Diverse Structural Motifs Research Articles

Understanding the Role of NHC Ditopic Ligand Substituents in the Molecular Diversity and Emissive Properties of Silver Complexes.

Silver bis(carbene) complexes featuring ditopic N-heterocyclic carbene (NHC) ligands have been synthesized which enable the assembly of supramolecular architectures via reaction with silver triflate. Through a systematic exploration of crystal structures and emissive properties, this study investigates the impact of the substituents on the NHC ditopic ligands [R-Im-2-Z-py], where R = Me, benzyl (Bz), or 2-naphthylmethyl (NaphCH2), and Z = H or Cl in the structural framework and emissive properties observed in the silver bis(carbene) or polynuclear species. Remarkably diverse structural motifs emerge in both of them, predominantly influenced by the choice of R wingtip and second by the Z substituent. Also the emissive quantum yield of the complexes is mostly governed by the selection of the R wingtip and further modulated by the Z substituent. Several of the mono and polynuclear complexes exhibit complex emissive profiles, including the observation of dual emission phenomena. Particularly noteworthy is the complex [Ag(NHC)]2]OTf (R = Bz, Z = Cl), which demonstrates an exceptionally intense single blue emission with a remarkable solid-state quantum yield (Φ) of 24%.

Evaluating the potential of hydrophilic interaction liquid chromatography for collagen peptide mapping analysis

This study presents a systematic approach for developing an innovative hydrophilic interaction liquid chromatography (HILIC) method for collagen peptide mapping analysis. The predominant post-translational modification (PTM) of collagen, proline hydroxylation, introduces polar hydroxyl groups throughout the collagen sequence, making HILIC a promising alternative to classical reversed-phase liquid chromatography (RPLC) approaches. This study employs sixteen model peptides, selected from in silico predicted tryptic peptides with zero missed cleavages and representing diverse physicochemical properties and structural motifs of collagen. The peptides were used as standards to conduct detailed chromatographic evaluation. Various HILIC stationary phases and mobile phases were systematically examined to identify optimal separation conditions for collagen peptides, contributing to a better understanding of peptide behavior in HILIC. The study also explores the effects of sample diluent and injection mode, comparing classical injection with the Performance Optimizing Injection Sequence (POISe), to determine their impact on HILIC performance. Introducing a plug of weak solvent (acetonitrile) prior to sample injection, effectively mitigates the mismatch in eluent strength between the fully aqueous sample diluent (resulting from tryptic digestion) and the mobile phase, addressing issues of peak distortion. Different injection volumes (from 0.5 to 8 µL) and acetonitrile ratios (1:1, 1:2, 1:5 and 1:10) were tested to optimize sample injection and increase sensitivity of collagen tryptic peptides.Following method optimization, HILIC was coupled with mass spectrometry (MS) to evaluate its effectiveness in analyzing collagen-digested samples. This evaluation included the assessment of peptide sequence coverage and the method ability to identify hydroxylation patterns, thereby demonstrating its potential for detailed peptide analysis.

Synthesis and biological studies of acetophenone-based novel chalcone, semicarbazone, thiosemicarbazone and indolone derivatives: Structure-Activity relationship, molecular docking, molecular dynamics, and kinetic studies

This study presents the synthesis and evaluation of nine acetophenone derivatives (1–9), with compounds 2, 4, 5, 6, 7, and 9 being novel and synthesized for the first time. These derivatives encompass diverse structural motifs including chalcone, thiosemicarbazone, semicarbazone, and indolone derivatives. The structures of synthesized compound were confirmed by NMR analysis. The synthesized compounds were assessed for their in vitro enzyme inhibition against acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and α-Glycosidase enzymes, as well as their antioxidant capacities using the DPPH radical scavenging assay. With Ki values ranging from 8.96±0.40 to 44.16±4.25 nM, these showed effective inhibition of AChE. However, the inhibitory characteristics of all drugs were almost the same. The Ki values of the two most active compounds, (3) and (4), were 8.96±0.40 and 11.33±0.58 nM, respectively. Regarding α-Glycosidase, they demonstrate that all novel compounds (1–9) have IC50 values between 30.16 and 133.98 µM, whereas the Ki values vary from 42.71±5.90 to 128.78±8.03 µM. Compound 4 emerged as a notable inhibitor, displaying significant inhibition against all used enzymes. Molecular docking studies revealed its exceptional binding affinities, corroborated by MM-GBSA ΔG binding free energies, and Glide Emodel scores. Compound 7 also exhibited promising inhibitory potential against α-Glycosidase. Docking scores for hAChE -12.207, for hBChE -10.140 and for α-Glycosidase -10.590 kcal/mol. The 250 ns molecular dynamics simulations confirmed the stability of the ligand-protein complexes, particularly with compound 4. The ligand-protein complexes were found extremely stable according to the MD simulations. Additionally, ADME predictions indicated favorable pharmacokinetic properties and drug-likeness for all compounds, further supporting their potential as orally active agents. Compound 4, in particular, stands out as a multitarget drug candidate, with strong inhibition against key enzymes implicated in neurodegenerative diseases and diabetes, suggesting its therapeutic potential in these conditions.

