Hierarchical Self-Assembly of Histidine-Functionalized Peptide Amphiphiles into Supramolecular Chiral Nanostructures

The effects of histidine substitution of aromatic residues on the amyloidogenic properties of the fragment 264-277 of nucleophosmin 1

Histidine (His) plays a key role in mediating protein interactions and its unique side chain determines pH responsive self-assembling processes and thus in the formation of nanostructures. In this study, To identify novel self-assembling bioinspired sequences, we analyzed a series of peptide sequences obtained through the point mutation of aromatic residues of 264-277 fragment of nucleophosmin 1 (NPM1) with single and double histidines. Through several orthogonal biophysical techniques and under different pH and ionic strength conditions we evaluated the effects of these substitutions in the amyloidogenic features of derived peptides. The results clearly indicate that both the type of aromatic mutated residue and its position can have different effect on amyloid-like behaviors. They corroborate the crucial role exerted by Tyr271 in the self-assembling process of CTD of NPM1 in AML mutated form and add novel insights in the accurate investigation of how side chain orientations can determine successful design of innovative bioinspired materials.

Lipopeptides as tools in catalysis, supramolecular, materials and medicinal chemistry

Lipopeptides are amphiphilic peptides in which an aliphatic chain is attached to either the C or N terminus of peptides. Their self-assembly - into micelles, vesicles, nanotubes, fibres or nanobelts - leads to applications in nanotechnology, catalysis or medicinal chemistry. Self-organization of lipopeptides is dependent on both the length of the lipid tail and the amino acid sequence, in which the chirality of the peptide sequence can be transmitted into the supramolecular species. This Review describes the use of lipopeptides to design synthetic advanced dynamic supramolecular systems, nanostructured materials or self-responsive delivery systems in the area of medical biotechnology. We examine the influence of external stimuli, the ability of lipopeptide-derived structures to adapt over time and their application as medicinal agents with antibacterial, antifungal, antiviral or anticancer activities. Finally, we discuss the catalytic efficiency of lipopeptides, with the aim of building minimal synthetic enzymes, and recent efforts to incorporate metals into lipopeptide assemblies.

Antibacterial and Cytocompatible pH-Responsive Peptide Hydrogel

A short peptide, FHHF-11, was designed to change stiffness as a function of pH due to changing degree of protonation of histidines. As pH changes in the physiologically relevant range, G' was measured at 0 Pa (pH 6) and 50,000 Pa (pH 8). This peptide-based hydrogel is antimicrobial and cytocompatible with skin cells (fibroblasts). It was demonstrated that the incorporation of unnatural AzAla tryptophan analog residue improves the antimicrobial properties of the hydrogel. The material developed can have a practical application and be a paradigm shift in the approach to wound treatment, and it will improve healing outcomes for millions of patients each year.

Urea-Modified Self-Assembling Peptide Amphiphiles That Form Well-Defined Nanostructures and Hydrogels for Biomedical Applications

Hydrogen bonding plays a critical role in the self-assembly of peptide amphiphiles (PAs). Herein, we studied the effect of replacing the amide linkage between the peptide and lipid portions of the PA with a urea group, which possesses an additional hydrogen bond donor. We prepared three PAs with the peptide sequence Phe-Phe-Glu-Glu (FFEE): two are amide-linked with hydrophobic tails of different lengths and the other possesses an alkylated urea group. The differences in the self-assembled structures formed by these PAs were assessed using diverse microscopies, nuclear magnetic resonance (NMR), and dichroism techniques. We found that the urea group influences the morphology and internal arrangement of the assemblies. Molecular dynamics simulations suggest that there are about 50% more hydrogen bonds in nanostructures assembled from the urea-PA than those assembled from the other PAs. Furthermore, in silico studies suggest the presence of urea-π stacking interactions with the phenyl group of Phe, which results in distinct peptide conformations in comparison to the amide-linked PAs. We then studied the effect of the urea modification on the mechanical properties of PA hydrogels. We found that the hydrogel made of the urea-PA exhibits increased stability and self-healing ability. In addition, it allows cell adhesion, spreading, and growth as a matrix. This study reveals that the inclusion of urea bonds might be useful in controlling the morphology, mechanical, and biological properties of self-assembled nanostructures and hydrogels formed by the PAs.

