Conformational Changes of Facially Amphiphilic meta-Poly(phenylene ethynylene)s in Aqueous Solution

Development of protein mimics for intracellular delivery

Designing delivery agents for therapeutics is an ongoing challenge. As treatments and desired cargoes become more complex, the need for improved delivery vehicles becomes critical. Excellent delivery vehicles must ensure the stability of the cargo, maintain the cargo's solubility, and promote efficient delivery and release. In order to address these issues, many research groups have looked to nature for design inspiration. Proteins, such as HIV-1 trans-activator of transcription (TAT) and Antennapedia homeodomain protein, are capable of crossing cellular membranes. However, due to the complexities of their structures, they are synthetically challenging to reproduce in the laboratory setting. Being able to incorporate the key features of these proteins that enable cell entry into simpler scaffolds opens up a wide range of opportunities for the development of new delivery reagents with improved performance. This review charts the development of protein mimics based on cell-penetrating peptides (CPPs) and how structure-activity relationships (SARs) with these molecules and their protein counterparts ultimately led to the use of polymeric scaffolds. These scaffolds deviate from the normal peptide backbone, allowing for simpler, synthetic procedures to make carriers and tune chemical compositions for application specific needs. Successful design of polymeric protein mimics would allow researchers to further understand the key features in proteins and peptides necessary for efficient delivery and to design the next generation of more efficient delivery reagents.

Synthetic mimics of antimicrobial peptides--a versatile ring-opening metathesis polymerization based platform for the synthesis of selective antibacterial and cell-penetrating polymers

Natural macromolecules exhibit an extensive arsenal of properties, many of which have proven difficult to recapitulate in simpler synthetic systems. Over the last couple of years, foldamers have emerged as one important step toward increased functionality in synthetic systems. While the great majority of work in this area has focused on folded structures, hence the name, more recent progress has centered on polymers that mimic protein function. These efforts have resulted in the design of relatively simple macromolecules; one example are the synthetic mimics of antimicrobial peptides (SMAMPs) that capture the central physicochemical features of their natural archetypes irrespective of the specific folded form. Here we present our recent efforts to create polymers which display biological activity similar to natural proteins, including antimicrobial and cell-penetrating peptides.

Double helix formation of oligoresorcinols in water: thermodynamic and kinetic aspects

We previously reported that the oligoresorcinols formed double-stranded helices in neutral water through interstrand aromatic interactions. In the present study, we synthesized a new series of oligomers from the 2mer to the 15mer to explore the thermodynamics, kinetics, and mechanism of the double helix formation of the oligoresorcinols in water. The double helix formation was dependent on the chain length of the oligomers and significantly affected by solvent, pH, salt, and temperature. The free energy change (-DeltaG) for the double helix formation linearly increased with the chain length from the 4mer to the 11mer (DeltaDeltaG = -0.94 kcal mol(-1) unit(-1)), whereas it did not change for the oligomers longer than the 11mer. The van't Hoff analysis of the 9mer revealed that the double helix formation was an enthalpically driven process (DeltaH = -27 +/- 1.5 kcal mol(-1) and DeltaS = -70 +/- 5 cal mol(-1) K(-1)), which was consistent with the upfield shifts in the (1)H NMR spectra and the hypochromicity of the absorption spectra as a result of the interstrand aromatic interactions in water. Furthermore, the kinetic analysis of the chain exchange reaction between the double helices of the optically active and optically inactive 11mers revealed a small DeltaS(double dagger), suggesting that the chain exchange proceeds not via the dissociation-association pathway, but via the direct exchange pathway.

Helicity induction and memory of the macromolecular helicity in a polyacetylene bearing a biphenyl pendant

A novel, cis-transoidal poly-(phenylacetylene) bearing a carboxybiphenyl group as the pendant (poly-1) was prepared by polymerization of (4'-ethoxycarbonyl-4-biphenylyl)acetylene with a rhodium catalyst followed by hydrolysis of the ester groups. Upon complexation with various chiral amines and amino alcohols in dimethyl sulfoxide (DMSO), the polymer exhibited characteristic induced circular dichroism (ICD) in the UV/Vis region due to the predominantly one-handed helix formation of the polymer backbone as well as an excess of a single-handed, axially twisted conformation of the pendant biphenyl group. Poly-1 complexed with (R)-2-amino-1-propanol showed unique time-dependent inversion of the macromolecular helicity. Furthermore, the preferred-handed helical conformation of poly-1 induced by a chiral amine was further "memorized" after the chiral amine was replaced with achiral 2-aminoethanol or n-butylamine in DMSO. In sharp contrast to the previously reported memory in poly((4-carboxyphenyl)acetylene), the present helicity memory of poly-1 was accompanied by memory of the twisted biphenyl chirality in the pendants. Unprecedentedly, the helicity memory of poly-1 with achiral 2-aminoethanol was found to occur simultaneously with inversion of the axial chirality of the biphenyl groups followed by memory of the inverted biphenyl chirality, thus showing a significant change in the CD spectral pattern.