Mechanistic model for epigenetic maintenance by methyl-CpG-binding domain proteins.

DNA methylation is a fundamental element of epigenetic regulation that is governed by the MBD protein superfamily, a group of "readers" that share a highly conserved methyl-CpG-binding domain (MBD) and mediate chromatin remodeler recruitment, transcription regulation, and coordination of DNA and histone modification. Previous work has characterized the binding affinity and sequence selectivity of MBD-containing proteins toward palindromes of 5-methylcytosine (5mC) containing 5mCpG dinucleotides, often referred to as single symmetrically methylated CpG sites. However, little is known about how MBD binding is influenced by the prototypical local clustering of methylated CpG sites and the presence of DNA structural motifs encountered, e.g., during DNA replication and transcription. Here, we use Single-Molecule Kinetics through Equilibrium Poisson Sampling (SiMKEPS) to measure precise binding and dissociation rate constants of the MBD of human protein MBD1 to DNAs with varying patterns of multiple methylated CpG sites and diverse structural motifs. MBD binding is promoted by two major properties of its DNA substrates: 1) tandem (consecutive) symmetrically methylated CpG sites in double-stranded DNA and secondary structures in single-stranded DNA; and 2) DNA forks. Based on our findings, we propose a mechanistic model for how MBD proteins contribute to epigenetic boundary maintenance between transcriptionally silenced and active genome regions.

High-Throughput Screening for Boride Superconductors.

A high-throughput screening using density functional calculations is performed to search for stable boride superconductors from the existing materials database. The workflow employs the fast frozen-phonon method as the descriptor to evaluate the superconducting properties quickly. Twenty-three stable candidates were identified during the screening. The superconductivity was obtained earlier experimentally or computationally for almost all found binary compounds. Previous studies on ternary borides are very limited. Our extensive search among ternary systems confirmed superconductivity in known systems and found several new compounds. Among these discovered superconducting ternary borides, TaMo2B2 shows the highest superconducting temperature of ∼12 K. Most predicted compounds were synthesized previously; therefore, our predictions can be examined experimentally. Our work also demonstrates that the boride systems can have diverse structural motifs that lead to superconductivity.

Metal-ring interactions in group 2 ansa-metallocenes: assessed with the local vibrational mode theory.

Ansa-metallocenes, a vital class of organometallic compounds, have attracted significant attention due to their diverse structural motifs and their pivotal roles in catalysis and materials science. We investigated 37 distinct group 2 ansa-metallocenes at the B3LYP-D3/def2-TZVP level of theory. Utilizing local mode force constants derived from our local vibrational mode theory, including a special force constant directly targeting the metal-ring interaction, we could unveil latent structural differences between solvated and non-solvated metallocenophanes and the influence of the solvent on complex stability and structure. We could quantify the intrinsic strength of the metal-cyclopentadienyl (M-Cp) bonds and the influence of the bridging motifs on the stiffness of the Cp-M-Cp angles, another determinant of complex stability. LMA was complemented by the analysis of electronic density, utilizing the quantum theory of atoms in molecules (QTAIM), which confirmed both the impact of solvent coordination on the strength of the M-Cp bond(s) and the influence of the bridging motif on the Cp-M-Cp angles. The specific effect of the ansa-motif on the M-Cp interaction was further elucidated by a comparison with linear/bent metallocene structures. In summary, our results identify the local mode analysis as an efficient tool for unraveling the intricate molecular properties of ansa-metallocenes and their unique structural features.

Gold-catalyzed cyclization and cycloaddition in natural product synthesis.

