Peptide and protein recognition by designed molecules

ProtTrans and multi-window scanning convolutional neural networks for the prediction of protein-peptide interaction sites

This study delves into the prediction of protein-peptide interactions using advanced machine learning techniques, comparing models such as sequence-based, standard CNNs, and traditional classifiers. Leveraging pre-trained language models and multi-view window scanning CNNs, our approach yields significant improvements, with ProtTrans standing out based on 2.1 billion protein sequences and 393 billion amino acids. The integrated model demonstrates remarkable performance, achieving an AUC of 0.856 and 0.823 on the PepBCL Set_1 and Set_2 datasets, respectively. Additionally, it attains a Precision of 0.564 in PepBCL Set 1 and 0.527 in PepBCL Set 2, surpassing the performance of previous methods. Beyond this, we explore the application of this model in cancer therapy, particularly in identifying peptide interactions for selective targeting of cancer cells, and other fields. The findings of this study contribute to bioinformatics, providing valuable insights for drug discovery and therapeutic development.

Ultrasensitive electrochemical sensor based on synergistic effect of Ag@MXene and antifouling cyclic multifunctional peptide for PD-L1 detection in serum

A sensing interface co-constructed from the two-dimensional conductive material (Ag@MXene) and an antifouling cyclic multifunctional peptide (CP) is described. While the large surface area of Ag@MXene loads more CP probes, CP binds to Ag@MXene to form a fouling barrier and ensure the structural rigidity of the targeting sequence. This strategy synergistically enhances the biosensor's sensitivity and resistance to contamination. The SPR results showed that the binding affinity of the CP to the target was 6.23 times higher than that of the antifouling straight-chain multifunctional peptide (SP) to the target. In the 10 mg/mL BSA electrochemical fouling test, the fouling resistance of Ag@MXene + CP (composite sensing interface of CP combined with Ag@MXene) was 30 times higher than that of the bare electrode. The designed electrochemical sensor exhibited good selectivity and wide dynamic response range at PD-L1 concentrations from 0.1 to 50 ng/mL. The lowest detection limit was 24.54 pg/mL (S/N = 3). Antifouling 2D materials with a substantial specific surface area, coupled with non-straight chain antifouling multifunctional peptides, offer a wide scope for investigating the sensitivity and antifouling properties of electrochemical sensors.

Therapeutic Potential of Nanocarrier Mediated Delivery of Peptides for Wound Healing: Current Status, Challenges and Future Prospective

Wound healing presents a complex physiological process that involves a sequence of events orchestrated by various cellular and molecular mechanisms. In recent years, there has been growing interest in leveraging nanomaterials and peptides to enhance wound healing outcomes. Nanocarriers offer unique properties such as high surface area-to-volume ratio, tunable physicochemical characteristics, and the ability to deliver therapeutic agents in a controlled manner. Similarly, peptides, with their diverse biological activities and low immunogenicity, hold great promise as therapeutics in wound healing applications. In this review, authors explore the potential of peptides as bioactive components in wound healing formulations, focusing on their antimicrobial, anti-inflammatory, and pro-regenerative properties. Despite the significant progress made in this field, several challenges remain, including the need for standardized characterization methods, optimization of biocompatibility and safety profiles, and translation from bench to bedside. Furthermore, developing multifunctional nanomaterial-peptide hybrid systems represents promising avenues for future research. Overall, the integration of nanomaterials made up of natural or synthetic polymers with peptide-based formulations holds tremendous therapeutic potential in advancing the field of wound healing and improving clinical outcomes for patients with acute and chronic wounds.

Vancomycin mimicry: towards new supramolecular antibiotics

Vancomycin is the best-known of the glycopeptide group antibiotics (GPAs), a family of agents which operate by binding the C-terminal deptide D-Ala-D-Ala. This anionic epitope is an interesting target because it plays a central role in bacterial cell wall synthesis, and is not readily modified by evolution. Accordingly, vancomycin has been in use for >60 years but has only provoked limited resistance. Agents which mimic vancomycin but are easier to synthesise and modify could serve as valuable weapons against pathogenic bacteria, broadening the scope of the GPAs and addressing the resistance that does exist. This article gives an overview of vancomycin's structure and action, surveys past work on vancomycin mimicry, and makes the case for renewed effort in the future.