Systems chemistry of peptide-assemblies for biochemical transformations

During the billions of years of the evolutionary journey, primitive polymers, involved in proto metabolic pathways with low catalytic activity, played critical roles in the emergence of modern enzymes with remarkable substrate specificity. The precise positioning of amino acid residues and the complex orchestrated interplay in the binding pockets of evolved enzymes promote covalent and non-covalent interactions to foster a diverse set of complex catalytic transformations. Recent efforts to emulate the structural and functional information of extant enzymes by minimal peptide based assemblies have attempted to provide a holistic approach that could help in discerning the prebiotic origins of catalytically active binding pockets of advanced proteins. In addition to the impressive sets of advanced biochemical transformations, catalytic promiscuity and cascade catalysis by such small molecule based dynamic systems can foreshadow the ancestral catalytic processes required for the onset of protometabolism. Looking beyond minimal systems that work close to equilibrium, catalytic systems and compartments under non-equilibrium conditions utilizing simple prebiotically relevant precursors have attempted to shed light on how bioenergetics played an essential role in chemical emergence of complex behaviour. Herein, we map out these recent works and progress where diverse sets of complex enzymatic transformations were demonstrated by utilizing minimal peptide based self-assembled systems. Further, we have attempted to cover the examples of peptide assemblies that could feature promiscuous activity and promote complex multistep cascade reaction networks. The review also covers a few recent examples of minimal transient catalytic assemblies under non-equilibrium conditions. This review attempts to provide a broad perspective for potentially programming functionality via rational selection of amino acid sequences leading towards minimal catalytic systems that resemble the traits of contemporary enzymes.

Modulating the Excited State Chirality of Dynamic Chemical Reactions in Chiral Micelles

Chirality generation and transfer is not only of critical importance in resolving the origin of biological homochirality, but also is of great significance for exploring the chirality-related functionalities in nanomaterials and supramolecular systems. Although modulating the ground state chirality in chiral nanomaterials has been widely demonstrated, it remains a big challenge to steer the excited state chirality (circularly polarized luminescence, CPL). Herein, we present a kind of chiral spherical micelles constructed by chiral cationic gemini surfactants, whose surfaces and cavities could co-assemble with hydrophilic and hydrophobic emitters concurrently. Subsequently, the hydrophilic and hydrophobic emitters could be endowed with CPL activity in the aqueous phase. Additionally, the cavities of such micelles can be regarded as the powerful chiral confined space, which could effectively modulate the excited state chirality of dynamic chemical reactions, enabling color-adjustable CPL emission.

Structure-function relationship of small peptides generated during the ripening of Spanish dry-cured ham: Peptidome, molecular stability and computational modelling

A systematic insight into the structure-function properties of small bioactive peptides is of great importance. Herein, peptidomics and computational methodology were adopted to investigate the stabilization patterns and building blocks of antioxidant peptides resulting from proteolysis during the ripening of Spanish dry-cured ham (9-24 months of processing). The results showed that native peptides underwent manufacture-induced steric/redox stress, while homogeneous/heterogeneous p-π/π-π interaction significantly improved the ABTS⁺ inhibition activity of hydrophobic peptides. However, for more hydrophilic peptides, the intrinsic π-interaction system (i.e., cation-π and π-π packing) substantially interfered with ABTS⁺/DPPH scavenging events when compared to the aromatic residues. Semi-quantitative peptidomics and molecular simulation/docking revealed that VFSSQGQSELILLQK and LCPSPDGLYL are two potential antioxidant peptides at the late ripening-drying. They had distinctive self-folding destinies following solvation owing to varying charged/hydrophobic properties of termini and hydrogen atom donor, allowing different flexibility of backbone and interactive surface towards free radicals ex situ followed by electron/proton transfer.

