Yousef M. Abul-Haija

Exploring the sequence space for (tri-)peptide self-assembly to design and discover new hydrogels

Peptides that self-assemble into nanostructures are of tremendous interest for biological, medical, photonic and nanotechnological applications. The enormous sequence space that is available from 20 amino acids probably harbours many interesting candidates, but it is currently not possible to predict supramolecular behaviour from sequence alone. Here, we demonstrate computational tools to screen for the aqueous self-assembly propensity in all of the 8,000 possible tripeptides and evaluate these by comparison with known examples. We applied filters to select for candidates that simultaneously optimize the apparently contradicting requirements of aggregation propensity and hydrophilicity, which resulted in a set of design rules for self-assembling sequences. A number of peptides were subsequently synthesized and characterized, including the first reported tripeptides that are able to form a hydrogel at neutral pH. These tools, which enable the peptide sequence space to be searched for supramolecular properties, enable minimalistic peptide nanotechnology to deliver on its promise.

Controlling Cancer Cell Fate Using Localized Biocatalytic Self-Assembly of an Aromatic Carbohydrate Amphiphile

We report on a simple carbohydrate amphiphile able to self-assemble into nanofibers upon enzymatic dephosphorylation. The self-assembly can be triggered by alkaline phosphatase (ALP) in solution or in situ by the ALP produced by osteosarcoma cell line, SaOs2. In the latter case, assembly and localized gelation occurs mainly on the cell surface. The gelation of the pericellular environment induces a reduction of the SaOs2 metabolic activity at an initial stage (≤7 h) that results in cell death at longer exposure periods (≥24 h). We show that this effect depends on the phosphatase concentration, and thus, it is cell-selective with prechondrocytes ATDC5 (that express ∼15-20 times lower ALP activity compared to SaOs2) not being affected at concentrations ≤1 mM. These results demonstrate that simple carbohydrate derivatives can be used in an antiosteosarcoma strategy with limited impact on the surrounding healthy cells/tissues.

Sequence adaptive peptide-polysaccharide nanostructures by biocatalytic self-assembly

Coassembly of peptides and polysaccharides can give rise to the formation of nanostructures with tunable morphologies. We show that in situ enzymatic exchange of a dipeptide sequence in aromatic peptide amphiphiles/polysaccharide coassemblies enables dynamic formation and degradation of different nanostructures depending on the nature of the polysaccharide present. This is achieved in a one-pot system composed of Fmoc-cysteic acid (CA) and Fmoc-lysine (K) plus phenylalanine amide (F) in the presence of thermolysin that, through dynamic hydrolysis and amide formation, gives rise to a dynamic peptide library composed of the corresponding Fmoc-dipeptides (CAF and KF). When the cationic polysaccharide chitosan is added to this mixture, selective amplification of the CAF peptide is observed giving rise to formation of nanosheets through coassembly. By contrast, upon addition of anionic heparin, KF is formed that gives rise to a nanotube morphology. The dynamic adaptive potential was demonstrated by sequential morphology changes depending on the sequence of polysaccharide addition. This first demonstration of the ability to access different peptide sequences and nanostructures, depending on the presence of biopolymers, may pave the way to biomaterials that can adapt their structure and function and may be of relevance in the design of materials able to undergo dynamic morphogenesis.

Pickering stabilized peptide gel particles as tunable microenvironments for biocatalysis

We demonstrate the preparation of peptide gel microparticles that are emulsified and stabilized by SiO2 nanoparticles. The gels are composed of aromatic peptide amphiphiles 9-fluorenylmethoxycarbonyldiphenylalanine (Fmoc-FF) coassembled with Fmoc-amino acids with different functional groups (S: serine; D: aspartic acid; K: lysine; and Y: tyrosine). The gel phase provides a highly hydrated matrix, and peptide self-assembly endows the matrix with tunable chemical environments which may be exploited to support and stabilize proteins. The use of Pickering emulsion to stabilize these gel particles is advantageous through avoidance of surfactants that may denature proteins. The performance of enzyme lipase B immobilized in pickering/gel microparticles with different chemical functionalities is investigated by studying transesterification in heptane. We show that the use of Pickering particles enhances the performance of the enzyme, which is further improved in gel-phase systems, with hydrophilic environment provided by Fmoc-FF/S giving rise to the best catalytic performance. The combination of a tunable chemical environment in gel phase and Pickering stabilization described here is expected to prove useful for areas where proteins are to be exploited in technological contexts such as biocatalysis and also in other areas where protein performance and activity are important, such as biosensors and bioinspired solar fuel devices.

Biocatalytic Self-Assembly Cascades

The properties of supramolecular materials are dictated by both kinetic and thermodynamic aspects, providing opportunities to dynamically regulate morphology and function. Herein, we demonstrate time-dependent regulation of supramolecular self-assembly by connected, kinetically competing enzymatic reactions. Starting from Fmoc-tyrosine phosphate and phenylalanine amide in the presence of an amidase and phosphatase, four distinct self-assembling molecules may be formed which each give rise to distinct morphologies (spheres, fibers, tubes/tapes and sheets). By varying the sequence or ratio in which the enzymes are added to mixtures of precursors, these structures can be (transiently) accessed and interconverted. The approach provides insights into dynamic self-assembly using competing pathways that may aid the design of soft nanostructures with tunable dynamic properties and life times.