Rational design of a sensitivity-enhanced tracer for discovering efficient APC-Asef inhibitors

The adenomatous polyposis coli (APC)–Rho guanine nucleotide exchange factor 4 (Asef) protein–protein interaction (PPI) is essential for colorectal cancer metastasis, making it a promising drug target. Herein, we obtain a sensitivity-enhanced tracer (tracer 7) with a high binding affinity (K_d = 0.078 μM) and wide signal dynamic range (span = 251 mp). By using tracer 7 in fluorescence-polarization assays for APC–Asef inhibitor screening, we discover a best-in-class inhibitor, MAI-516, with an IC₅₀ of 0.041 ± 0.004 μM and a conjugated transcriptional transactivating sequence for generating cell-permeable MAIT-516. MAIT-516 inhibits CRC cell migration by specifically hindering the APC–Asef PPI. Furthermore, MAIT-516 exhibits no cytotoxic effects on normal intestinal epithelial cell and colorectal cancer cell growth. Overall, we develop a sensitivity-enhanced tracer for fluorescence polarization assays, which is used for the precise quantification of high-activity APC–Asef inhibitors, thereby providing insight into PPI drug development.

The adenomatous polyposis coli (APC)–Asef protein interaction is essential for colorectal cancer metastasis. Here, the authors present the rational design of a sensitivity-enhanced tracer for fluorescence polarization assays, enabling them to discover more efficient APC–Asef interaction inhibitors.

Binary and Ternary Complexes of Cucurbit[8]uril with Tryptophan, Phenylalanine, and Tyrosine: A Computational Study

Selective binding of amino acids, peptides, and proteins by synthetic molecules and elucidation of the geometry and dynamics of the resulting complexes and their strengths are active areas of contemporary research. In recent work, we analyzed via molecular dynamics (MD) simulations the complexes formed between cucurbit[7]uril (CB7) and three aromatic amino acids: tryptophan (W), phenylalanine (F), and tyrosine (Y). Herein, we continue this line of research by performing MD simulations lasting 100 ns to investigate the formation, stabilities, binding modes, dynamics, and specific host-guest noncovalent interactions contributing to the formation of the binary (1:1) and ternary (2:1) complexes in aqueous solution between W, F, and Y amino acids and cucurbit[8]uril (CB8). All complexes were found to be stable, with the binding in each complex dominated by one mode (except for the F-CB8 complex, which had two) characterized by encapsulation of the aromatic side chains of the amino acids within the cavity of CB8 and the exclusion of their ammonium and carboxylate groups. Using the molecular mechanics/Poisson-Boltzmann surface area method to estimate the individual contributions to the overall free energies of binding, results revealed that the key role is played by the amino acid side chains in stabilizing the complexes through their favorable van der Waals interactions with the CB8 cavity and the importance of favorable electrostatic interactions between the carbonyl portal of CB8 and the ammonium group of the amino acid. Visual analysis of structures of the ternary complexes indicated the presence of π-π stacking between the aromatic side chains of the included amino acids. The insights provided by this work may be of value for further efforts aiming to employ the recognition properties of CB8 toward amino acids in applications requiring more elaborate recognition of short peptides and proteins.

A versatile enrichment of functionalized calixarene as a facile sensor for amino acids

Amino acids have become the most important part of the human biological system due to their roles in the living processes. Role of amino acids stretches beyond their traditional role as a building block for proteins, deficiency of the same could lead to decreased immunity, digestive problems, depression, fertility issues, lower mental alertness, slowed growth in children, and many other health issues. The acute detection of amino acids is necessary to determine the human health domain. Here in this review, we summarize and study the calixarenes as a complex detailed being of an immeasurable value and its utilization for the amino acids' detection. The key factors responsible such as noncovalent forces, LOD and supramolecular chemistry of calixarenes with amino acids are described well. This study presents the most recent efforts made for the development of potential and highly efficient calixarene based sensors for the detection of amino acids.

Antibodies targeting enzyme inhibition as potential tools for research and drug development

Antibodies have transformed biomedical research and are now being used for different experimental applications. Generally, the interaction of enzymes with their specific antibodies can lead to a reduction in their enzymatic activity. The effect of the antibody is dependent on its narrow i.e. the regions of the enzyme to which it is directed. The mechanism of this inhibition is rarely a direct combination of the antibodies with the catalytic site, but is rather due to steric hindrance, barring the substrate access to the active site. In several systems, however, the interaction with the antibody induces conformational changes on the enzyme that can either inhibit or enhance its catalytic activity. The extent of enzyme inhibition or enhancement is, therefore, a reflection of the nature and distribution of the various antigenic determinants on the enzyme molecule. Currently, the mode of action of many enzymes has been elucidated at the molecular level. We here review the molecular mechanisms and recent trends by which antibodies inhibit the catalytic activity of enzymes and provide examples of how specific antibodies can be useful for the neutralization of biologically active molecules.