New antimicrobial self-assembling short lipopeptides

Lipopeptides are an exceptional example of amphiphilic molecules that self-assemble into functional structures with applications in the areas of nanotechnology, catalysis or medicinal chemistry. Herein, we report a library of 21 short lipopeptides, together with their supramolecular characterization and antimicrobial activity against both Gram-negative (E. coli) and Gram-positive (S. aureus) strains. This study shows that simple lipoamino acids self-assemble into micellar or vesicular structures, while incorporating dipeptides capable of stablishing hydrogen bonds results in the adoption of advanced fibrilar structures. The self-assembly effect has proven to be key to achieve antimicrobial activity.

De novo design of a pH-triggered self-assembled β-hairpin nanopeptide with the dual biological functions for antibacterial and entrapment

BACKGROUND

Acid-tolerant enteric pathogens can evade small intestinal acid barriers, colonize and infect the intestinal tract. However, broad-spectrum antibiotics are not the best therapeutic strategy because of the disruption of intestinal flora caused by its indiscriminate antimicrobial activity against beneficial and harmful bacteria. So that is what inspired us to combine pH regulation with nanotechnology to develop a pH-triggered site-targeted antimicrobial peptide with entrapping function.

RESULTS

A pH-triggered dual biological functional self-assembled peptide (SAP) was designed according to the features of amino-acid building blocks and the diagonal cation-π interaction principle. The results of characterization experiments showed that changes in pH conditions could trigger microstructural transformation of the nanopeptide from nanospheres to nanofibers. The subsequent antibacterial and toxicity experiments determined that SAP had great antimicrobial activity against Escherichia coli, Salmonella typhimurium, Listeria monocytogenes, and Bacillus cereus above 15.6 μg/mL under acidic conditions by disrupting bacterial membrane integrity, excellent biocompatibility in vitro even at 250 μg/mL and high tolerance in physical environment. Moreover, at peptide concentrations greater than 62.5 μg/mL, SAP showed the entrapment property, which played an important role in phagocytic clearance in infection forces. Meanwhile, the in vivo results revealed that SAP possessed excellent therapeutic effect and good biosafety.

CONCLUSIONS

Our study revealed the antibacterial activity of a short β-hairpin forming self-assembled peptide, and established an innovative design strategy for peptide-based nanomaterials and a new treatment strategy for gastrointestinal bacterial infections.

(Macro)molecular self-assembly for hydrogel drug delivery

Hydrogels prepared via self-assembly offer scalable and tunable platforms for drug delivery applications. Molecular-scale self-assembly leverages an interplay of attractive and repulsive forces; drugs and other active molecules can be incorporated into such materials by partitioning in hydrophobic domains, affinity-mediated binding, or covalent integration. Peptides have been widely used as building blocks for self-assembly due to facile synthesis, ease of modification with bioactive molecules, and precise molecular-scale control over material properties through tunable interactions. Additional opportunities are manifest in stimuli-responsive self-assembly for more precise drug action. Hydrogels can likewise be fabricated from macromolecular self-assembly, with both synthetic polymers and biopolymers used to prepare materials with controlled mechanical properties and tunable drug release. These include clinical approaches for solubilization and delivery of hydrophobic drugs. To further enhance mechanical properties of hydrogels prepared through self-assembly, recent work has integrated self-assembly motifs with polymeric networks. For example, double-network hydrogels capture the beneficial properties of both self-assembled and covalent networks. The expanding ability to fabricate complex and precise materials, coupled with an improved understanding of biology, will lead to new classes of hydrogels specifically tailored for drug delivery applications.

