Recognition Of Small Molecules Research Articles

Ultrasensitive and rapid colorimetric detection of paraquat via a high specific VHH nanobody

Rapid and quantitative detection of paraquat is crucial because of its high toxicity. Here, we developed an ultrasensitive time-resolved fluorescence immunochromatographic assay (TRFICA) strip based on our synthesized variable domain of heavy chain antibody (VHH, also called Nanobody) for paraquat detection. Briefly, the specific immunogen selected from six designed antigens was employed to immunize alpaca, and a high-efficiency capacity of 1.6 × 1013 pfu mL−1 phage display nanobody library was established for biopanning against paraquat. The selected nanobody exhibited high sensitivity (limit of detection (LOD) was 0.0090 ng mL−1 and IC50 was 0.0588 ng mL−1 in buffer) and stability to high temperatures and denaturants. The molecular docking results indicated that the π-π, cation-π, and hydrogen bond interactions between paraquat and the pocket-like structures of complementarity-determining regions (CDRs) in VHH played a critical role in the antibody-paraquat recognition, competition, and affinity processes. The constructed TRFICA recognized paraquat through a quantitative analysis using the strip reader, and showed no cross-reactivity with other herbicides, and a semi-quantitative analysis using the naked eye. Notably, the potential practical applications of the TRFICA evaluated by performing a quantitative analysis of paraquat in food samples (vegetables, fruits, and grain products) and biological samples (blood and urine) showed a recovery rate range between 76.7% and 133.3% with inter-assay coefficient variation lower than 18.5%. The nanobody from phage display libraries was effective for small molecule recognition and detection, and it is a vital tool for immunoassay.

Energetics of a protein disorder-order transition in small molecule recognition.

Many proteins recognise other proteins via mechanisms that involve the folding of intrinsically disordered regions upon complex formation. Here we investigate how the selectivity of a drug-like small molecule arises from its modulation of a protein disorder-to-order transition. Binding of the compound AM-7209 has been reported to confer order upon an intrinsically disordered ‘lid’ region of the oncoprotein MDM2. Calorimetric measurements revealed that truncation of the lid region of MDM2 increases the apparent dissociation constant of AM-7209 250-fold. By contrast, lid truncation has little effect on the binding of the ligand Nutlin-3a. Insights into these differential binding energetics were obtained via a complete thermodynamic analysis that featured adaptive absolute alchemical free energy of binding calculations with enhanced-sampling molecular dynamics simulations. The simulations reveal that in apo MDM2 the ordered lid state is energetically disfavoured. AM-7209, but not Nutlin-3a, shows a significant energetic preference for ordered lid conformations, thus shifting the balance towards ordering of the lid in the AM-7209/MDM2 complex. The methodology reported herein should facilitate broader targeting of intrinsically disordered regions in medicinal chemistry.

Three-pole wheel paddle luminescent metal organic frameworks (LMOFs) based on the oxygen substituted triazine tricarboxylic acid ligand: recognition and detection of small drug molecules and aromatic amine molecules.

Luminescent metal organic frameworks (LMOFs) are considered to be a type of promising optical sensing material due to their designable and tunable functions, and stable pore structures. Therefore, the preparation of LMOFs has become a research hotspot in recent years. As we know, triazine carboxylic acid ligands are conducive for constructing LMOF materials due to their large π electron conjugated system. In this work, two crystalline materials [Cd3(TCPT)2]·0.5DMF·4H2O (1) and (H3O)[Zn2(TCPT)(μ2-OH)2]·0.5DMF·3H2O (2) were obtained by the reaction of the triazine carboxylic acid ligand 2,4,6-tris(4-carboxyphenoxy)-1,3,5-triazine (H3TCPT), as an extended carboxylate arm, and d10 transition metal salts. Their structures were determined by single crystal X-ray diffraction and characterized by infrared spectroscopy (IR), ultraviolet visible spectroscopy (UV-vis), fluorescence spectroscopy, powder X-ray diffraction (PXRD) and thermogravimetric analysis (TG). The experimental results showed that complexes 1 and 2 show excellent fluorescent emission behavior. Thus, we explored their fluorescence sensing properties. To our delight, the results showed that they both had the ability to sense small organic drug molecules and aromatic amine molecules containing o-phenylenediamine (OPD), m-phenylenediamine (MPD) and p-phenylenediamine (PPD). In general, the practical applications of a MOF material are usually limited because of the relatively harsh synthesis methods. In this aspect, we studied the synthesis method in detail to obtain the optimal reaction conditions for the large-scale synthesis of 1 and 2. The preparation of the two LMOF materials only required about 3 hours of heating time and they could be prepared on a large scale, which is significant for the practical applications of LMOFs.