Synthesis of a pH-independent bifurcated amphiphile

An efficient synthetic method for preparing bifurcated amphiphiles has been developed such that the functionality for attachment is located at the interface between the lipophilic and hydrophilic side chains. Attachment of the amphiphile to the repeat units of polymeric substrates enables the rapid preparation of amphiphilic homopolymers.

Conformationally rigid proteomimetics: a case study in designing antimicrobial aryl oligomers

The promise of proteomics to provide a vast library of protein structural data is exciting to scientists desiring an unprecedented understanding of the relationship between protein structure and function. This powerful knowledge will provide insight into the design rules for proteomimetics which are oligomers and polymers that can be more stable and inexpensive to produce than natural proteins, but still emulate the main biological function of the natural molecule. This Emerging Area article is intended to stimulate discussion on innovative strategies to design the next generation of proteomimetics. Specifically we will examine the design evolution of facially amphiphilic aryl oligomers, compounds that act as synthetic mimics of antimicrobial peptides (SMAMPs) and are known to interact with lipid bilayers. An increasingly important goal in the field of antimicrobial polymers is to develop strategies to rationally design membrane-binding SMAMPs, that are highly cell-selective, from any preferred backbone and molecular weight. It is expected that lessons learned from studying these oligomers can be applied to other systems where mimics are desired to interact with extended surfaces and where it would be most productive to consider mimicking the protein of interest with a large molecule. Obvious examples include disrupting protein-protein interactions or binding long tracts of DNA to control gene expression.

Infectious Disease: Connecting Innate Immunity to Biocidal Polymers

Infectious disease is a critically important global healthcare issue. In the U.S. alone there are 2 million new cases of hospital-acquired infections annually leading to 90,000 deaths and 5 billion dollars of added healthcare costs. Couple these numbers with the appearance of new antibiotic resistant bacterial strains and the increasing occurrences of community-type outbreaks, and clearly this is an important problem. Our review attempts to bridge the research areas of natural host defense peptides (HDPs), a component of the innate immune system, and biocidal cationic polymers. Recently discovered peptidomimetics and other synthetic mimics of HDPs, that can be short oligomers as well as polymeric macromolecules, provide a unique link between these two areas. An emerging class of these mimics are the facially amphiphilic polymers that aim to emulate the physicochemical properties of HDPs but take advantage of the synthetic ease of polymers. These mimics have been designed with antimicrobial activity and, importantly, selectivity that rivals natural HDPs. In addition to providing some perspective on HDPs, selective mimics, and biocidal polymers, focus is given to the arsenal of biophysical techniques available to study their mode of action and interactions with phospholipid membranes. The issue of lipid type is highlighted and the important role of negative curvature lipids is illustrated. Finally, materials applications (for instance, in the development of permanently antibacterial surfaces) are discussed as this is an important part of controlling the spread of infectious disease.

Spin System Assignment of Homo-o-Phenylene Ethynylene Oligomers

We previously reported the synthesis and solution characterization of short o-phenylene ethynylene (oPE) foldamers. Proton correlation techniques are not adequate for NMR assignment in these compounds as the ethynylene linkers interrupt proton connectivity. In order to facilitate structural characterization and more fully harness the power of NMR, it is necessary to know the sequence of spin systems along the molecular backbone. For example, spin system assignment is required to unambiguously assign NOE correlations for structural determination of folded forms in solution. Therefore, we developed a method to assign the aromatic spin systems in these compounds using HMBC experiments. This has been performed for tetrameric (Es4), pentameric (Es5), and hexameric (Es6) oligomers and is expected to prove useful for this class of foldamers in general. The proton assignments obtained by this technique have been useful toward confirming the previous hypotheses of helical folding in oPE systems.

