve quickly the elucidation of protein structure and stability.     

Enantioselective synthesis of 2-arylpiperidines from chiral lactams. A concise synthesis of (-)-anabasine

Cyclodehydration of achiral or racemic aryl-delta-oxoacids with (R)-phenylglycinol stereoselectively affords chiral non-racemic bicyclic lactams, from which the enantiodivergent synthesis of (R)- and (S)-2-phenylpiperidine, the diastereodivergent synthesis of cis- and trans-3-ethyl-2-phenylpiperidine, and the enantioselective synthesis of the piperidine alkaloid (-)-anabasine is reported.     

Synthesis of microcin SF608

The first total synthesis of aquatic peptide microcin SF608 is described. Coupling of L-Hpla with the dipeptide L-Phe-L-Choi followed by coupling with agmatine and a deprotection step gave microcin SF608. In addition, the levorotatory character of L-Hpla (5) was thoroughly established, and the conformational analysis of L-Choi containing peptides 1 and 8-10 was performed using NMR spectroscopy to examine the cis-trans isomer equilibrium of the L-Phe-L-Choi amide bond.     

Synthetic Haptens and Monoclonal Antibodies to the Cyanotoxin Anatoxin‐a

Early warning systems for monitoring toxic events may benefit from the availability of monoclonal antibodies enabling the sensitive and specific detection of anatoxin‐a, a cyanotoxin involved in numerous cases of animal poisoning resulting from toxic algal blooms in freshwaters. Through the synthesis of three functionalized derivatives of anatoxin‐a, we have succeeded in generating the first‐ever reported immunoreagents (bioconjugates and antibodies) suitable for the development of immunoanalytical approaches aimed at rapid and onsite detection of this harmful cyanotoxin.     

Synthesis of Azabicyclic Building Blocks for Daphniphyllum Alkaloid Intermediates Featuring N‐Trichloroacetyl Enamide 5‐endo‐trig Radical Cyclizations

A general procedure is reported for the synthesis of cis ring fused azapolycyclic compounds bearing an all‐carbon quaternary stereocenter at the ring fusion and an adequate functionalization for the assembly of new rings leading to advanced synthetic intermediates for Daphniphyllum alkaloid synthesis. The key carbon?carbon bond‐forming step in this approach is a radical cyclization of an N‐cycloalkenyl trichloroacetamide derivative involving a tetrasubstituted enamide to achieve polyfunctionalized lactams.     

Long‐Term Photostability in Terephthalate Metal–Organic Frameworks

Prolonged (weeks) UV/Vis irradiation under Ar of UiO‐66(Zr), UiO66 Zr‐NO₂, MIL101 Fe, MIL125 Ti‐NH₂, MIL101 Cr and MIL101 Cr(Pt) shows that these MOFs undergo photodecarboxylation of benzenedicarboxylate (BDC) linker in a significant percentage depending on the structure and composition of the material. Routine characterization techniques such as XRD, UV/Vis spectroscopy and TGA fail to detect changes in the material, although porosity and surface area change upon irradiation of powders. In contrast to BCD‐containing MOFs, zeolitic imidazolate ZIF‐8 does not evolve CO₂ or any other gas upon irradiation.