Detection of salinomycin and lasalocid in chicken liver by icELISA based on functional bispecific single-chain antibody (scDb) and interpretation of molecular recognition mechanism

Salinomycin (SAL) and lasalocid (LAS) are widely used as ionophore antibiotics for coccidiosis control. However, their common use as feed additives has led to the occurrence of feed cross-contamination, which has toxic effects on non-target animals. There have been few reports on multiple-residue detection for SAL and LAS in recent years. In this study, two single-chain antibody fragments (scFvs) capable of specifically recognizing SAL and LAS were constructed. Using LAS-scFv and SAL-scFv as parent antibodies, a complete bispecific single-chain diabody (scDb) against both LAS and SAL was built using splicing by overlap extension polymerase chain reaction (SOE-PCR). In addition, the key amino acid sites and interaction energy of antibody variable regions for small-molecule recognition were preliminarily studied by homology modeling and molecular docking. Finally, IC50 values of 12.9 and 8.6ng/mL, with a linear range of 6.9-24.0 and 4.7-16.0ng/mL, were obtained for LAS-scFv and SAL-scFv, respectively. An indirect competitive enzyme-linked immunosorbent assay (icELISA) method was established using scDb to obtain an IC50 of 3.5ng/mL for LAS and 4.1ng/mL for SAL, which showed better sensitivity and specificity than those of the parent scFv antibodies. The recoveries of LAS and SAL in chicken liver were 89.2-92.7%(CV<4.7%) and 88.6-90.2% (CV<6.8%)), respectively.

Family of Structurally Related Bioconjugates Yields Antibodies with Differential Selectivity against Ketamine and 6-Hydroxynorketamine.

The dissociative-hypnotic compound ketamine is being used in an increasingly wide range of therapeutic contexts, including anesthesia, adjunctive analgesia, treatment-resistant depression, but it also continues to be a notable substance of abuse. No specific antidotes exist for ketamine intoxication or overdose. Immunopharmacotherapy has demonstrated the ability to offer overdose protection through production of highly specific antibodies that prevent psychoactive drug penetration across the blood-brain barrier, although antiketamine antibodies have not yet been assessed or optimized for use in this approach. Moreover, generation of specific antibodies also provides an opportunity to address the role of 6-hydroxynorketamine metabolites in ketamine's rapid-acting antidepressant effect through selective restriction of metabolite access to the central nervous system. Hapten design is a critical element for tuning immune recognition of small molecules, as it affects the presentation of the target antigen and thus the quality and selectivity of the response. Here, we report the synthesis and optimization of carrier protein and conjugation conditions for an initial hapten, norketamine-N-COOH (NK-N-COOH), to optimize vaccination conditions and assess the functional consequences of such vaccination on ketamine-induced behavioral alterations occurring at dissociative-like (50 mg/kg) doses. Iterating from this initial approach, two additional haptens, ketamine-N-COOH (KET-N-COOH) and 6-hydroxynorketamine-N-COOH (HNK-N-COOH), were synthesized to target either ketamine or 6-hydroxynorketamine with greater selectivity. The ability of these haptens to generate antiketamine, antinorketamine, and anti-6-hydroxynorketamine immune responses in mice was then assessed using enzyme-linked immunosorbent assay (ELISA) and competitive surface plasmon resonance (SPR) methods. All three haptens provoked immune responses in vivo, although the KET-N-COOH and 6-HNK-N-COOH haptens yielded antibodies with 5- to 10-fold improvements in affinity for ketamine and/or 6-hydroxynorketamine, as compared to NK-N-COOH. Regarding selectivity, vaccines bearing a KET-N-COOH hapten yielded an antibody response with approximately equivalent Kd values against ketamine (86.4 ± 3.2 nM) and 6-hydroxynorketamine (74.1 ± 7.8 nM) and a 90-fold weaker Kd against norketamine. Contrastingly, 6-HNK-N-COOH generated the highest affinity and most selective antibody profile, with a 38.3 ± 4.7 nM IC50 against 6-hydroxynorketamine; Kd values for ketamine and norketamine were 33- to 105-fold weaker, at 1290 ± 281.5 and 3971 ± 2175 nM, respectively. Overall, these findings support the use of rational hapten design to generate antibodies capable of distinguishing between structurally related, yet mechanistically distinct, compounds arising from the same precursor molecule. As applied to the production of the first-reported anti-6-hydroxynorketamine antibodies to date, this approach demonstrates a promising path forward for identifying the individual and combinatorial roles of ketamine and its metabolites in supporting rewarding effects and/or rapid-acting antidepressant activity.