A Supramolecular Antidote to Macromolecular Toxins Prepared through Coassembly of Macrocyclic Amphiphiles

Poisoning is a leading cause of admission to medical emergency departments and intensive care units. Supramolecular detoxification, which involves injecting supramolecular receptors that bind with toxins to suppress their biological activity, is an emerging strategy for poisoning treatment; it has few requirements and a broad application scope. However, it is still a formidable challenge to design supramolecular therapeutic materials as an antidote to macromolecular toxins, because the large size, flexible conformation, and presence of multiple and diverse binding sites of biomacromolecules hinder their recognition. Herein, a supramolecular antidote to macromolecular toxins is developed through the coassembly of macrocyclic amphiphiles, relying on heteromultivalent recognition between the coassembled components and toxic macromolecules. The coassembly of amphiphilic cyclodextrin and calixarene strongly and selectively captures melittin, a toxin studied herein; this imparts various therapeutic effects such as inhibiting the interactions of melittin with cell membranes, alleviating melittin cytotoxicity and hemolytic toxicity, reducing the mortality rate of melittin-poisoned mice, and mitigating damage to major organs. The use of the proposed antidote overcomes the limitation of supramolecular detoxification applicability to only small-molecular toxins. The antidote can also detoxify other macromolecular toxins as long as selective and strong binding is achieved because of the coassembling tunability.

Substrate Protection in Controlled Enzymatic Transformation of Peptides and Proteins

Proteins are involved in practically every single biological process. The many enzymes involved in their synthesis, cleavage, and posttranslational modification (PTM) carry out highly specific tasks with no usage of protecting groups. Yet, the chemists' strategy of protection/deprotection potentially can be highly useful, for example, when a specific biochemical reaction catalyzed by a broad-specificity enzyme needs to be inhibited, during infection of cells by enveloped viruses, in the invasion and spread of cancer cells, and upon mechanistic investigation of signal-transduction pathways. Doing so requires highly specific binding of peptide substrates in aqueous solution with biologically competitive affinities. Recent development of peptide-imprinted cross-linked micelles allows such protection and affords previously impossible ways of manipulating peptides and proteins in enzymatic transformations.

Indicator displacement assays: from concept to recent developments

Overcoming the synthetic burden related to covalently connected receptors with appropriate indicators for sensing various analytes via an indicator spacer receptor (ISR) approach, the indicator displacement assay (IDA) seems to be a very sophisticated and versatile supramolecular sensing paradigm, and it has taken the phenomenon of molecular recognition to the next level in the realm of host-guest chemistry. Due to the unavailability of a comprehensive report on what has been done in the last decade in relation to IDAs, we decided to set down this account illustrating diverse indicator displacement assays (IDAs) in detail from the concept stage to recent developments relating to the detection of cationic, anionic, and neutral analytes. The authors conclude this account with future perspectives and highlight the limitations and challenges relating to IDAs which need to be overcome in order to realize the full potential of this popular sensing phenomenon. While we were finalizing our account for publication, a tutorial review by the research groups of Anslyn, Sessler, and Sun was published, which focuses mainly on diverse aspects of the chemistry related to IDAs. As can be seen, our review, besides discussing various basic IDA concepts, has a vast collection of information published in the past decade and hence, hopefully, will be very informative for the supramolecular community. We believe that this work will offer new insights for the construction of novel sensors operating through the IDA approach.

Modulation of Src Kinase Activity by Selective Substrate Recognition with Pseudopeptidic Cages

The selective recognition of tyrosine residues in peptides is an appealing approach to inhibiting their tyrosine kinase (TK)-mediated phosphorylation. Herein, we describe pseudopeptidic cages that efficiently protect substrates from the action of the Src TK enzyme, precluding the corresponding Tyr phosphorylation. Fluorescence emission titrations show that the most efficient cage inhibitors strongly bind the peptide substrates with a very good correlation between the binding constant and the inhibitory potency. Structural insights and additional control experiments further support the proposed mechanism of selective supramolecular protection of the substrates. Moreover, the approach also works in a completely different kinase-substrate system. These results illustrate the potential of supramolecular complexes for the efficient and selective modulation of TK signaling.

Sequence-selective recognition of cationic amphipathic tripeptides with similar structures in aqueous solutions by cucurbit[7]uril

Sequence-selective recognition of cationic amphipathic peptides by synthetic receptors is significant to biological applications, but it is still a great challenging task. Here we first study the binding characteristics of receptor cucurbit[7]uril (CB[7]) to the smallest aromatic tripeptides X1GG (X1 = tryptophan (W), phenylalanine (F), and tyrosine (Y)) and basic tripeptides X2GG (X2 = arginine (R), lysine (K), and histidine (H)) by molecular dynamics simulations. The study indicates that the sidechains of aromatic X1 residues can be encapsulated into the CB[7] cavity, while the sidechains of basic X2 residues prefer to locate at the CB[7] portal. Based on that, we consider hydrophobic aromatic residues as the N-terminus, the smallest glycine (G) as the 2nd-residue and basic residues as the C-terminus, and design nine tripeptides X1GX2 (X1 = F, Y, W and X2 = H, K, R). We found that there is a great influence of the C-terminal basic residue of X1GX2 on binding with CB[7] due to the introduction of a new binding site between CB[7] and the sidechain of the C-terminal residue. Interestingly, CB[7] can differentiate WGR and WGK with similar structures efficiently because of their eight orders of magnitude difference in the association constant (Ka). Besides, for WGR, YGR, and YGK with a nanomolar binding affinity (Ka > 109 M-1), on reversing the sequence order of the 2nd-residue and 3rd-residue, their Ka reduces by about at least 1000-fold, implying the sequence dependence of CB[7] on recognizing these tripeptides. These results predict the potential applications of CB[7] in recognizing cationic amphipathic peptides.