SAPdb: A database of short peptides and the corresponding nanostructures formed by self-assembly

Nanostructures generated by self-assembly of peptides yield nanomaterials that have many therapeutic applications, including drug delivery and biomedical engineering, due to their low cytotoxicity and higher uptake by targeted cells owing to their high affinity and specificity towards cell surface receptors. Despite the promising implications of this rapidly expanding field, there is no dedicated resource to study peptide nanostructures. This study endeavours to create a repository of short peptides, which may prove to be the best models to study ordered nanostructures formed by peptide self-assembly. SAPdb has a repertoire of 1049 entries of experimentally validated nanostructures formed by the self-assembly of small peptides. It consists of 328 tripeptides, 701 dipeptides, and 20 single amino acids with some conjugate partners. Each entry encompasses comprehensive information about the peptide, such as chemical modifications, the type of nanostructure formed, experimental conditions like pH, temperature, solvent required for the self-assembly, etc. Our analysis indicates that peptides containing aromatic amino acids favour the formation of self-assembling nanostructures. Additionally, we observed that these peptides form different nanostructures under different experimental conditions. SAPdb provides this comprehensive information in a hassle-free tabulated manner at a glance. User-friendly browsing, searching, and analysis modules have been integrated for easy data retrieval, data comparison, and examination of properties. We anticipate SAPdb to be a valuable repository for researchers engaged in the burgeoning arena of nanobiotechnology. It is freely available at https://webs.iiitd.edu.in/raghava/sapdb.

High-Throughput Peptide Derivatization toward Supramolecular Diversification in Microtiter Plates

The evolution of life on earth eventually leads to the emergence of species with increased complexity and diversity. Similarly, evolutionary chemical space exploration in the laboratory is a key step to pursue the structural and functional diversity of supramolecular systems. Here, we present a powerful tool that enables rapid peptide diversification and employ it to expand the chemical space for supramolecular functions. Central to this strategy is the exploitation of palladium-catalyzed Suzuki-Miyaura cross-coupling reactions to direct combinatorial synthesis of peptide arrays in microtiter plates under an open atmosphere. Taking advantage of this in situ library design, our results unambiguously deliver a fertile platform for creating a set of intriguing peptide functions including green fluorescent protein-like peptide emitters with chemically encoded emission colors, hierarchical self-assembly into nano-objects, and macroscopic hydrogels. This work also offers opportunities for quickly surveying the diversified peptide arrays and thereby identifying the structural factors that modulate peptide properties.

Alpha helical surfactant-like peptides self-assemble into pH-dependent nanostructures

A designed surfactant-like peptide is shown, using a combination of cryogenic-transmission electron microscopy and small-angle X-ray scattering, to have remarkable pH-dependent self-assembly properties. Peptide Arg₃-Leu₁₂ (R₃L₁₂) forms a network of peptide nanotubes at pH 9 and below. These are associated with α-helical conformation in a "cross-α" nanotube structure, in which peptide dimers lie perpendicular to the nanotube axis, with arginine coated inner and outer nanotube walls. In contrast, this peptide forms decorated vesicular aggregates at higher pH values, close to the pK_a of the arginine residues. These structures are associated with a loss of α-helical order as detected through X-ray scattering, circular dichroism and FTIR spectroscopy, the latter technique also revealing a loss of ordering of leucine side chains. This suggests a proposed model for the decorated or patchy vesicular structures that comprises disordered peptide as the matrix of the membrane, with small domains of ordered peptide dimers forming the minority domains. We ascribe this to a lipid-raft like phase separation process, due to conformational disordering of the leucine hydrophobic chains. The observation of the self-assembly of a simple surfactant-like peptide into these types of nanostructure is remarkable, and peptide R₃L₁₂ shows unique pH-dependent morphological and conformational behaviour, with the potential for a range of future applications.

Effect of C12H25O– substituent position on the self-assembly behaviour of C6H5COO–Ala–Ala dipeptide

Intramolecular hydrogen bonding and steric hindrance of side chain lead the different molecular packing of dipeptides and the morphological transformation of self-assemblies’ nanostructures.