Ab initio multi-level layered elongation method and its application to local interaction analysis between DNA bulge and ligand molecules.

A multi-level layered elongation method was developed for efficiently analyzing the electronic states of local structures in large bio/nano-systems at the full ab initio level of theory. The original elongation method developed during the last three decades in our group has focused on the system in one direction from one terminal to the other terminal to sequentially construct the electronic states of a polymer, called a theoretical synthesis of polymers. In this study, an important region termed the central (C) part is targeted in a large polymer and the remainder are terminal (T) parts. The electronic structures along with polymer elongation are calculated repeatedly from both end T parts to the C central part at the same time. The important C part is treated with large basis sets (high level) and the other regions are treated with small basis sets (low level) in the ab initio theoretical framework. The electronic structures besides the C part can be reused for other systems with different structures at the C part, which renders the method computationally efficient. This multi-level layered elongation method was applied to the investigation on DNA single bulge recognition of small molecules (ligands). The reliability and validity of our approach were examined in comparison with the results obtained by direct calculations using a conventional quantum chemical method for the entire system. Furthermore, stabilization energies by the formation of the complex of bulge DNA and a ligand were estimated with basis set superposition error corrections incorporated into the elongation method.

Covalently bridged pillararene-based oligomers: from construction to applications.

Covalently bridged pillararene-based oligomers (CBPOs) are formed by covalent bonding of pillararene monomers, and they play a critical role in expanding the multi-disciplinary application of pillararenes due to their excellent molecular complexing ability, specially designed geometry and multifunctional linking groups. This article provides a comprehensive review of the synthesis and applications of CBPOs. The design and synthetic strategies of a series of CBPOs (dimers, trimers, tetramers and others) are first introduced. Many CBPOs with multi-cavities and unique geometry are very attractive and efficient building blocks for constructing novel smart supramolecular polymers (SPs) with different topological structures through host-guest interactions. We describe the methods of constructing various SPs based on CBPOs in detail. Furthermore, the extensive applications of CBPOs and CBPO-based SPs in recognition and detection of ions and organic small molecules, selective adsorption and separation, artificial light-harvesting systems, catalysis, drug delivery systems, and others are systematically introduced. Finally, the future challenges and perspectives for CBPOs are also highlighted.

Determination of the binding of natural products to the human c-myb oncogene promoter G-quadruplex DNA by capillary electrophoresis and electrospray ionization mass spectrometry