Toward Light-Controlled Supramolecular Peptide Dimerization

The selective photodeprotection of the NVoc-modified FGG tripeptide yields the transformation of its 1:1 receptor-ligand complex with cucurbit[8]uril into a homoternary FGG₂@CB8 assembly. The resulting light-induced dimerization of the model peptide provides a tool for the implementation of stimuli-responsive supramolecular chemistry in biologically relevant contexts.

Sequence-Selective Protection of Peptides from Proteolysis

Proteolysis of proteins and peptides is involved in the infection of cells by enveloped viruses and also in the invasion and spread of cancer cells. Shutting down broad‐specificity proteases, however, is problematic because normal functions by these proteases will be affected. Herein, nanoparticle receptors were prepared from molecular imprinting for complex biological peptides. Their strong and selective binding enabled them to protect their targeted sequences from proteolysis in aqueous solution at stoichiometric amounts. Generality of the method was demonstrated by the protection of hydrophobic and hydrophilic peptides from different proteases, selective protection of a segment of a long peptide, and selective protection of a targeted peptide in a mixture. Most interestingly, two receptors targeting different parts of a long peptide could work in cooperation to protect the overall sequence, highlighting the versatility of the method.

Selective Recognition of Amino Acids and Peptides by Small Supramolecular Receptors

To this day, the recognition and high affinity binding of biomolecules in water by synthetic receptors remains challenging, while the necessity for systems for their sensing, transport and modulation persists. This problematic is prevalent for the recognition of peptides, which not only have key roles in many biochemical pathways, as well as having pharmacological and biotechnological applications, but also frequently serve as models for the study of proteins. Taking inspiration in nature and on the interactions that occur between several receptors and peptide sequences, many researchers have developed and applied a variety of different synthetic receptors, as is the case of macrocyclic compounds, molecular imprinted polymers, organometallic cages, among others, to bind amino acids, small peptides and proteins. In this critical review, we present and discuss selected examples of synthetic receptors for amino acids and peptides, with a greater focus on supramolecular receptors, which show great promise for the selective recognition of these biomolecules in physiological conditions. We decided to focus preferentially on small synthetic receptors (leaving out of this review high molecular weight polymeric systems) for which more detailed and accurate molecular level information regarding the main structural and thermodynamic features of the receptor biomolecule assemblies is available.

Synthesis and Glycosidase Inhibition Properties of Calix[8]arene-Based Iminosugar Click Clusters

A set of 6- to 24-valent clusters was constructed with terminal deoxynojirimycin (DNJ) inhibitory heads through C6 or C9 linkers by way of Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) reactions between mono- or trivalent azido-armed iminosugars and calix[8]arene scaffolds differing in their valency and their rigidity but not in their size. The power of multivalency to upgrade the inhibition potency of the weak DNJ inhibitor (monovalent DNJ K_i being at 322 and 188 µM for C6 or C9 linkers, respectively) was evaluated on the model glycosidase Jack Bean α-mannosidase (JBα-man). Although for the clusters with the shorter C6 linker the rigidity of the scaffold was essential, these parameters had no influence for clusters with C9 chains: all of them showed rather good relative affinity enhancements per inhibitory epitopes between 70 and 160 highlighting the sound combination of the calix[8]arene core and the long alkyl arms. Preliminary docking studies were performed to get insights into the preferred binding modes.

Allosteric Signal Amplification Sensing Using a Bisthiourea-Binaphthyl-Polythiophene Conjugate: A Positive Homotropic Allosterim Case

The development of signal amplification systems has attracted much attention and presents a highly challenging objective. Herein, we reveal the amplification processes using a newly synthesized bisthiourea-binaphthyl-polythiophene conjugate. The spectral data, behavior of supramolecular complexation, and thermodynamic parameters with calculation support comprehensively elucidated the factors that control the outcomes of the signal amplification. The present work provides a new perspective on functional chemosensors and an attractive alternative to conventional amplification systems.