Amphiphilic phenylalanine derivatives that temporally generate reactive oxygen species from water in the presence of Au(iii) ions

Amphiphilic derivatives of phenylalanine (ADFs) have strong self-assembling propensities and yield low molecular weight hydrogels on multiple occassions. The interaction of ADFs with metal ions can result in the morphological changes in the self-assemblies. Herein, we report the interesting consequences of the interaction between four N-protected ADFs with Au(iii) ions. In the case of ADF 1, the original nanofibrillar morphology of the self-assemblies spontaneously transformed into uniform nanoglobules of ∼80 nm in diameter upon addition of Au(iii) ions. A subsequent reduction of the Au(iii) ions to Au(0) nanoparticles (AuNPs) and the surface decoration of the nanoglobules with AuNPs were observed in the course of the next six to eight hours. Simultaneously, multiple reactive oxygen species (ROS) such as hydrogen peroxide (H₂O₂), hydroxyl radicals (˙OH), singlet oxygen and superoxide ions were also found to be present in the reaction medium. These ROS originate from water used as the reaction medium. The ROS production and the reduction of Au(iii) were inhibited upon deaeration of the reaction medium and the use of heavy water (D₂O) or organic solvents as the reaction medium, while an increase in the pH of the aqueous medium intensified both these processes. We exploited the temporal ROS generation using the mixture of 1 and Au(iii) ions towards anticancer therapy by enhancing the intracellular ROS levels. It is expected that this effort can be expanded into a viable anticancer therapy in the near future by modulating the amount and the rate of ROS-generation through judicious choice of the peptidic ligands and metal ions.

Enhanced Stability of Peptide Nanofibers Coated with a Conformal Layer of Polydopamine

The susceptibility of self-assembled materials to changes of environmental conditions and mechanical forces often limits their utility for many applications. In this work, the surface of nanofibers formed by β-sheet peptide self-assemblies were coated by polydopamine (PDA) deposition. This conformal coating process rendered the nanofiber dimensions and internal π-stacking chirality impervious to changes in pH, temperature, and physical processing by spin-coating onto a silicon wafer. Whereas sonication-induced shearing of the dopamine/naphthalenediimide-dilysine (DA/NDI-KK) composite irreversibly shortened the nanofibers into 100-200 nm segments, the uncoated nanofibers unraveled into single strands upon similar treatment. Additionally, the PDA-coated nanofibers could be wrapped by an additional layer comprised of a positively charged polyelectrolyte polymer.

Hierarchical chirality expression of gemini surfactant aggregates via equilibrium between chiral nucleotide and nonchiral mono-anions

The assembling behaviors of nonchiral dicationic amphiphilic molecules (gemini) in the presence of the mixture of chiral anionic nucleotides and nonchiral anions are investigated. We demonstrate that subtle balance of various physico-chemical parameters and the competition between chiral and nonchiral anions at the interface of gemini assemblies influences the expression of molecular chirality at the micrometer scale through the hierarchical molecular assembly.

Peptide interdigitation-induced twisted nanoribbons as chiral scaffolds for supramolecular nanozymes

Establishing reliable strategies for rationally manipulating the organization of peptide building blocks and thereby precisely creating chiral nanostructures is challenging, while meaningful toward development of advanced functional materials. Here we report on a peptide-interdigitating mechanism for the reliable self-assembly of lipid-inspired amphiphiles (LIPIAs) into robust twisted nanoribbons by grafting domains to one alkyl tail of lipids as an extended element. Peptide interdigitation promoted the self-assembly of LIPIAs into twisted or flat nanoribbons driven by antiparallel or parallel β-sheet hydrogen bonds, respectively, strongly associated with the connecting direction of the incorporated domains. We found that the LIPIAs containing N-terminus-connected domains with either bulky or small side chain groups formed twisted nanoribbons in a broad pH range, thus implying a sequence- and pH-independent strategy for creation of robust chiral nanostructures. Integrating the resulting twisted nanoribbons with gold nanoparticles led to supramolecular nanozymes exhibiting the excellent catalytic activity and enantioselectivity of asymmetric oxidation of 3,4-dihyroxy-phenylalanine molecules. Our finding demonstrates that the peptide-interdigitating mechanism is a reliable strategy for precise creation of chiral nanostructures serving as chiral matrices for supramolecular nanozymes with improved catalytic performance, thus potentially paving the way towards advanced biomimetic systems resembling natural systems.