Mechanistic insights into phosphatase triggered self-assembly including enhancement of biocatalytic conversion rate

We report on the mechanistic investigation of alkaline phosphatase (AP) triggered self-assembly and hydrogelation of Fmoc-tyrosine (Fmoc-Y). We studied separately the biocatalytic conversion using HPLC, changes in supramolecular interactions and chirality using CD and fluorescence spectroscopy, nanostructure formation by AFM and gelation by oscillatory rheometry. Three consecutive stages could be distinguished (which may overlap, depending on the enzyme concentration). Typically, the phosphorylated Fmoc-Y (Fmoc-pY) undergoes rapid and complete dephosphorylation, followed by formation of aggregates which reorganise into nanofibres and consequently give rise to gelation. We observed a remarkable enhancement of catalytic activity during the early stages of the self-assembly process, providing evidence for enhancement of enzymatic activation by the supramolecular structures formed. Overall, this study provides a further step in understanding biocatalytic self-assembly.

Versatile pectin grafted poly (N-isopropylacrylamide) : modulated targeted drug release

This study describes synthesis and optimization of pectin grafted poly(N-isopropylacrylamide) hydrogels as vehicles for colon-targeted theophylline model drug release. The gels were prepared in the presence of N, N′–methylenebisacrylamide (MBAA) crosslinker and ceric ammonium nitrate (CAN) initiator under N2 atmosphere. Optimum conditions, in terms of percent of grafting (%G), were determined as follows: pectin = 1.0 g, [NIPAAm] = 26.51 mM, [MBAA] = 0.65 mM, [CAN] = 0.073 mM, polymerization temperature = 30°C and time = 4.0 h. Hydrogels were characterized by FTIR, TGA, DSC, XRD and SEM. The formed hydrogel did not have a thermo-sensitivity behavior. The in vitro percent drug release was studied in terms of different percent of grafting and different polymerization temperatures under two pH values namely 5.5 and 7.4. Conclusively, the optimum colon-targeted vehicle properties that provide the least drug release at pH5.5 and the most drug release at pH7.4 were as follows: [NIPAAm] = 26.51 mM and [MBAA] = 0.56 mM, polymerization temperature = 30°C and %G = 55.5.

Enzyme-responsive hydrogels for biomedical applications

This chapter highlights recent developments in enzyme-responsive gels. The focus is on peptide-based small-molecule hydrogels, for biomedical applications. The use of enzymes in this context provides a powerful methodology for controlled assembly, taking advantage of both biological selectivity and catalytic amplification. The building blocks for self-assembly and basic design rules for small molecule peptide gelators are discussed first. This is followed by a discussion of key features of biocatalytic self-assembly of hydrogels, focusing on control of nanoscale organization and consequent function. Finally, the potential applications of the enzyme-responsive hydrogels as biomaterials are discussed in the areas of cell culture, drug delivery, biosensing, and control of cell fate.

Exploring Strategies To Bias Sequence in Natural and Synthetic Oligomers and Polymers

Millions of years of biological evolution have driven the development of highly sophisticated molecular machinery found within living systems. These systems produce polymers such as proteins and nucleic acids with incredible fidelity and function. In nature, the precise molecular sequence is the factor that determines the function of these macromolecules. Given that the ability to precisely define sequence emerges naturally, the fact that biology achieves unprecedented control over the unit sequence of the monomers through evolved enzymatic catalysis is incredible. Indeed, the ability to engineer systems that allow polymer synthesis with precise sequence control is a feat that technology is yet to replicate in artificial synthetic systems. This is the case because, without access to evolutionary control for finely tuned biological catalysts, the inability to correct errors or harness multiple competing processes means that the prospects for digital control of polymerization have been firmly bootstrapped to biological systems or limited to stepwise synthetic protocols. In this Account, we give an overview of strategies that have been used over the last 5 years in efforts to program polymer synthesis with sequence control in the laboratory. We also briefly explore how the use of robotics, algorithms, and stochastic chemical processes might lead to new understanding, mechanisms, and strategies to achieve full digital control. The aim is to see whether it is possible to go beyond bootstrapping to biological polymers or stepwise chemical synthesis. We start by describing nonenzymatic techniques used to obtain sequence-controlled natural polymers, a field that lends itself to direct application of insights gleaned from biology. We discuss major advances, such as the use of rotaxane-based molecular machines and templated approaches, including the utilization of biological polymers as templates for purely synthetic chains. We then discuss synthetic polymer chemistry, whose array of techniques allows the production of polymers with enormous structural and functional diversity, but so far with only limited control over the unit sequence itself. Synthetic polymers can be subdivided into multiple classes depending on the nature of processes used to synthesize them, such as by addition or condensation. Consequently, varied approaches for sequence control have been demonstrated in the area, including but not limited to click reactions, iterative solid-phase chemistry, and exploiting the chemical affinity of the monomers themselves. In addition to those, we highlight the importance of environmental bias in possible control of polymerization at the single-unit level, such as using catalyst switching or external stimuli. Even the most successful experimental sequence control approach needs appropriate tools to verify its scope and validity; therefore, we devote part of the present Account to possible analytical approaches to sequence readout, starting with well-established tandem mass spectrometry techniques and touching on those more applicable to specific classes of processes, such as diffusion-ordered NMR spectroscopy. Finally, we discuss progress in modeling and automation of sequence-controlled polymers. We postulate that developments in analytical chemistry, bioinformatics, and computer modeling will lead to new ways of exploring the development of new strategies for the realization of sequence control by means of sequence bias. This is the case because treating the assembly of polymers as a network of chemical reactions will enable the development of control strategies that can bias the outcome of the polymer assembly. The grand aim would be the synthesis of complex polymers in one step with a precisely defined digital sequence.

Data for: "Biocatalytic Self-Assembly on Magnetic Nanoparticles"

This dataset comprises of 8 Microsoft Excel xlsx files. The files contain the raw data for CD, HPLC and FRET analytical measurements. The titles of the file indicate to which measurements the data belong. Data embargo until 31/01/18