M. Reza Ghadiri

Self Assembling Organic Nanotubes

Hollow tubular structures of molecular dimensions perform diverse biological functions in nature. Examples include scaffolding and packaging roles played by cytoskeletal microtubules and viral coat proteins, respectively, as well as the chemical transport and screening activities of membrane channels. In the preparation of such tubular assemblies, biological systems make extensive use of self-assembling and self-organizing strategies. Owing to numerous potential applications in areas such as chemistry, biology, and materials science considerable effort has recently been devoted to preparation of artificial nanotubular structures. This article reviews design principles and the preparation of synthetic organic nanotubes, with special emphasis on noncovalent processes such as self-assembly and self-organization.

A Single-Molecule Nanopore Device Detects DNA Polymerase Activity with Single-Nucleotide Resolution

The ability to monitor DNA polymerase activity with single-nucleotide resolution has been the cornerstone of a number of advanced single-molecule DNA sequencing concepts. Toward this goal, we report the first observation of the base-by-base DNA polymerase activity with single-base resolution at the single-molecule level. We describe the design and characterization of a supramolecular nanopore device capable of detecting up to nine consecutive DNA polymerase-catalyzed single-nucleotide primer extensions with high sensitivity and spatial resolution (<or=2.4 A). The device is assembled in a suspended lipid membrane by threading and mechanically capturing a single strand of DNA-PEG copolymer inside an alpha-hemolysin protein pore. Single-nucleotide primer extensions result in successive displacements of the template DNA strand within the protein pore, which can be monitored by the corresponding stepped changes in the ion current flowing through the pore under an applied transmembrane potential. The system described thus represents a promising advance toward nanopore-mediated single-molecule DNA sequencing concept and, in addition, might be applicable to studying a number of other biopolymer-protein interactions and dynamics.

Peptide Nanotubes and Beyond

Self-assembling peptide nanotubes (such as the cyclic peptide for which the calculated crystal structure is shown on the right) display a wide range of structural and functional capabilities that have enabled their application in biological as well as materials science. Recent advances in the field and future directions are discussed.

A chiroselective peptide replicator.

The origin of homochirality in living systems is often attributed to the generation of enantiomeric differences in a pool of chiral prebiotic molecules, but none of the possible physiochemical processes considered can produce the significant imbalance required if homochiral biopolymers are to result from simple coupling of suitable precursor molecules. This implies a central role either for additional processes that can selectively amplify an initially minute enantiomeric difference in the starting material, or for a nonenzymatic process by which biopolymers undergo chiroselective molecular replication. Given that molecular self-replication and the capacity for selection are necessary conditions for the emergence of life, chiroselective replication of biopolymers seems a particularly attractive process for explaining homochirality in nature. Here we report that a 32-residue peptide replicator, designed according to our earlier principles, is capable of efficiently amplifying homochiral products from a racemic mixture of peptide fragments through a chiroselective autocatalytic cycle. The chiroselective amplification process discriminates between structures possessing even single stereochemical mutations within otherwise homochiral sequences. Moreover, the system exhibits a dynamic stereochemical ‘editing’ function; in contrast to the previously observed error correction, it makes use of heterochiral sequences that arise through uncatalysed background reactions to catalyse the production of the homochiral product. These results support the idea that self-replicating polypeptides could have played a key role in the origin of homochirality on Earth.

Organische Nanoröhren durch Selbstorganisation

Rohrenformige molekulare Strukturen nehmen in der Natur verschiedenste biologische Funktionen wahr, erwahnt seien ihre Rolle beim Aufbau des Gerusts der Mikrotubuli des Cytoskeletts, die Verpackungsfunktion viraler Hullenproteine und ihre Funktion beim Transport von Molekulen sowie beim Screening von Transmembrankanalen. Beim Aufbau solcher tubularer Strukturen nutzen biologische Systeme ausgiebig die Selbstassoziation und Selbstorganisation molekularer Einheiten. Wegen der zahlreichen Anwendungsmoglichkeiten in der Chemie, der Biologie und den Materialwissenschaften wurden in der letzten Zeit betrachtliche Anstrengungen zur Herstellung kunstlicher Nanorohren unternommen. Dieser Aufsatz gibt einen Uberblick uber die Prinzipien des Designs und der Herstellung synthetischer organischer Nanorohren mit dem Schwerpunkt auf Aggregation uber nichtkovalente Wechselwirkungen wie der Selbstorganisation und Selbstassoziation.