Harnessing the PD-L1 interface peptide for positron emission tomography imaging of the PD-1 immune checkpoint

Interface peptides that mediate protein–protein interactions (PPI) are a class of important lead compounds for designing PPI inhibitors. However, their potential as precursors for radiotracers has never been exploited. Here we report that the interface peptides from programmed death-ligand 1 (PD-L1) can be used in positron emission tomography (PET) imaging of programmed cell death 1 (PD-1) with high accuracy and sensitivity. Moreover, the performance differentiation between murine PD-L1 derived interface peptide (mPep-1) and human PD-L1 derived interface peptide (hPep-1) as PET tracers for PD-1 unveiled an unprecedented role of a non-critical residue in target binding, highlighting the significance of PET imaging as a companion diagnostic in drug development. Collectively, this study not only provided a first-of-its-kind peptide-based PET tracer for PD-1 but also conveyed a unique paradigm for developing imaging agents for highly challenging protein targets, which could be used to identify other protein biomarkers involved in the PPI networks.

Leveraging interface peptides in PD-L1 for PET imaging of PD-1, providing a new paradigm for radiotracer development.

Design, synthesis, structural analysis and biochemical studies of stapled AIF(370-394) analogues as ligand of CypA

BACKGROUND

The neuronal apoptotic process requires the nuclear translocation of Apoptosis Inducing Factor (AIF) in complex with Cyclophilin A (CypA) with consequent chromatin condensation and DNA degradation events. Targeting CypA by delivering an AIF-blocking peptide (AIF(370-394)) provides a significant neuroprotection, demonstrating the biological relevance of the AIF/CypA complex. To date pharmaceutical compounds targeting this complex are missing.

METHODS

We designed and synthesized a set of mono and bicyclic AIF(370-394) analogs containing both disulfide and 1,2,3-triazole bridges, in the attempt to both stabilize the peptide conformation and improve its binding affinity to CypA. Peptide structures in solution and in complex with CypA have been studied by circular dichroism (CD), Nuclear Magnetic Resonance (NMR) and molecular modeling. The ability of stapled peptides to interact with CypA was evaluated by using Epic Corning label free technique and Isothermal Titration Calorimetry experiments.

RESULTS

We identified a stapled peptide analogue of AIF(370-394) with a ten-fold improved affinity for CypA. Molecular modeling studies reveal that the new peptide acquires β-turn/β-fold structures and shares with the parent molecule the same binding region on CypA.

CONCLUSIONS

Data obtained provide invaluable assistance in designing new ligand of CypA for therapeutic approaches in neurodegenerative diseases.

GENERAL SIGNIFICANCE

Due to the crucial role of AIF/CypA complex formation in neurodegeneration, identification of selective inhibitors is of high importance for targeted therapies. We describe new bicyclic peptide inhibitors with improved affinity for CypA, investigating the kinetic, thermodynamic and structural effects of conformational constraints on the protein-ligand interaction, and their utility for drug design.

Cationic Pillar[6]arene Induces Cell Apoptosis by Inhibiting Protein Tyrosine Phosphorylation Via Host-Guest Recognition

We reported for the first time that cationic pillar[6]arene (cPA6) could tightly bind to peptide polymer (MW~20–50 kDa), an artificial substrate for tyrosine (Tyr) phosphorylation, and efficiently inhibit Tyr protein phosphorylation through host–guest recognition. We synthesized a nanocomposite of black phosphorus nanosheets loaded with cPA6 (BPNS@cPA6) to explore the effect of cPA6 on cells. BPNS@cPA6 was able to enter HepG2 cells, induced apoptosis, and inhibited cell proliferation by reducing the level of Tyr phosphorylation. Furthermore, BPNS@cPA6 showed a stronger ability of inhibiting cell proliferation in tumor cells than in normal cells. Our results revealed the supramolecular modulation of enzymatic Tyr phosphorylation by the host–guest recognition of cPA6.

A graphene oxide-aided triple helical aggregation-induced emission biosensor for highly specific detection of charged collagen peptides

Aggregation-induced emission (AIE) probes have emerged as promising "turn-on" sensing tools for DNA and proteins, and the AIE biosensors conjugated with graphene oxide (GO) have shown improved selectivity. Collagen is an essential structural protein in the human body, and its degraded products are involved in a plethora of severe diseases. Collagen has a high content of charged amino acids, while EOG represents one of the most abundant charged triplets in Type I collagen. We, herein, for the first time report the construction of a GO-aided AIE biosensor for the detection of charged collagen peptides. We have shown that an AIE fluorophore TPE conjugated with a triple helical peptide TPE-PRG possesses strong fluorescence due to the restriction of intramolecular rotation of TPE in the trimer state. The adsorption of the probe TPE-PRG by GO leads to efficient fluorescence quenching, while the addition of target collagen peptide EOG releases the probe peptide from the GO surface and recovers its fluorescence. We have demonstrated that the TPE-PRG/GO complex provides a highly specific "turn-on" sensing platform for the target collagen peptide with a typical charged amino acid-rich sequence. The assay has shown little interference from other biomolecules, and it can also effectively distinguish the target charged collagen peptide from its single amino acid mutant type. The development of robust analytical assays for charged collagen peptides could pronouncedly extend our capability to investigate the pathology of collagen diseases, showing great potential for their molecular diagnosis.

