Binding Of Molecules Research Articles

Applications of Cell-Based Protein Array Technology to Preclinical Safety Assessment of Biological Products.

Off-target evaluation is essential in preclinical safety assessments of novel biotherapeutics, supporting lead molecule selection, endpoint selection in toxicology studies, and regulatory requirements for first-in-human trials. Off-target interaction of a therapeutic antibody and antibody derivatives has been historically assessed via the Tissue Cross-Reactivity (TCR) study, in which the candidate molecule is used as a reagent in immunohistochemistry (IHC) to assess binding of the candidate molecule to a panel of human tissue sections. The TCR approach is limited by the performance of the therapeutic as an IHC reagent, which is often suboptimal to outright infeasible. Furthermore, binding of the therapeutic in IHC conditions typically has poor in vitro to in vivo translation and lacks qualitative data of the identity of putative off-targets limiting the decisional value of the data. More recently, cell-based protein arrays (CBPA) that allow for screening against a large portion of the human membrane proteome and secretome have emerged as a complement, and likely a higher value alternative, to IHC-based off-target assessment. These arrays identify specific protein interactions and may be useful for testing nontraditional antibody-based therapeutic formats that are unsuitable for TCR studies. This article presents an overview of CBPA technologies in the context of TCR and off-target assessment studies. Selected case examples and strategic considerations covering a range of different modalities are presented.

Deciphering Binding Potential of Naphthalimide-Coumarin Conjugate with c-MYC G-Quadruplex for Developing Anticancer Agents: A Spectroscopic and Molecular Modeling Approach.

It has been well accumulated that G-quadruplex (G4-DNA) has great anticancer relevance, and various heterocyclic moieties have been synthesized and examined as potent G4-DNA binders with promising anticancer activity. Here, we have synthesized a series of naphthalimide-triazole-coumarin conjugates by substituting various amines and further examine their anticancer activity against 60 human cancer cell lines at 10 μM. One and five dose concentration results reveal low values of MG-MID GI50 for compounds including 8a (3.18 μM), 8b (13.11 μM), 8e (7.68 μM) and 8f (1.75 μM). Further cell apoptosis manifests that all compounds can induce cell apoptosis in cancer cells by stabilizing the c-MYC promoter G-quadruplex. Therefore, the G-quadruplex-mediated pathway may be responsible for the apoptosis that these naphthalimide-coumarin compounds caused in cancer cells. Therefore, multispectroscopic techniques are employed to evaluate the binding of molecules with c-MYC G4-DNA where all four molecules readily bind to G4-DNA and stabilize it with a high binding constant, leading to inhibition of cancer cells and apoptosis of cancer cells. Binding studies toward ct-DNA disclose that these compounds do not interact with ds-DNA and thus selectively target G4-DNA to exert their anticancer activity. All the active compounds have greater affinity toward Human Serum Albumin (HSA) and can readily bind with HSA with a binding constant of 12 × 104 M-1 (8a), 13.0 × 104 M-1 (8b), 14.2 × 104 M-1 (8e), 16.3 × 104 M-1 (8f). Thus, the results disclose that inhibition and killing of cancer cells by these derivatives feasibly occur due to their ability to interact with c-MYC G-quadruplex forming promoters and their high affinity toward HSA unfold potent anticancer agents and can be taken further for clinical trials.

Deep Learning of CYP450 Binding of Small Molecules by Quantum Information.

Drug-drug interaction can lead to diminished therapeutic effects or increased toxicity, posing significant risks, especially in polypharmacy, and cytochrome P450 plays an indispensable role in this interaction. Cytochrome P450, responsible for the metabolism and detoxification of most drugs, metabolizes about 90% of Food and Drug Administration-approved drugs, making early detection of potential drug-drug interactions. Over the years, in-silico modeling has become a valuable tool for predicting drug-drug interactions. Still, conventional molecular descriptors focusing on the structural properties of drugs often overlook complex electronic interactions critical for accurate predictions. To address this, we implemented the Manifold Embedding of Molecular Surface (MEMS) approach, which retains the quantum mechanical characteristics of molecules. MEMS-generated electronic attributes were embedded and featurized for deep learning using the DeepSets architecture, where our models achieved high accuracy, particularly for cytochrome P450 enzyme 1A2 (CYP1A2), with F1 scores reaching up to 0.866. This study highlights the potential of integrating detailed electronic properties with deep learning to improve predictive models for drug-drug interactions, addressing the limitations of traditional molecular descriptors and machine-learning techniques.

MAI-TargetFisher: A proteome-wide drug target prediction method synergetically enhanced by artificial intelligence and physical modeling.