The relationship between a drug and its target directly affects its pharmacology and efficacy. Drug-target binding ability and binding stoichiometry are essential characterization data in pharmaceutical research. The c-myb proto-oncogene encodes a crucial transcription factor that is involved in proliferation, differentiation, and maturation during hematopoiesis. Recent studies have found that the human oncogene c-myb is overexpressed in cancer tissues such as colorectal cancer. C-myb has become a potential therapeutic target for colorectal cancer, leukemia, and other cancers. A guanine (G)-rich DNA sequence located in the promoter region of c-myb can be spontaneously folded to form an intra-molecular G-quadruplex (G4) with cationic induction. The specific recognition of small molecules can stabilize this G4 folding, thus regulating the transcription and expression of c-myb. In this study, pressure assisted capillary electrophoresis frontier analysis (PACE-FA) combined with electrospray ionization mass spectrometry (ESI-MS) was used to investigate the interactions between the human c-myb promoter G4 and natural product molecules. In PACE-FA, an external pressure (no more than 13.8 kPa) in the same direction of the migration of the analyte was used in capillary electrophoresis frontier analysis (CE-FA), which greatly sped up the analysis while maintaining the accuracy of the results. Meanwhile, the combination of PACE-FA and ESI-MS could rapidly determine the affinity and stoichiometric relationship between binding molecules and targets. First, the intramolecular parallel-stranded G4 formation of the c-myb promoter sequence in the presence of cations (K+, NH4+) was investigated by circular dichroism (CD) and ESI-MS. Then, ESI-MS was used to rapidly screen the natural products for candidate molecules that bound the target G4 DNA. The binding interactions were measured by mixing the c-myb DNA with each natural product separately in a 1:4 molar ratio, and then directly infusing these mixtures into the ESI-MS system. From the ESI-MS spectra, IRa values calculated from the relative intensities of DNA and its complex ions were used to probe the binding affinities of the natural products. This parameter denotes the relative binding affinity for a small molecule with the G4 DNA. Three natural products were identified through the screen, and their binding affinities to G4 DNA were ranked as follows:pseudolaric acid B > scopolamine butylbromide > nuciferine. Considering that both specific and non-specific binding existed in the solution phase, a free solution method using PACE-FA was developed to further test the binding ability of these products to the c-myb promoter G4 DNA. In the PACE-FA experiments, the pre-equilibrated mixture of the c-myb G4 DNA and the selected ligand was injected into the capillary prior to separation. Upon applying voltage and an external pressure (6.9 kPa) to the capillary, different species of analytes in the sample migrated at their own rates due to their different sizes and charges. The results showed that scopolamine butylbromide could bind specifically to target G4 DNA with 1:1 stoichiometry and a binding constant of 1.18×105 L/mol. Nuciferine's binding to G4 DNA showed a linear increasing trend due to nonspecific binding; thus nuciferine is a nonspecific binder. Although pseudolaric acid B showed high affinity for the c-myb G4 DNA and 1:1 and 1:2 G4-bound complex ions were observed in ESI-MS measurements, the PACE-FA results indicated that pseudolaric acid B did not bind to target G4 DNA in free solution. Therefore, scopolamine butylbromide could be the best candidate to regulate the transcription of the c-myb oncogene, and is expected to be a precursor for anticancer drugs. In this work, PACE-FA has allowed for significant improvements to the conventional CE-FA technique. This combination of PACE-FA and ESI-MS not only reduced the time needed for binding analysis, but also improved the accuracy and specificity of the affinity analysis compared to conventional binding approaches. Furthermore, this combination could be used to screen other targeted drug candidates and to evaluate their interaction mechanisms.

Hierarchically Molecular Imprinted Porous Particles for Biomimetic Kidney Cleaning.

Blood purification by adsorption of excessive biomolecules is vital for maintaining human health. Here, inspired by kidney self-purification, which removes a number of biomolecules with different sizes simultaneously, hierarchical molecular-imprinted inverse opal particles integrated with a herringbone microfluidic chip for efficient biomolecules cleaning are presented. The particle possesses combinative porous structure with both surface and interior imprints for the specific recognition of small molecules and biomacromolecules. Additionally, the presence of the herringbone mixer largely improve the adsorption efficiency due to enhanced mixing. Moreover, the inverse opal framework of the particles give rise to optical sensing ability for self-reporting of the adsorption states. These features, together with its reusability, biosafety, and biocompatibility, make the platform highly promising for clinical blood purification and artificial kidney construction.

Supporting SARS-CoV-2 Papain-Like Protease Drug Discovery: In silico Methods and Benchmarking.