Functional Disruption of the Cancer-Relevant Interaction between Survivin and Histone H3 with a Guanidiniocarbonyl Pyrrole Ligand

The protein Survivin is highly upregulated in most cancers and considered to be a key player in carcinogenesis. We explored a supramolecular approach to address Survivin as a drug target by inhibiting the protein-protein interaction of Survivin and its functionally relevant binding partner Histone H3. Ligand L1 is based on the guanidiniocarbonyl pyrrole cation and serves as a highly specific anion binder in order to target the interaction between Survivin and Histone H3. NMR titration confirmed binding of L1 to Survivin's Histone H3 binding site. The inhibition of the Survivin-Histone H3 interaction and consequently a reduction of cancer cell proliferation were demonstrated by microscopic and cellular assays.

Supramolecular assemblies controlled by cucurbit[n]uril size (n = 6, 7, 8 and 10)

The differing cavity size of the Q[n] determines the binding interactions between the benzyl substituted 4-pyrrolidinopyridinium salt and each Q[n]. Single crystal X-ray diffraction of the guest as well as two host–guest complexes is reported.

Design and Applications of Small Molecular Probes for Calcium Detection

The physiological significance of calcium ions such as the role in cellular signalling, cell growth, etc. have driven the development of methods to detect and monitor the level of Ca²⁺ ions, both in vivo and in vitro. Although various approaches for the detection of calcium ions have been reported, methods based on small molecular fluorescent probes have unique advantages including small probe size, easy monitoring of detection processes and applicability in biological systems. In this review article, we will discuss the progress in the development of Ca²⁺ -binding fluorescent probes by taking into account the types of chelating groups that have been employed for Ca²⁺ binding.

General Method for Peptide Recognition in Water through Bioinspired Complementarity

A general method for peptide recognition has been elusive despite decades of research. Strong binding and selectivity among closely related peptides are necessary for biological applications but have been difficult to achieve with synthetic receptors. With inspiration from highly specific protein-protein and protein-ligand interactions, protein-sized, water-soluble imprinted nanoparticles were prepared via templated polymerization of peptides within cross-linked micelles. Combination of hydrophobic and polar interactions afforded micromolar to submicromolar binding affinities for selected tripeptides. A "golden pair" of functional monomers was identified to enhance both the affinity and selectivity of binding, and enabled differentiation of subtly different sequences including single-point variation of lysine by arginine and insertion of a single glycine at the N- or C-terminus. Biological peptides (β-amyloid peptides) afforded even stronger binding (tens of nanomolar) due to a larger number of complementary interactions between the host and the guest, opening doors to a wide range of biological applications.

Diverse Properties of Guanidiniocarbonyl Pyrrole-Based Molecules: Artificial Analogues of Arginine

The guanidinium moiety, which is present in active sites of many enzymes, plays an important role in the binding of anionic substrates. In addition, it was also found to be an excellent binding motif for supramolecular chemistry. Inspired by Nature, scientists have developed artificial receptors containing guanidinium scaffolds that bind to a variety of oxoanions through hydrogen bonding and charge pairing interactions. However, the majority of binding studies is restricted to organic solvents. Polyguanidinium based molecules can form efficient complexes in aqueous solvents due to strong electrostatic interactions. However, they only have moderate association constants, which are significantly decreased in the presence of competing anions and salts. Hence, to improve the binding affinity of the guanidinium moiety, our group developed the cationic guanidiniocarbonyl pyrrole (GCP) moiety. This rigid planar analogue binds efficiently to oxoanions, like carboxylates even in aqueous solvents. The lower p K_a value (7-8) of GCP compared to guanidinium derivatives (p K_a 13) favors the formation of strong, hydrogen bonded ion pairs. In addition, carboxylate binding is further enhanced by additional amide hydrogen bond donors located at the five position of the pyrrole core. Moreover, the design has allowed for introducing secondary interactions between receptor side chains and guest molecules, which allows for optimizing binding specificity and selectivity. The spectroscopic data confirmed stabilization of guanidiniocarbonyl pyrrole/oxoanion complexes through a combination of ion pairing and multiple hydrogen bonding interactions. The key role of the ionic interaction in a polar solvent, is demonstrated by a zwitterion derivative of the guanidiniocarbonyl pyrrole, which self-assembles in both dimethyl sulfoxide and pure water with association constants of K > 10¹⁰ M^-1 and K = 170 M^-1, respectively. In this Account, we discuss strategies for making GCP functionalized compounds, in order to boost their ability to bind oxoanions. Then we explore how these building blocks have been incorporated into different synthetic molecules and peptide sequences, highlighting examples that demonstrated the versatility of this binding scaffold. For instance, the high oxoanion binding property of GCP-based compounds was exploited to generate a detectable signal for sensing applications, thus improving selectivity and sensitivity in aqueous solution. Moreover, peptides and molecules containing GCP have shown excellent gene transfections properties. Furthermore, the self-assembly and zwitterionic behavior of zwitterionic GCP analogues was used to develop variety of supramolecular architectures such as stable supramolecular β-helix structure, linear supramolecular oligomers, one-dimensional rods or two-dimension sheets, fibers, vesicles, soft nanospheres, as well as stimuli responsive supramolecular gels.