Covering: 2016 to mid 2023Transition metal catalysis, known for its remarkable capacity to expedite the assembly of molecular complexity from readily available starting materials in a single operation, occupies a central position in contemporary chemical synthesis. Within this landscape, gold-catalyzed reactions present a novel and versatile paradigm, offering robust frameworks for accessing diverse structural motifs. In this review, we highlighted a curated selection of publications in the past 8 years, focusing on the deployment of homogeneous gold catalysis in the ring-forming step for the total synthesis of natural products. These investigations are categorized based on the specific ring formations they engender, accentuating the prevailing gold-catalyzed methodologies applied to surmount intricate challenges in natural products synthesis.

Phage Display of Two Distinct Warheads to Inhibit Challenging Proteins.

Falling in between traditional small molecules and antibodies in size, peptides are emerging as a privileged therapeutic modality, one that can harness the benefits of both small molecule and antibody drugs. To discover potential peptide therapeutics, it is highly desirable to have high throughput screening platforms that can assess peptides with diverse and non-natural functional motifs. With this contribution, we present a novel phage library that incorporates two distinct designer groups. As an example, a pair of reversible covalent warheads was installed onto phage-displayed peptides to target a cysteine and a lysine. The double modification is realized by sequential modification of an N-terminal cysteine and then an internal cysteine using chemoselective chemistry. Screening of this double-warhead-presenting library against TEV protease readily revealed peptide inhibitors with single-digit micromolar potency. Importantly, our structure-activity studies demonstrate that both covalent warheads make important contributions to TEV protease inhibition. We envision that our strategy of double phage modification can be readily extended to build phage libraries with diverse structural motifs, allowing facile expansion of the chemical space coverable by phage display.

Kinesin and myosin motors compete to drive rich multiphase dynamics in programmable cytoskeletal composites.

The cellular cytoskeleton relies on diverse populations of motors, filaments, and binding proteins acting in concert to enable nonequilibrium processes ranging from mitosis to chemotaxis. The cytoskeleton's versatile reconfigurability, programmed by interactions between its constituents, makes it a foundational active matter platform. However, current active matter endeavors are limited largely to single force-generating components acting on a single substrate-far from the composite cytoskeleton in cells. Here, we engineer actin-microtubule (MT) composites, driven by kinesin and myosin motors and tuned by crosslinkers, to ballistically restructure and flow with speeds that span three orders of magnitude depending on the composite formulation and time relative to the onset of motor activity. Differential dynamic microscopy analyses reveal that kinesin and myosin compete to delay the onset of acceleration and suppress discrete restructuring events, while passive crosslinking of either actin or MTs has an opposite effect. Our minimal advection-diffusion model and spatial correlation analyses correlate these dynamics to structure, with motor antagonism suppressing reconfiguration and demixing, while crosslinking enhances clustering. Despite the rich formulation space and emergent formulation-dependent structures, the nonequilibrium dynamics across all composites and timescales can be organized into three classes-slow isotropic reorientation, fast directional flow, and multimode restructuring. Moreover, our mathematical model demonstrates that diverse structural motifs can arise simply from the interplay between motor-driven advection and frictional drag. These general features of our platform facilitate applicability to other active matter systems and shed light on diverse ways that cytoskeletal components can cooperate or compete to enable wide-ranging cellular processes.

Rise and fall of Mott insulating gaps in YNiO3 paramagnets as a reflection of symmetry breaking and remaking