Self-Assembling Sequence-Adaptive Peptide Nucleic Acids

Adaptable DNA Analogs The defining feature of DNA as a genetic blueprint is its capacity for self-replication. In the cell, however, the replication process requires the assistance of multiple elaborate enzymes. How then at the origin of life could DNA or its precursor replicate before enzymes were present? Ura et al. (p. 73, published online 11 June) have achieved the long-sought goal of preparing a synthetic DNA analog that can dynamically adapt its sequence in free solution. Their analog (as yet only studied in relatively short, 20-unit oligomers) replaces DNAs sugar and phosphate backbone by a peptide strand in which cysteines reversibly bind the conventional DNA bases through thioester tethers. These strands can pair with complementary sequences of true DNA and furthermore swap one tethered base for another if different DNA templating strands are added to the solution in succession. A synthetic DNA analog can dynamically adapt its sequence in response to changing templates. Several classes of nucleic acid analogs have been reported, but no synthetic informational polymer has yet proven responsive to selection pressures under enzyme-free conditions. Here, we introduce an oligomer family that efficiently self-assembles by means of reversible covalent anchoring of nucleobase recognition units onto simple oligo-dipeptide backbones [thioester peptide nucleic acids (tPNAs)] and undergoes dynamic sequence modification in response to changing templates in solution. The oligomers specifically self-pair with complementary tPNA strands and cross-pair with RNA and DNA in Watson-Crick fashion. Thus, tPNA combines base-pairing interactions with the side-chain functionalities of typical peptides and proteins. These characteristics might prove advantageous for the design or selection of catalytic constructs or biomaterials that are capable of dynamic sequence repair and adaptation.

Photoswitchable Hydrogen‐Bonding in Self‐Organized Cylindrical Peptide Systems

The new photochromic supramolecular system 1 is based on the E→Z isomerization of an azobenzene substituted with cyclic peptides with alternating D- and L-α-amino acids. This system allows reversible switching between inter- and intramolecularly assembled cylindrical β-sheet structures in solution as well as in thin films at the air-water interface. Moreover, the system displays the rarely observed quantitative photoinduced E→Z isomerization.

Probing the bioactive conformation of an archetypal natural product HDAC inhibitor with conformationally homogeneous triazole-modified cyclic tetrapeptides.

Fooling enzymes with mock amides: Analogues of apicidin, a cyclic-tetrapeptide inhibitor of histone deacetylase (HDAC), were designed with a 1,4- or 1,5-disubstituted 1,2,3-triazole in place of a backbone amide bond to fix the bond in question in either a trans-like or a cis-like configuration. Thus, the binding affinity of distinct peptide conformations (see picture) could be probed. One analogue proved in some cases to be superior to apicidin as an HDAC inhibitor.

Systemic Antibacterial Activity of Novel Synthetic Cyclic Peptides

ABSTRACT Cyclic peptides with an even number of alternating d,l-α-amino acid residues are known to self-assemble into organic nanotubes. Such peptides previously have been shown to be stable upon protease treatment, membrane active, and bactericidal and to exert antimicrobial activity against Staphylococcus aureus and other gram-positive bacteria. The present report describes the in vitro and in vivo pharmacology of selected members of this cyclic peptide family. The intravenous (i.v.) efficacy of six compounds with MICs of less than 12 μg/ml was tested in peritonitis and neutropenic-mouse thigh infection models. Four of the six peptides were efficacious in vivo, with 50% effective doses in the peritonitis model ranging between 4.0 and 6.7 mg/kg against methicillin-sensitive S. aureus (MSSA). In the thigh infection model, the four peptides reduced the bacterial load 2.1 to 3.0 log units following administration of an 8-mg/kg i.v. dose. Activity against methicillin-resistant S. aureus was similar to MSSA. The murine pharmacokinetic profile of each compound was determined following i.v. bolus injection. Interestingly, those compounds with poor efficacy in vivo displayed a significantly lower maximum concentration of the drug in serum and a higher volume of distribution at steady state than compounds with good therapeutic properties. S. aureus was unable to easily develop spontaneous resistance upon prolonged exposure to the peptides at sublethal concentrations, in agreement with the proposed interaction with multiple components of the bacterial membrane canopy. Although additional structure-activity relationship studies are required to improve the therapeutic window of this class of antimicrobial peptides, our results suggest that these amphipathic cyclic d,l-α-peptides have potential for systemic administration and treatment of otherwise antibiotic-resistant infections.

A virocidal amphipathic α-helical peptide that inhibits hepatitis C virus infection in vitro

An amphipathic α-helical peptide (C5A) derived from the membrane anchor domain of the hepatitis C virus (HCV) NS5A protein is virocidal for HCV at submicromolar concentrations in vitro. C5A prevents de novo HCV infection and suppresses ongoing infection by inactivating both extra- and intracellular infectious particles, and it is nontoxic in vitro and in vivo at doses at least 100-fold higher than required for antiviral activity. Mutational analysis indicates that C5As amphipathic α-helical structure is necessary but not sufficient for its virocidal activity, which depends on its amino acid composition but not its primary sequence or chirality. In addition to HCV, C5A inhibits infection by selected flaviviruses, paramyxoviruses, and HIV. These results suggest a model in which C5A destabilizes viral membranes based on their lipid composition, offering a unique therapeutic approach to HCV and other viral infections.