Chiral Poly(ureidophthalimide) Foldamers in Water

Poly(ureidophthalimide)s decorated with hydrophilic side chains, that ensure solubility in aqueous media, have been synthesized and characterized by UV/Vis and circular dichroism (CD) spectroscopy. Temperature and concentration dependent CD measurements in water have revealed an almost temperature and concentration independent Cotton effect, indicative for a strong intramolecular organization. Similar studies in THF demonstrate the dynamic nature of the secondary architecture, a characteristic of foldamers. In addition, the bisignated Cotton effect in water is opposite in sign to that in THF, suggestive for a solvent-dependent preference for one helical handedness. Mixing experiments prove the dominance of water in determining the handedness of the helical architecture. The solvent allows for control over the helical architecture and thus governs the supramolecular synthesis.

Meta-linked poly(phenylene ethynylene) conjugated polyelectrolyte featuring a chiral side group: helical folding and guest binding

A water soluble, meta-linked poly(phenylene ethynylene) featuring chiral and optically active side groups based on L-alanine (mPPE-Ala) has been studied by using absorption, fluorescence, and circular dichroism spectroscopy. Studies of mPPE-Ala in methanol/water solvent mixtures show that the polymer folds into a helical conformation, and the extent of helical folding increases with the volume % water in the solvent. The presence of the helical conformation is signaled by the appearance of a broad, excimer-like visible fluorescence band, combined with a strong bisignate circular dichroism signal in the region of the pi,pi absorption of the polymer backbone. The circular dichroism signal exhibits negative chirality, suggesting that the left-handed (M-form) of the helix is in enantiomeric excess. Binding of the metallointercalator [Ru(bpy)2(dppz)]2+ (where bpy = 2,2-bipyridine and dppz = dipyrido[3,2-a:2',3'-c]phenazine) with the helical polymer is accompanied by the appearance of the orange-red photoluminescence from the metal complex. This effect is directly analogous to that observed when [Ru(bpy)2(dppz)]2+ binds to DNA via intercalation, suggesting that the metal complex binds to mPPE-Ala by intercalating between the pi-stacked phenylene ethynylene residues. Cationic cyanine dyes also bind to the periphery of the helical polymer in a manner that is interpreted as "groove binding". A circular dichroism signal is observed that is believed to arise from exciton coupling within the chiral cyanine dye chromophore aggregate that is formed as the dye molecules are oriented by the helical mPPE-Ala "template".

Solvophobic and Steric Effects of Side Groups on Polymer Folding: Molecular Modeling Studies of Amine-Functionalized m-Poly(phenyleneethynylene) Foldamers in Aqueous Solution

The folding behavior of five different amine-functionalized m-poly(phenyleneethynylene) (m-PPE) oligomers containing 24 phenyl rings (12 residues, where a residue includes 2 phenyl rings) in water was examined by using a combination of molecular dynamics (MD) and replica exchange molecular dynamics (REMD) simulation techniques. The REMD method employed the highly parallelized GROMACS MD software and a modified OPLS-AA force field to simulate 44 replicas of each solvated system in parallel, with temperatures ranging from 300 to 577 K. Our results showed that the REMD method was more effective in predicting the helical conformation of the m-PPE in water, from an extended structure, than canonical MD methods in the same simulation time. Furthermore, we observed from canonical MD simulations of the explicitly solvated helical m-PPEs at 300 K that the radius of gyration, average helix inner diameter, and average helix pitch of the helical structure all pass through a minima when the side group is R = OC(2)H(5) as R is changed from R = H through OC(4)H(9).

Molecular Dynamics Simulations of Helix-Forming, Amine-Functionalized m-Poly(phenyleneethynylene)s

We present here the results of all-atom and united-atom molecular dynamics (MD) simulations that were used to examine the folding behavior of an amine-functionalized m-poly(phenyleneethynylene) (m-PPE) oligomer in aqueous environment. The parallelized GROMACS MD simulation code and OPLS force field were used for multiple MD simulations of m-PPE oligomers containing 24 phenyl rings in extended, coiled and helix conformations separately in water to determine the minimum energy conformation of the oligomer in aqueous solvent and what interactions are most important in determining this structure. Simulation results showed that the helix is the preferred minimum energy conformation of a single oligomer in water and that Lennard-Jones interactions are the dominant forces for the stabilization of the helix. In addition, these solvophobic interactions are strong enough to maintain the helix conformation at temperatures up to 523 K.