The coronavirus disease 19 (COVID-19) is a rapidly growing pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Its papain-like protease (SARS-CoV-2 PLpro) is a crucial target to halt virus replication. SARS-CoV PLpro and SARS-CoV-2 PLpro share an 82.9% sequence identity and a 100% sequence identity for the binding site reported to accommodate small molecules in SARS-CoV. The flexible key binding site residues Tyr269 and Gln270 for small-molecule recognition in SARS-CoV PLpro exist also in SARS-CoV-2 PLpro. This inspired us to use the reported small-molecule binders to SARS-CoV PLpro to generate a high-quality DEKOIS 2.0 benchmark set. Accordingly, we used them in a cross-benchmarking study against SARS-CoV-2 PLpro. As there is no SARS-CoV-2 PLpro structure complexed with a small-molecule ligand publicly available at the time of manuscript submission, we built a homology model based on the ligand-bound SARS-CoV structure for benchmarking and docking purposes. Three publicly available docking tools FRED, AutoDock Vina, and PLANTS were benchmarked. All showed better-than-random performances, with FRED performing best against the built model. Detailed performance analysis via pROC-Chemotype plots showed a strong enrichment of the most potent bioactives in the early docking ranks. Cross-benchmarking against the X-ray structure complexed with a peptide-like inhibitor confirmed that FRED is the best-performing tool. Furthermore, we performed cross-benchmarking against the newly introduced X-ray structure complexed with a small-molecule ligand. Interestingly, its benchmarking profile and chemotype enrichment were comparable to the built model. Accordingly, we used FRED in a prospective virtual screen of the DrugBank1 database. In conclusion, this study provides an example of how to harness a custom-made DEKOIS 2.0 benchmark set as an approach to enhance the virtual screening success rate against a vital target of the rapidly emerging pandemic.

Ninhydrin Revisited: Quantitative Chirality Recognition of Amines and Amino Alcohols Based on Nondestructive Dynamic Covalent Chemistry.

A novel approach to chiral recognition of small molecules using the classical ninhydrin agent is introduced. Well-defined dynamic covalent chemistry with amines and amino alcohols was developed and applied to quantitative ee sensing with good accuracy using a straightforward mixing protocol and subsequent circular dichroism measurements. This chiroptical assay is fast, broadly useful, practical and repurposes an inexpensive reagent known for more than 100 years in a new application.

Abstract 6361: Identification of mitochondrial RNA polymerase inhibitors via deep convolutional neural networks: A therapeutic strategy for cancer metabolism

Abstract Dysregulated metabolism is a hallmark of cancer and a substantial subset of many cancers rely on oxidative phosphorylation (OXPHOS) for growth and viability, including AML, breast cancer, lung cancer, glioblastoma, ovarian and pancreatic cancer. The electron transport chain (ETC) in mitochondria contains both nuclear DNA- and mitochondrial DNA-encoded subunits. Mitochondrial DNA-encoded subunits are essential for ETC function and are transcribed by the mitochondrial RNA polymerase POLRMT. We have previously validated POLRMT as an anticancer target in acute myeloid leukemia models. The challenge of inhibiting POLRMT with small molecules will arise from both a) selectivity to off targets and b) transport of the drug to the mitochondria. There exist several small nucleoside / nucleotide analogues that are known to inhibit RNA polymerase. However, this target space is rife with the opportunity for off-target activities and toxicity. Therefore, we targeted a novel pocket with the aim of finding novel chemical matter. Using AtomNet, an artificial intelligence platform that utilizes deep convolutional neural networks to predict small molecule recognition, a virtual library of 8 million compounds was screened against POLRMT. The top 72 hit compounds were tested in OCI-AML2 human acute myeloid leukemia cells for a potential decrease of mitochondrial RNA levels (MT-ND1) using reverse transcriptase polymerase chain reaction (RT-PCR). OCI-AML2 cells were treated with compounds at 0.1, 1 or 10 micromolar for 72 hours, 3 days or 6 days or with the positive control POLRMT ribonucleoside analogue inhibitor, 4'-azidocytidine. Gene expression was normalized to 18S. Twelve compounds demonstrated a time-dependent decrease in mitochondrial gene expression. In summary, these data indicate that functional inhibitors of human POLRMT can be identified rapidly via deep convolutional neural networks and machine learning techniques. Financial relationships: RL received an Artificial Intelligence Molecular Screening Award from Atomwise, and funding from the Centre for Collaborative Drug Research, Toronto, Canada. JW is an employee of Atomwise. Citation Format: Noor-Ul-Ain Khalid, Jeffrey M. Warrington, Rebecca Rachelle Laposa. Identification of mitochondrial RNA polymerase inhibitors via deep convolutional neural networks: A therapeutic strategy for cancer metabolism [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6361.