Computational target identification plays a pivotal role in the drug development process. With the significant advancements of deep learning methods for protein structure prediction, the structural coverage of human proteome has increased substantially. This progress inspired the development of the first genome-wide small molecule targets scanning method. Our method aims to localize drug targets and detect potential off-target effects early in the drug discovery process, thereby improving the success rate of drug development. We have constructed a high-quality database of protein structures with annotated potential binding sites, covering 82% of the protein-coding genome. On the basis of this database, to enhance our search capabilities, we have integrated computational techniques, including both artificial intelligence-based and biophysical model-based methods. This integration led to the development of a target identification method called Multi-Algorithm Integrated Target Fisher (MAI-TargetFisher). MAI-TargetFisher leverages the complementary strengths of various methods while minimizing their weaknesses, enabling precise database navigation to generate a reliably ranked set of candidate targets for an active query molecule. Importantly, our work is the first comprehensive scan of protein surfaces across the entire human genome, aimed at evaluating potential small molecule binding sites on each protein. Through a series of evaluations on benchmark and a target identification task, the results demonstrate the high hit rates and good reliability of our method under the validation of wet experiments. We have also made available a freely accessible web server at https://bailab.siais.shanghaitech.edu.cn/mai-targetfisher for non-commercial use.

Structural and Dynamical Response of Lipid Bilayers to Solvation of an Amphiphilic Anesthetic.

The structural response of 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC)/water bilayers to addition and subsequent solvation of a small amphiphilic molecule - an anesthetic benzyl alcohol - was studied by means of solid-state NMR (2H NMR, 31P NMR) spectroscopy and low-angle X-ray diffraction. The sites of binding of this solute molecule within the bilayer were determined - the solute was shown to partition between several sites in the bilayer and the equilibrium was shown to be dynamic and dependent on the level of hydration and temperature. At the same time, it was shown that solubilization of benzyl alcohol reached a solubility limit and was terminated when the ordering profile of DMPC hydrocarbon chains adopted finite limiting values throughout the whole chain. Such findings were made probably for the first time for any lipid bilayer system and possibly have more general implications for dissolution of other small-molecule amphiphilic solutes in lipid bilayer systems other than DMPC. The limit to the hydrocarbon chain profile is probably a more general property and corresponds to the balance of intrabilayer and interbilayer forces established in combination with the elastic properties of the bilayer system that still consists of one single phase just before the solute forms an excess phase. It is not necessary to quantify the contribution of each individual intrabilayer and interbilayer force acting within such a bilayer system. A model of the dependence of surface density of lipid chains on the chain segment order parameter was also developed - an empirical mathematical model based on experimental data was derived and it was proposed to represent a relationship between intrinsic bilayer forces and bilayer deformation characteristics and might be proven to be of more general significance in the future.

Reducing Measurement Deviation by Metastable DNA Probes for Aptamer Thermodynamic Characterization.

DNA reaction equilibrium-based calculations have great potential in thermodynamic characterization, but their widespread applications are hindered by significant measurement deviation of equilibrium concentration. Here, we report the advantages of metastable DNA hybridization in reducing quantification deviation of equilibrium concentration and propose a universal and standardized strategy for measuring aptamer binding energy, termed metastable DNA reference calorimetry (MDRC). We built different MDRC-based algorithms tailored to different aptamer binding models, enabling the calculation of thermodynamic parameters for aptamers with one or more binding sites. Our correlative model, considering the cross-effects between different binding sites, showed that for ATP aptamers with two binding sites, binding of the first ATP molecule would decrease its affinity for the second at low temperatures and even completely inhibit this binding at high temperatures. Moreover, the thermodynamic parameters of protein-specific aptamers were calculated to elucidate the universality of the method. The successful analysis of cell-specific aptamers further demonstrated MDRC's applicability in complex biological systems.

Enhanced Sampling Simulations of RNA-Peptide Binding Using Deep Learning Collective Variables.

Enhanced sampling (ES) simulations of biomolecular recognition, such as binding small molecules to proteins and nucleic acid targets, protein-protein association, and protein-nucleic acid interactions, have gained significant attention in the simulation community because of their ability to sample long-time scale processes. However, a key challenge in implementing collective variable (CV)-based enhanced sampling methods is the selection of appropriate CVs that can distinguish the system's metastable states and, when biased, can effectively sample these states. This challenge is particularly acute when the binding of a flexible molecule to a conformationally rich host molecule is simulated, such as the binding of a peptide to an RNA. In such cases, a large number of CVs are required to capture the conformations of both the host and the guest as well as the binding process. Using such a large number of descriptors is impractical in any enhanced sampling simulation method. In our work, we used the recently developed deep targeted discriminant analysis (Deep-TDA) method to design CVs to study the binding of a cyclic peptide, L22, to a TAR RNA of HIV, which is a prototypical system. The Deep-TDA CV, obtained from a nonlinear combination of important contact pairs between the L22 peptide and the host RNA backbone atoms, along with the RNA apical loop RMSD as the second CV were used in the on-the-fly probability-based enhanced sampling (OPES) simulation to sample the reversible binding and unbinding of the L22 peptide to the TAR RNA target. The OPES simulation delineated the mechanism of peptide binding and unbinding to and from the RNA and enabled the calculation of the underlying free energy landscape. Our results demonstrate the potential of the Deep-TDA method for designing CVs to study complex biomolecular recognition processes.