Molecular Dynamics Investigations Suggest a Non-specific Recognition Strategy of 14-3-3σ Protein by Tweezer: Implication for the Inhibition Mechanism

The supramolecular complex formed between protein and designed molecule has become one of the most efficient ways to modify protein functions. As one of the more well-studied model systems, 14-3-3 family proteins play an important role in regulating intracellular signaling pathways via protein-protein interactions. In this work, we selected 14-3-3σ as the target protein. Molecular dynamics simulations and binding free energy calculations were applied to identify the possible binding sites and understand its recognition ability of the supramolecular inhibitor, the tweezer molecule (CLR01). On the basis of our simulation, major interactions between lysine residues and CLR01 come from the van der Waals interactions between the long alkyl chain of lysine and the cavity formed by the norbornadiene and benzene rings of the inhibitor. Apart from K214, which was found to be crystallized with this inhibitor, other lysine sites have also shown their abilities to form inclusion complexes with the inhibitor. Such non-specific recognition features of CLR01 against 14-3-3σ can be used in the modification of protein functions via supramolecular chemistry.

Correlations between secondary structure- and protein-protein interface-mimicry: the interface mimicry hypothesis

An active segment of the research community designing small molecules ("minimalist mimics" of peptide fragments) to interfere with protein-protein interactions have based their studies on an implicit hypothesis. Here we refer to this as the Secondary Structure Hypothesis, that might be defined as, "If a small molecule can orient amino acid side-chains in directions that resemble side-chains of the parent secondary structure at the interface, then that small molecule is a candidate to perturb the protein-protein interaction". Rigorous tests of this hypothesis require co-crystallization of minimalist mimics with protein receptors, and comparison of the bound conformations with the interface secondary structures they were designed to resemble. Unfortunately, to the best of our knowledge, there is no such analysis in the literature, and it is unlikely that enough examples will emerge in the near future to test the hypothesis. Research described here was designed to challenge this hypothesis from a different perspective. In a previous study, preferred conformations of a series of novel minimalist mimics were simulated then systematically overlaid on >240 000 crystallographically characterized protein-protein interfaces. Select data from that overlay procedure revealed chemotypes that overlay side chains on various PPI interfaces with a relatively high frequency of occurrence. The first aim of this work was to determine if good secondary structure mimics overlay frequently on PPI interfaces. The second aim of this work was to determine if overlays of preferred conformers at interface regions involve secondary structures. Thus situations where these conformations overlaid extremely well on PPI interfaces were analyzed to determine if secondary structures featured the PPI regions where these molecules overlaid in the previous study. Combining conclusions from these two studies enabled us to formulate a hypothesis that is complementary to the Secondary Structure Hypothesis, but, unlike this, is supported by abundant data. We call this the Interface Mimicry Hypothesis.

In Silico Approaches for TRP Channel Modulation

The implication of several TRP ion channels (e.g., TRPV1) in diverse physiological and pathological processes has signaled them as pivotal drug targets. Consequently, the identification of selective and potent ligands for these channels is of great interest in pharmacology and biomedicine. However, a major challenge in the design of modulators is ensuring the specificity for their intended targets. In recent years, the emergence of high-resolution structures of ion channels facilitates the computer-assisted drug design at molecular levels. Here we describe some computational methods and general protocols to discover channel modulators, including homology modelling, docking and virtual screening, and structure-based peptide design.

Bisphosphonate ligand mediated ultrasensitive capacitive protein sensor: complementary match of supramolecular and dynamic chemistry

A powerful polymeric protein sensor was constructed by microcontact imprinting taking advantage of the specific interaction between a bisphosphonate binding monomer and lysine/arginine residues on the surface of trypsin.