Molecular Features for Probing Small Amphiphilic Molecules with Self-Assembled Monolayer-Protected Nanoparticles.

The sensing of small molecules poses the challenge of developing devices able to discriminate between compounds that may be structurally very similar. Here, attention has been paid to the use of self-assembled monolayer (SAM)-protected gold nanoparticles since they enable a modular approach to tune single-molecule affinity and selectivity simply by changing functional moieties (i.e., covering ligands), along with multivalent molecular recognition. To date, the discovery of monolayers suitable for a specific molecular target has relied on trial-and-error approaches, with ligand chemistry being the main criterion used to modulate selectivity and sensitivity. By using molecular dynamics, we showcase that either individual molecular characteristics and/or collective features such as ligand flexibility, monolayer organization, ligand local ordering, and interfacial solvent properties can also be exploited conveniently. The knowledge of the molecular mechanisms that drive the recognition of small molecules on SAM-covered nanoparticles will critically expand our ability to manipulate and control such supramolecular systems.

High resolution crystal structure of a KRAS promoter G-quadruplex reveals a dimer with extensive poly-A π-stacking interactions for small-molecule recognition.

Aberrant KRAS signaling is a driver of many cancers and yet remains an elusive target for drug therapy. The nuclease hypersensitive element of the KRAS promoter has been reported to form secondary DNA structures called G-quadruplexes (G4s) which may play important roles in regulating KRAS expression, and has spurred interest in structural elucidation studies of the KRAS G-quadruplexes. Here, we report the first high-resolution crystal structure (1.6 Å) of a KRAS G-quadruplex as a 5′-head-to-head dimer with extensive poly-A π-stacking interactions observed across the dimer. Molecular dynamics simulations confirmed that the poly-A π-stacking interactions are also maintained in the G4 monomers. Docking and molecular dynamics simulations with two G4 ligands that display high stabilization of the KRAS G4 indicated the poly-A loop was a binding site for these ligands in addition to the 5′-G-tetrad. Given sequence and structural variability in the loop regions provide the opportunity for small-molecule targeting of specific G4s, we envisage this high-resolution crystal structure for the KRAS G-quadruplex will aid in the rational design of ligands to selectively target KRAS.

InVivo Bioengineering of Fluorescent Conductive Protein-Dye Microfibers.

SummaryEngineering protein-based biomaterials is extremely challenging in bioelectronics, medicine, and materials science, as mechanical, electrical, and optical properties need to be merged to biocompatibility and resistance to biodegradation. An effective strategy is the engineering of physiological processes in situ, by addition of new properties to endogenous components. Here we show that a green fluorescent semiconducting thiophene dye, DTTO, promotes, in vivo, the biogenesis of fluorescent conductive protein microfibers via metabolic pathways. By challenging the simple freshwater polyp Hydra vulgaris with DTTO, we demonstrate the stable incorporation of the dye into supramolecular protein-dye co-assembled microfibers without signs of toxicity. An integrated multilevel analysis including morphological, optical, spectroscopical, and electrical characterization shows electrical conductivity of biofibers, opening the door to new opportunities for augmenting electronic functionalities within living tissue, which may be exploited for the regulation of cell and animal physiology, or in pathological contexts to enhance bioelectrical signaling.

Applying support-vector machine learning algorithms toward predicting host-guest interactions with cucurbit[7]uril.