The ${\mathrm{YNiO}}_{3}$ nickelate is a paradigm $d$-electron oxide that manifests the intriguing temperature-mediated sequence of three phases transitions from (i) magnetically ordered insulator to (ii) paramagnetic (PM) insulator and then to (iii) PM metal. Such phenomena raised the question of the nature of the association of magnetism and structural symmetry breaking with the appearance in (i) and (ii) and disappearance in (iii) of insulating band gaps. It is demonstrated here that first-principles mean-field--like density-functional theory (DFT), driven by molecular dynamics temperature evolution, can describe not only the origin of the magnetically long-range ordered insulating phase (i), but also the creation of an insulating paramagnet (ii) that lacks spin- long-range order, and of a metallic paramagnet (iii) as temperature rises. This approach provides the patterns of structural and magnetic symmetry breaking at different temperatures, in parallel with band gaps obtained when the evolving geometries are used as input to DFT electronic band-structure calculations. This disentangles the complex interplay among spin, charge, and orbital degrees of freedom. Analysis shows that the success in describing the rise and fall of the insulating band gaps along the phase transition sequence is enabled by allowing sufficient flexibility in describing diverse local structural and magnetic motifs as input to DFT. This entails the use of sufficiently large supercells that allow expressing structural disproportionation of octahedra, as well as a description of PM phases as a distribution of local magnetic moments (rather than using a single averaged moment). It appears that the historic dismissal of mean-field--like DFT as being unable to describe such Mott-like transitions was premature, as it was based on consideration of averaged crystallographic unit cells, a description that washes out local symmetry-breaking motifs. The magnetically ordered insulating ${\mathrm{YNiO}}_{3}$ phase (i) and the PM insulating phase (ii) result in DFT from allowing symmetry breaking, evident already by considering the athermal internal energy. In contrast, the PM metallic phase (iii) is formed thermally by smearing out thus weakening symmetry breaking. Analysis of snapshots of the different forms of structural vs magnetic symmetry breaking shows that only the loss of the polymorphous distribution of magnetic moments existing in (ii) causes the fall of the band gap, resulting in the metallic state in (iii). The interesting conclusion is that such a description of the rise [in phases (i) and (ii)] and fall [in phase (iii)] of the insulating gap does not rely on the traditional Mott-like strong correlation understanding, but on breaking and remaking of magnetic and structural symmetries reflected in energy lowering.

Counterintuitive Chemistry: Carbene Stabilization of Zero-Oxidation State Main Group Species

Carbenes have evolved from transient laboratory curiosities to a robust, diverse, and surprisingly impactful ligand class. A variety of different carbenes have significantly contributed to the development of low-oxidation state main group chemistry. This Perspective focuses upon advances in the chemistry of carbene complexes containing main group element cores in the formal oxidation state of zero, including their diverse synthetic strategies, unusual bonding and structural motifs, and utility in transition metal coordination chemistry and activation of small molecules.

Synthesis of I(III)/S(VI) reagents and their reactivity in photochemical cycloaddition reactions with unsaturated bonds

The development of novel methodologies for the introduction of the sulfoxonium group under mild conditions is appealing but remains underexplored. Herein we report the synthesis of a class of hypervalent iodine reagents with a transferrable sulfoxonium group. These compounds enable mixed iodonium-sulfoxonium ylide reactivity. These well-defined reagents are examined in visible-light-promoted cyclization reactions with a wide range of unsaturated bonds including alkenes, alkynes, nitriles, and allenes. Two distinct cyclization pathways are identified, which are controlled by the substituent of the unsaturated bond. The cycloaddition protocol features simple operation, mild reaction conditions, and excellent functional group tolerance, affording a broad range of sulfoxonium-containing cyclic structures in moderate to excellent yields. Furthermore, the sufoxonium group in the product can be transformed into diverse functional groups and structural motifs via single electron transfer and transition-metal catalysis.

Unique three‐component co‐assembly among AIEgen, L‐GSH, and Ag+ for the formation of helical nanowires

AbstractNature has selected, produced, and evolved numerous molecular architectural motifs over billions of years for particular bio‐functions. During this process, molecular self‐assembly plays a critically important role. Inspired by these delicate assemblies, scientists devote themselves to developing various sophisticated complexes assembled by diverse and numerous structural motifs. By far, most of the examples focus on single‐molecule self‐assembly or co‐assembly between two molecules, seldom works report the co‐assembly among three building blocks due to the substantially increased complexity and decreased controllability. Here we report a novel three‐component co‐assembly among L‐glutathione (L‐GSH), AgNO3, and an aggregation‐induced emission luminogen (AIEgen), namely triphenylamine–pyridinium (abbreviated to TPA‐Py). TPA‐Py, L‐GSH, and Ag+ co‐assemble into numerous long and ordered nanowires with left‐handed helices, which show remarkable AIE properties that can be observed by naked eyes. This effect is only detected in this system, the replacement of TPA‐Py with other AIEgens, L‐GSH with other cysteine derivatives or anions, Ag+ with other metal ions, could not lead to the unique AIE effect, which endows this system with high specificity and controllability. This work provides new insight into the design of biomolecule recognition systems and discloses that ternary co‐assembly could become a facile route to build sophisticated nanobiomaterials.