Cyclopenta[d]isoxazoline β-Turn Mimics: Synthetic Approach, Turn Driving Force, Scope, and Limitations

Model β-turn inducers were prepared from constrained oxazanorbornene aminols. Taking advantage of the starting materials geometry, new diastereoisomeric compounds were synthesized, introducing different amino acidic residues. The products were spectroscopically characterized (VT and NMR titration). Temperature coefficients in dimethyl sulfoxide denote the existence of an intramolecular hydrogen bond. Chiroptical properties disclosed a β-turn arrangement of the synthesized compounds. The fused isoxazoline ring constraints the cyclopentane moiety, stabilizing a boatlike conformation that ensures the turn efficiency but limiting the accessibility to hindered amino acids.

Molecular Recognition of Methionine-Terminated Peptides by Cucurbit[8]uril

This Article describes the molecular recognition of peptides containing an N-terminal methionine (Met) by the synthetic receptor cucurbit[8]uril (Q8) in aqueous solution and with submicromolar affinity. Prior work established that Q8 binds with high affinity to peptides containing aromatic amino acids, either by simultaneous binding of two aromatic residues, one from each of two different peptides, or by simultaneous binding of an aromatic residue and its immediate neighbor on the same peptide. The additional binding interface of two neighboring residues suggested the possibility of targeting nonaromatic peptides, which have thus far bound only weakly to synthetic receptors. A peptide library designed to test this hypothesis was synthesized and screened qualitatively for Q8 binding using a fluorescent indicator displacement assay. The large fluorescence response observed for several Met-terminated peptides suggested strong binding, which was confirmed quantitatively by the determination of submicromolar equilibrium dissociation constant values for Q8 binding to MLA, MYA, and MFA using isothermal titration calorimetry (ITC). This discovery of high affinity binding to Met-terminated peptides and, more generally, to nonaromatic peptides prompted a detailed investigation of the determinants of binding in this system using ITC, electrospray ionization mass spectrometry, and 1H NMR spectroscopy for 25 purified peptides. The studies establish the sequence determinants required for high-affinity binding of Met-terminated peptides and demonstrate that cucurbit[ n]uril-mediated peptide recognition does not require an aromatic residue for high affinity. These results, combined with the known ability of cucurbit[ n]urils to target N-termini and disordered loops in folded proteins, suggest that Q8 could be used to target unmodified, Met-terminated proteins.

Sequence-Selective Recognition of Peptides in Aqueous Solution: A Supramolecular Approach through Micellar Imprinting

Sequence-selective recognition of peptides in water has been one of the most important and yet unsolved problems in bioorganic and supramolecular chemistry. The motivation comes from not only the importance of these molecules in biology but also the fundamental challenges involved in the research. Molecular imprinting in doubly cross-linked surfactant micelles offers a unique solution to this problem by creating a "supramolecular code" on the micelle surface that matches the structural features of the peptide chain. Hydrophobic "dimples" are constructed on imprinted micelles that match the hydrophobic side chains of the peptide precisely in size and shape. Polar binding functionalities are installed at correct positions to interact with specific acidic and basic groups on the peptide. Secondary hydrogen-bonding and electrostatic interactions are introduced through imprinting to enhance the binding affinity and specificity further. Binding affinities of tens of nanomolar are readily achieved in water for biological peptides with over a dozen residues. Excellent binding selectivity is observed even for subtly different peptides. The synthesis of these protein-sized nanoparticles involves a one-pot reaction complete within 2 days; purification requires nothing but precipitation and solvent washing. These features make the molecularly imprinted nanoparticles (MINPs) highly promising peptide-binding "artificial antibodies" for chemical and biological applications.

Exfoliated Nanosheets of a CuII Coordination Polymer Modulate Enzyme Activity of α-Chymotrypsin

A 2D coordination polymer derived from 5-azidoisophthalic acid (AIA) and Cu(NO₃ )₂ was designed with the aim of modulating the activity of a digestive enzyme α-chymotrypsin (ChT). The coordination polymer namely {[Cu_0.5 (μ-AIA)_0.5 (H₂ O)]⋅2 H₂ O}_α (CP1) was successfully synthesized and fully characterized by single-crystal X-ray diffraction (SXRD). An exfoliated nanosheet (ENS) of CP1 was readily produced by overnight stirring of hand-ground CP1 crystals dispersed in DMSO. ENS(CP1) was demonstrated to be acting as an inhibitor of ChT; as much as ≈97 % inhibition of ChT was achieved with 100 μm of ENS(CP1) using N-succinyl-l-phenylalanine-p-nitroanilide (SPNA) as substrate. Enzyme kinetics data revealed that the inhibition of ChT followed a competitive pathway. An enzyme assay under varying ionic strength and varying concentration of free histidine revealed that the active site His-57 participated in coordination with the Cu^II metal center of ENS(CP1) thereby preventing the substrate (SPNA) from binding with the enzyme resulting in efficient inhibition.