pH-Controlled Chiral Packing and Self-Assembly of a Coumarin Tetrapeptide

A coumarin-tetrapeptide conjugate, EFEK(DAC)-NH₂ (1), is reported to undergo a pH-dependent interconversion between nanotubes and nanoribbons. An examination of zeta potential measurements, circular dichroism (CD) spectra, and microscopy imaging (transmission electron microscopy and atomic force microscopy) identified three different self-assembly regimes based on pH: (1) pH 2-5, positively charged, left-handed helical nanotubes; (2) pH 6-8, negatively charged, right-handed helical nanoribbons; and (3) pH ≥ 9.0, a monomeric/disassembled peptide. The nanotubes exhibited uniform diameters of 41 ± 5 nm and wall thicknesses of 4.8 ± 0.8 nm, whereas the nanoribbons existed as either flat or twisted sheets ranging in width from 11 to 60 nm with heights of 8 ± 1 nm. The UV-vis and CD spectra of the most common antiparallel, β-sheet conformation of 1-dimer were simulated at the B3LYP/def2svpd level of theory in implicit water. These studies indicated that the transition from nanotubes to nanoribbons was coupled to an M → P helical inversion of the coumarin packing orientation, respectively, within the nanostructures. The assembly process was driven by β-sheet aggregation and π-π interactions, leading to the formation of nanoribbons, which progressively wound into helical ribbons and laterally grew into smooth nanotubes as the pH decreased.

Self-assembled micro-fibres by oxime connection of linear peptide amphiphiles

Linear peptide amphiphiles are excellent biocompatible scaffolds for the hierarchical self-assembly of one-dimensional nano-structures in aqueous media. However, their structural exploration and screening of self-assembling properties are often limited by time-consuming synthesis and purification steps. We here describe the application of an oxime bond as a powerful synthetic tool towards the conjugation of peptide heads bearing a hydroxylamine group with hydrophobic aldehyde tails. This methodology allowed the quick preparation of a small library of oxime-connected peptide amphiphiles, whose supramolecular screening revealed nano-to-micro-fibrillation with dependency on their chemical structure. These results demonstrate the simplicity and the synthetic potential of the oxime conjugation for the preparation of peptide amphiphiles with improved self-assembling capabilities.

Self-Assembly and Chiral Recognition of Chiral Cationic Gemini Surfactants

Chiral cationic gemini surfactants 1,4-bis(dodecyl- N, N-dimethylammonium bromide)-2,3-butanediol (12-4(OH)₂-12) including racemate, mesomer, and two enantiomers were synthesized and their self-assembly in aqueous solution has been comparatively investigated by tensiometry, conductometry, ¹H NMR, small-angle neutron scattering, cryogenic transmission electron microscopy, and cryogenic scanning electron microscopy. The chirality at spacer induces different self-assembly behaviors due to the hydrogen-bonding interaction between the hydroxyl groups at the chiral centers. The stereochemistry of the spacer has little effect on the release of the counterions from the surfactant headgroups and on the molecular packing at the air-water interface. The critical micelle concentration (CMC) decreases in the order of racemate > enantiomer > mesomer. Above the CMC, the aggregates of enantiomers transit from small spherical micelles to rodlike and wormlike micelles with increasing concentration, whereas the mesomer and racemate aggregates transform from spherical micelles to rodlike micelles and platelet-like aggregates. The differences may be because the mesomer and racemate molecules mainly form intermolecular hydrogen bonds between the -OH groups, but the enantiomer molecules dominantly form intramolecular hydrogen bonds. Furthermore, it was found that the chiral micelles formed by the enantiomers exhibit enantioselection ability for bilirubin (BR) enantiomers. The recognition capability can be adjusted by the micellar structure, i.e., the rodlike micelles are better than either small spherical micelles or wormlike micelles, which might possess different chiral cavities, controlling BR shape and location. These results demonstrate that the aggregates of chiral gemini surfactants can be used to mimic the chiral recognition in biological membrane.