Rapid syntheses of N-fused heterocycles via acyl-transfer in heteroaryl ketones

The wide-ranging potencies of bioactive N-fused heterocycles inspire the development of synthetic transformations that simplify preparation of their complex, diverse structural motifs. Heteroaryl ketones are ubiquitous, readily available, and inexpensive molecular scaffolds, and are thus synthetically appealing as precursors in preparing N-fused heterocycles via intramolecular acyl-transfer. To best of our knowledge, acyl-transfer of unstrained heteroaryl ketones remains to be demonstrated. Here, we show an acyl transfer-annulation to convert heteroaryl ketones to N-fused heterocycles. Driven via aromatisation, the acyl of a heteroaryl ketone can be transferred from the carbon to the nitrogen of the corresponding heterocycle. The reaction commences with the spiroannulation of a heteroaryl ketone and an alkyl bromide, with the resulting spirocyclic intermediate undergoing aromatisation-driven intramolecular acyl transfer. The reaction conditions are optimised, with the reaction exhibiting a broad substrate scope in terms of the ketone and alkyl bromide. The utility of this protocol is further demonstrated via application to complex natural products and drug derivatives to yield heavily functionalised N-fused heterocycles.

Widespread occurrence of covalent lysine\u2013cysteine redox switches in proteins

We recently reported the discovery of a lysine–cysteine redox switch in proteins with a covalent nitrogen–oxygen–sulfur (NOS) bridge. Here, a systematic survey of the whole protein structure database discloses that NOS bridges are ubiquitous redox switches in proteins of all domains of life and are found in diverse structural motifs and chemical variants. In several instances, lysines are observed in simultaneous linkage with two cysteines, forming a sulfur–oxygen–nitrogen–oxygen–sulfur (SONOS) bridge with a trivalent nitrogen, which constitutes an unusual native branching cross-link. In many proteins, the NOS switch contains a functionally essential lysine with direct roles in enzyme catalysis or binding of substrates, DNA or effectors, linking lysine chemistry and redox biology as a regulatory principle. NOS/SONOS switches are frequently found in proteins from human and plant pathogens, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and also in many human proteins with established roles in gene expression, redox signaling and homeostasis in physiological and pathophysiological conditions.

A facile synthesis of a novel family of heterotricyclic hybrids: Spiro-pyrrolopyridazines

An efficient strategy for the synthesis of spiro-pyrrolopyridazines has been developed. When reacted with hydrazine monohydrate, spiro-2H-pyrroles with a 1,4-diketone functionality produced a novel family of heterotricyclic hybrids, spiro-pyrrolopyridazines, specifically spiro{cyclohexane-1,5'-pyrrolo[3,4-d]pyridazine} systems. The condensation reaction of spiro-2H-pyrroles with hydrazine monohydrate in refluxing 1-butanol proceeded well and afforded spiro-pyrrolopyridazines in good to high yields. The reaction was found to be general for variety of spiro-2H-pyrroles and demonstrated good tolerance to a variety of aromatic and heteroaromatic groups with electron-withdrawing and electron-donating substituents. The synthesis of heterotricyclic spiro-pyrrolopyridazine hybrids may exhibit potential to deliver diverse structural motifs that aid the drug discovery efforts.

Structural Mechanisms in Soft Fibrous Tissues: A Review

Through years of evolution, biological soft fibrous tissues have developed remarkable functional properties, unique hierarchical architectures, and -most notably, an unparalleled and extremely efficient deformation ability. Whereas the structure-function relationship is well-studied in natural hard materials, soft materials are not getting similar attention, despite their high prevalence in nature. These soft materials are usually constructed as fiber-reinforced composites consisting of diverse structural motifs that result in an overall unique mechanical behavior with large deformations. Biomimetics of their mechanical behavior is currently a significant bioengineering challenge. The unique properties of soft fibrous tissues stem from their structural complexity, which, unfortunately, also hinders our ability to generate adequate synthetic analogs, such that autografts remain the “gold standard” materials for soft-tissue repair and replacement. This review seeks to understand the structural and deformation mechanisms of soft collagenous tissues, with a particular emphasis on tendon and ligaments, the annulus fibrosus (AF) in the intervertebral disc (IVD), skin, and blood vessels. We examined and compared different mechanical and structural motifs in these different tissue types, which are subjected to complex and varied mechanical loads, to isolate the mechanisms of their deformation behavior. Herein, we focused on their composite structure from a perspective of the different building blocks, architecture, crimping patterns, fiber orientation, organization and their structure-function relationship. In the second part of the review, we presented engineered soft composite applications that used these structural motifs to mimic the structural and mechanical behavior of soft fibrous tissues. Moreover, we demonstrated new methodologies and materials that use biomimetic principles as a guide. These novel architectural materials have tailor-designed J-shaped large deformations behavior. Structural motifs in soft composites hold valuable insights that could be exploited to generate the next generation of materials. They actually have a two-fold effect: 1) to get a better understanding of the complex structure-function relationship in a simple material system using reverse biomimetics and 2) to develop new and efficient materials. These materials could revolutionize the future tailor-designed soft composite materials together with various soft-tissue repair and replacement applications that will be mechanically biocompatible with the full range of native tissue behaviors.

