A Peptide-Based Oscillator.

Living organisms are replete with rhythmic and oscillatory behavior at all levels, to the extent that oscillations have been termed as a defining attribute of life. Recent studies of synthetic oscillators that mimic such functions have shown decayed cycles in batch-mode reactions or sustained oscillatory kinetics under flow conditions. Considering the hypothesized functionality of peptides in early chemical evolution and their central role in current bio-nanotechnology, we now reveal a peptide-based oscillator. Oscillatory behavior was achieved by coupling coiled-coil-based replication processes as positive feedback to controlled initiation and inhibition pathways in a continuously stirred tank reactor (CSTR). Our results stress that assembly into the supramolecular structure and specific interactions with the replication substrates are crucial for oscillations. The replication-inhibition processes were first studied in batch mode, which produced a single damped cycle. Thereafter, combined experimental and theoretical characterization of the replication process in a CSTR under different flow and environmental (pH, redox) conditions demonstrated reasonably sustained oscillations. We propose that studies in this direction might pave the way to the design of robust oscillation networks that mimic the autonomous behavior of proteins in cells (e.g., in the cyanobacterial circadian clock) and hence hint at feasible pathways that accelerated the transition from simple peptides to extant enzymes.

Signaling in Systems Chemistry: Programing Gold Nanoparticles Formation and Assembly Using a Dynamic Bistable Network.

Living cells exploit bistable and oscillatory behaviors as memory mechanisms, facilitating the integration of transient stimuli into sustained molecular responses that control downstream functions. Synthetic bistable networks have also been studied as memory entities, but have rarely been utilized to control orthogonal functions in coupled dynamic systems. We herein present a new cascade pathway, for which we have exploited a well-characterized switchable peptide-based replicating network, operating far from equilibrium, that yields two alternative steady-state outputs, which in turn serve as the input signals for consecutive processes that regulate various features of Au nanoparticle shape and assembly. This study further sheds light on how bridging together the fields of systems chemistry and nanotechnology may open up new opportunities for the dynamically controlled design of functional materials.

A chemically fueled non-enzymatic bistable network.

One of the grand challenges in contemporary systems chemistry research is to mimic life-like functions using simple synthetic molecular networks. This is particularly true for systems that are out of chemical equilibrium and show complex dynamic behaviour, such as multi-stability, oscillations and chaos. We report here on thiodepsipeptide-based non-enzymatic networks propelled by reversible replication processes out of equilibrium, displaying bistability. Accordingly, we present quantitative analyses of the bistable behaviour, featuring a phase transition from the simple equilibration processes taking place in reversible dynamic chemistry into the bistable region. This behaviour is observed only when the system is continuously fueled by a reducing agent that keeps it far from equilibrium, and only when operating within a specifically defined parameter space. We propose that the development of biomimetic bistable systems will pave the way towards the study of more elaborate functions, such as information transfer and signalling.

Investigations of Peptide-Based Biocompatible Injectable Shape-Memory Hydrogels: Differential Biological Effects on Bacterial and Human Blood Cells.

Here, we report the self-assembly of Amoc (9-anthracenemethoxycarbonyl)-capped dipeptides, which self-assemble to form injectable, self-healable, and shape-memory hydrogels with inherent antibacterial properties. Amoc-capped dipeptides self-assemble to form nanofibrillar networks, which are established by several spectroscopic and microscopic techniques. The inherent antibacterial properties of hydrogels are evaluated using two Gram-positive Staphylococcus aureus, Bacillus subtilis and three Gram-negative Escherichia coli, Pseudomonas aeruginosa, and Salmonella typhi bacteria. These hydrogels exhibit potent antibacterial efficacy against Gram-positive and Gram-negative bacteria. The minimum inhibitory concentrations (MIC50) for the hydrogels on Gram-positive bacteria are in the range of 10-200 µM hydrogelator concentrations. The biocompatibility and cytotoxicity of the hydrogels are evaluated using 3-(4,5-dimethythiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT), hemolysis, and lipid peroxidation (LPO) assay on human blood cells. The hydrogels are hemocompatible and they decrease LPO values on human red blood cells probably via increased cellular stability against oxidative stress. Furthermore, MTT data show that the hydrogels are biocompatible and promote cell viability and proliferation on cultured human white blood cells. Taken together, these results may suggest that our designed injectable hydrogels could be useful to prevent localized bacterial infections.

Ethyl 2-cyano-2-(2-nitrobenzenesulfonyloxyimino)acetate (o-NosylOXY): a recyclable coupling reagent for racemization-free synthesis of peptide, amide, hydroxamate, and ester.

Ubiquitousness of amide and ester functionality makes coupling reactions extremely important. Although numerous coupling reagents are available, methods of preparation of the common and efficient reagents are cumbersome. Those reagents generate a substantial amount of chemical waste and lack recyclability. Ethyl 2-cyano-2-(2-nitrobenzenesulfonyloxyimino)acetate (o-NosylOXY), the first member of a new generation of coupling reagents, produces byproducts that can be easily recovered and reused for the synthesis of the same reagent, making the method more environmentally friendly and cost-effective. The synthesis of amides, hydroxamates, peptides, and esters using this reagent is described. The synthesis of the difficult sequences, for example, the islet amyloid polypeptide (22-27) fragment (with a C-terminal Gly, H-Asn-Phe-Gly-Ala-Ile-Leu-Gly-NH2) and acyl carrier protein (65-74) fragment (H-Val-Gln-Ala-Ala-Ile-Asp-Tyr-Ile-Asn-Gly-OH), following the solid-phase peptide synthesis (SPPS) protocol and Amyloid ß (39-42) peptide (Boc-Val-Val-IIe-Ala-OMe), following solution-phase strategy is demonstrated. Remarkable improvement is noticed with respect to reaction time, yield, and retention of stereochemistry. A mechanistic investigation and recyclability are also described.

Ethyl 2-cyano-2-(4-nitrophenylsulfonyloxyimino)acetate-mediated Lossen rearrangement: single-pot racemization-free synthesis of hydroxamic acids and ureas from carboxylic acids.

Ethyl 2-cyano-2-(4-nitrophenylsulfonyloxyimino)acetate (4-NBsOXY) mediated Lossen rearrangement and its application for the synthesis of ureas is demonstrated. Required hydroxamic acids for the Lossen rearrangements were synthesized from carboxylic acids using the same reagent. Finally, reaction of an amine with the produced isocyanate resulted in urea. Good yields without racemization were achieved under milder and simpler reaction conditions. Reactions are compatible with common N-protecting groups, such as Boc, Fmoc, Cbz, and benzyl, as well as various OH protecting groups, such as (t)Bu and Bzl. Conversion from carboxylic acid to urea is achieved in one pot. Most importantly, byproducts Oxyma [ethyl 2-cyano-2-(hydroxyimino)acetate] and 4-nitrobenzenesulfonic acid can be recovered easily and can be recycled to prepare the reagent. Thus, the method is environmentally friendly and cost-effective.