Controlling Supramolecular Chiral Nanostructures by Self-Assembly of a Biomimetic β-Sheet-Rich Amyloidogenic Peptide

Squid sucker ring teeth (SRT) have emerged as a promising protein-only, thermoplastic biopolymer with an increasing number of biomedical and engineering applications demonstrated in recent years. SRT is a supra-molecular network whereby a flexible, amorphous matrix is mechanically reinforced by nanoconfined β-sheets. The building blocks for the SRT network are a family of suckerin proteins that share a common block copolymer architecture consisting of amorphous domains intervened by smaller, β-sheet forming modules. Recent studies have identified the peptide A1H1 (peptide sequence AATAVSHTTHHA) as one of the most abundant β-sheet forming domains within the suckerin protein family. However, we still have little understanding of the assembly mechanisms by which the A1H1 peptide may assemble into its functional load-bearing domains. In this study, we conduct a detailed self-assembly study of A1H1 and show that the peptide undergoes β-strands-driven elongation into amyloid-like fibrils with a rich polymorphism. The nanostructure of the fibrils was elucidated by small and wide-angle X-ray scattering (SAXS and WAXS) and atomic force microscopy (AFM). The presence of His-rich and Ala-rich segments results in an amphiphilic behavior and drives its assembly into fibrillar supramolecular chiral aggregates with helical ribbon configuration in solution, with the His-rich region exposed to the solvent molecules. Upon increase in concentration, the fibrils undergo gel formation, while preserving the same mesoscopic features. This complex phase behavior suggests that the repeat peptide modules of suckerins may be manipulated beyond their native biological environment to produce a wider variety of self-assembled amyloid-like nanostructures.

Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments

In bionanotechnology, the field of creating functional materials consisting of bio-inspired molecules, the function and shape of a nanostructure only appear through the assembly of many small molecules together. The large number of building blocks required to define a nanostructure combined with the many degrees of freedom in packing small molecules has long precluded molecular simulations, but recent advances in computational hardware as well as software have made classical simulations available to this strongly expanding field. Here, we review the state of the art in simulations of self-assembling bio-inspired supramolecular systems. We will first discuss progress in force fields, simulation protocols and enhanced sampling techniques using recent examples. Secondly, we will focus on efforts to enable the comparison of experimentally accessible observables and computational results. Experimental quantities that can be measured by microscopy, spectroscopy and scattering can be linked to simulation output either directly or indirectly, via quantum mechanical or semi-empirical techniques. Overall, we aim to provide an overview of the various computational approaches to understand not only the molecular architecture of nanostructures, but also the mechanism of their formation.

Self-assembly behaviours of peptide-drug conjugates: influence of multiple factors on aggregate morphology and potential self-assembly mechanism

Peptide-drug conjugates (PDCs) as self-assembly prodrugs have the unique and specific features to build one-component nanomedicines. Supramolecular structure based on PDCs could form various morphologies ranging from nanotube, nanofibre, nanobelt to hydrogel. However, the assembly process of PDCs is too complex to predict or control. Herein, we investigated the effects of extrinsic factors on assembly morphology and the possible formation of nanostructures based on PDCs. To this end, we designed a PDC consisting of hydrophobic drug (S)-ketoprofen (Ket) and valine-glutamic acid dimeric repeats peptide (L-VEVE) to study their assembly behaviour. Our results showed that the critical assembly concentration of Ket-L-VEVE was 0.32 mM in water to form various nanostructures which experienced from micelle, nanorod, nanofibre to nanoribbon. The morphology was influenced by multiple factors including molecular design, assembly time, pH and hydrogen bond inhibitor. On the basis of experimental results, we speculated the possible assembly mechanism of Ket-L-VEVE. The π-π stacking interaction between Ket molecules could serve as an anchor, and hydrogen bonded-induced β-sheets and hydrophilic/hydrophobic balance between L-VEVE peptide play structure-directing role in forming filament-like or nanoribbon morphology. This work provides a new sight to rationally design and precisely control the nanostructure of PDCs based on aromatic fragment.