Structures of synthetic helical filaments and tubes based on peptide and peptido-mimetic polymers.

AbstractSynthetic peptide and peptido-mimetic filaments and tubes represent a diverse class of nanomaterials with a broad range of potential applications, such as drug delivery, vaccine development, synthetic catalyst design, encapsulation, and energy transduction. The structures of these filaments comprise supramolecular polymers based on helical arrangements of subunits that can be derived from self-assembly of monomers based on diverse structural motifs. In recent years, structural analyses of these materials at near-atomic resolution (NAR) have yielded critical insights into the relationship between sequence, local conformation, and higher-order structure and morphology. This structural information offers the opportunity for development of new tools to facilitate the predictable and reproduciblede novodesign of synthetic helical filaments. However, these studies have also revealed several significant impediments to the latter process – most notably, the common occurrence of structural polymorphism due to the lability of helical symmetry in structural space. This article summarizes the current state of knowledge on the structures of designed peptide and peptido-mimetic filamentous assemblies, with a focus on structures that have been solved to NAR for which reliable atomic models are available.

Fused-azepinones: Emerging scaffolds of medicinal importance.

Hymenialdisine an alkaloid of oroidin class has drawn the attention of researchers owing to its unique structural features and interesting biological properties. Hymenialdisine exhibited promising inhibitory activity against a number of therapeutically important kinases viz., CDKs, GSK-3β etc., and showed anti-cancer, anti-inflammatory, anti-HIV, neuroprotective, anti-fouling, anti-plasmodium properties. Hymenialdisine and other structurally related oroidin alkaloids such as dibromo-hymenialdisine, stevensine, hymenin, axinohydantoin, spongicidines A-D, latonduines and callyspongisines contain pyrrolo[2,3-c] azepin-8-one core in common. Keeping in view of the interesting structural and therapeutic features of HMD, several structural modifications were carried around the fused-azepinone core which resulted in a number of diverse structural motifs like indolo-azepinones, paullones, aza-paullones, darpones and 5,7-dihydro-6H-benzo[b]pyrimido[4,5-d] azepin-6-one. In this review, an attempt is made to collate and review the structures of diverse hymenialdisine and related fused-azepinones of synthetic/natural origin and their biological properties.

Speeding drug discovery targeting RNAs: An iterative “RNA selection-compounds screening cycle“ for exploring RNA-small molecule pairs

RNA is an emerging target of next-generation drug development. Recently, new small molecules targeting RNAs were discovered by several pharmaceutical companies. Methods have been reported to identify small molecules targeting a specific RNA sequence and structural motif, however, because of diverse sequence and structural motifs potentially present in the druggable functional RNAs, large sets of structure–activity relationships (SARs) information of small molecule – RNA interactions will be required for the acceleration and efficient startup of the discovery programs toward unprecedented RNA targets. Here we describe our iterative RNA selection and compounds screening to accumulate rich information about small molecules – RNA interaction. The RNAs that selectively bind to the initial molecular target, compound 1 from our in-house chemical library (JT-library), was isolated using in vitro selection technique from a hairpin-structured RNA library mimicking precursor microRNA (pre-miRNA). Then, we engineered pre-let-7f-2 to create its mutant that can bind to compound 1 by embedding the in vitro selected RNA motif for compound 1 in the hairpin loop region. The obtained mutant pre-let-7f-2-loop-mt was used as a target for screening 316 analogs of compound 1. A surface plasmon resonance (SPR) -based screening was performed against pre-let-7f-2-loop-mt-immobilized sensor surface and we obtained four compounds that can bind to the RNA. Among these four compounds, three compounds showed higher affinity to pre-let-7f-2-loop-mt than the parental compound 1, which suggests the feasibility of our strategy for gathering the SAR information on small molecule – RNA interactions. We demonstrated only one cycle of RNA selection and compounds screening in the present study, but can continue this cycle with the selected molecule to gain new RNAs and even new RNA motifs and gather much SAR information with improved accuracy.