Machine learning is a valuable tool in the development of chemical technologies but its applications into supramolecular chemistry have been limited. Here, the utility of kernel-based support vector machine learning using density functional theory calculations as training data is evaluated when used to predict equilibrium binding coefficients of small molecules with cucurbit[7]uril (CB[7]). We find that utilising SVMs may confer some predictive ability. This algorithm was then used to predict the binding of drugs TAK-580 and selumetinib. The algorithm did predict strong binding for TAK-580 and poor binding for selumetinib, and these results were experimentally validated. It was discovered that the larger homologue cucurbit[8]uril (CB[8]) is partial to selumetinib, suggesting an opportunity for tunable release by introducing different concentrations of CB[7] or CB[8] into a hydrogel depot. We qualitatively demonstrated that these drugs may have utility in combination against gliomas. Finally, mass transfer simulations show CB[7] can independently tune the release of TAK-580 without affecting selumetinib. This work gives specific evidence that a machine learning approach to recognition of small molecules by macrocycles has merit and reinforces the view that machine learning may prove valuable in the development of drug delivery systems and supramolecular chemistry more broadly.

Small molecule recognition of disease-relevant RNA structures.

Targeting RNAs with small molecules represents a new frontier in drug discovery and development. The rich structural diversity of folded RNAs offers a nearly unlimited reservoir of targets for small molecules to bind, similar to small molecule occupancy of protein binding pockets, thus creating the potential to modulate human biology. Although the bacterial ribosome has historically been the most well exploited RNA target, advances in RNA sequencing technologies and a growing understanding of RNA structure have led to an explosion of interest in the direct targeting of human pathological RNAs. This review highlights recent advances in this area, with a focus on the design of small molecule probes that selectively engage structures within disease-causing RNAs, with micromolar to nanomolar affinity. Additionally, we explore emerging RNA-target strategies, such as bleomycin A5 conjugates and ribonuclease targeting chimeras (RIBOTACs), that allow for the targeted degradation of RNAs with impressive potency and selectivity. The compounds discussed in this review have proven efficacious in human cell lines, patient-derived cells, and pre-clinical animal models, with one compound currently undergoing a Phase II clinical trial and another that recently garnerd FDA-approval, indicating a bright future for targeted small molecule therapeutics that affect RNA function.

Structure-Dependent Guest Recognition with Flexible Ferrocene-Based Aromatic Oligoamide β-Sheet Mimics.

A series of aromatic oligoamides incorporating an inherently flexible ferrocene dicarboxylic acid unit was synthesized. Solid state, solution, and computational studies on these systems indicated that the aromatic strands can adopt a syn parallel stacked conformation. This results in modular β-sheet-like molecular clefts that display structure-dependent recognition of small polar molecules. NMR and theoretical studies of the host-guest interaction support an in cleft binding mode and allowed the selectivity of the oligomers to be rationalized on the basis of minor changes in functional-group presentation on the edge of the aromatic strands.

Porphyrinic zirconium-based MOF with exposed pyrrole Lewis base site as a luminescent sensor for highly selective sensing of Cd2+ and Br− ions and THF small molecule

In this study, with meso-tetra(4-carboxyphenyl)porphyrin (TCPP) as the ligand, a unique zirconium-based metal-organic framework, namely PCN-224, has been prepared and used as a fluorescent sensor for sensitive and selective recognition of cations, anions, and small organic molecules. During metal ions detection, PCN-224 displays fluorescence enhancing towards Cd2+ cation. More interestingly, this is the first report of MOF-based sensors for detecting Br− via fluorescence enhancement mechanism. Furthermore, the prepared PCN-224 can perform as fluorescence “turn-off” sensor for highly sensitive detection of THF in methanol solution. Therefore, this work presents a Zr-based MOF sensor towards the detection of Cd2+ cation, Br− anion and THF small molecule with quick response, significant sensitivity and desirable selectivity.

(Strept)avidin as a template for ligands other than biotin: An overview.

Chicken avidin and bacterial streptavidin are workhorses in biotechnology. We have used avidin as a scaffold protein to develop avidin variants with novel ligand-binding affinity, so-called antidins. This article covers the strategy applied in the development of antidins. Using a phage display developed for avidin, immobilized ligands were used to select binders from a phage pool displaying avidin variants with randomized sequence in the protein loops. Antidins binding various ligands with nanomolar affinity were obtained. Antidins have already been demonstrated to be suitable for a diagnostic assay measuring serum progesterone levels and they offer a promising alternative to antibodies for the recognition of small molecules.