Development and Use of DJ-1 Affinity Microcolumns to Screen and Study Small Drug Candidates for Parkinson’s Disease

BackgroundDJ-1 is a protein whose mutation causes rare heritable forms of Parkinson’s disease (PD) and is of interest as a target for treating PD and other disorders. This work used high performance affinity microcolumns to screen and examine the binding of small molecules to DJ-1, as could be used to develop new therapeutics or to study the role of DJ-1 in PD. Non-covalent entrapment was used to place microgram quantities of DJ-1 in an unmodified form within microcolumns, which were then used in multiple studies to analyze binding by model compounds and possible drug candidates to DJ-1. ResultsSeveral factors were examined in optimizing the entrapment method, including the addition of a reducing agent to maintain a reduced active site cysteine residue in DJ-1, the concentration of DJ-1 employed, and the entrapment times. Isatin was used as a known binding agent (dissociation constant, ∼2.0 μM) and probe for DJ-1 activity. This compound gave good retention on 2.0 cm × 2.1 mm inner diameter DJ-1 microcolumns made under the final entrapment conditions, with a typical retention factor of 14 and elution in ∼8 min at 0.50 mL/min. These DJ-1 microcolumns were used to evaluate the binding of small molecules that were selected in silico to bind or not to bind DJ-1. A compound predicted to have good binding with DJ-1 gave a retention factor of 122, an elution time of ∼15 min at 0.50 mL/min, and an estimated dissociation constant for this protein of 0.5 μM. SignificanceThese chromatographic tools can be used in future work to screen additional possible binding agents for DJ-1 or adapted for examining drug candidates for other proteins. This work represents the first time protein entrapment has been deployed with DJ-1, and it is the first experimental confirmation of binding to DJ-1 by a small lead compound selected in silico.

A novel poly(amidoamine)-modified electrolyte-insulator-semiconductor-based biosensor for label-free detection of ATP.

Adenosine triphosphate (ATP) is crucial for cellular activity. The need for ATP detection in the field of biomedicine is rapidly increasing. Several biosensor-based approaches have been developed as a result of the growing demand for ATP detection. An electrolyte-insulator-semiconductor (EIS) sensor is a type of field-effect device that has the ability to detect surface-potential changes with a specific level of sensitivity. In this study, a label-free ATP detection biosensor based on poly(amidoamine)-modified EIS sensors was developed, in which an ATP-sensitive aptamer (Apt) was utilized as the sensitive element and the EIS sensor was used as the transducer. It is possible to monitor the binding of charged molecules, such as aptamers using EIS sensors in a label-free manner with a straightforward setup. To improve the coupling efficiency of Apt with the EIS sensor, a positively charged polyelectrolyte, i.e., poly (amidoamine) (PAMAM) dendrimers, was utilized to modify the surface of the EIS sensors to attach the negatively charged Apt through electrostatic attraction. The adsorptive binding of Apt and ATP results in a change in the capacitance of the EIS sensor. During the process of surface modification, the electrochemical measurements of capacitance-voltage (C-V) curves and constant-capacitance (ConCap) characteristics were utilized as indicators for the corresponding processes of EIS sensor surface modification. The measurement results indicated that this biosensor was able to detect ATP with high sensitivity and good specificity. The detection range of ATP was from 0.1 nM to 100 nM and the detection limit was as low as 0.12 nM. This biosensor has the potential to be utilized in the detection of ATP in the surrounding microenvironment of cells and tissues, with promising prospects for application in the field of biomedicine such as energy and metabolism monitoring of cells and tissues.

Recent progress towards the development of fluorescent probes for the detection of disease-related enzymes.

Normal physiological functions as well as regulatory mechanisms for various pathological conditions depend on the activity of enzymes. Thus, determining the in vivo activity of enzymes is crucial for monitoring the physiological metabolism and diagnosis of diseases. Traditional enzyme detection methods are inefficient for in vivo detection, which have different limitations, such as high cost, laborious, and inevitable invasive procedures, low spatio-temporal resolution, weak anti-interference ability, and restricted scope of application. Because of its non-destructive nature, ultra-environmental sensitivity, and high spatiotemporal resolution, fluorescence imaging technology has emerged as a potent tool for the real-time visualization of live cells, thereby imaging the motility of proteins and intracellular signalling networks in tissues and cells and evaluating the binding and attraction of molecules. In the last few years, significant advancements have been achieved in detecting and imaging enzymes in biological systems. In this regard, the high sensitivity and unparalleled spatiotemporal resolution of fluorescent probes in association with confocal microscopy have garnered significant interest. In this review, we focus on providing a concise summary of the latest developments in the design of fluorogenic probes used for monitoring disease-associated enzymes and their application in biological imaging. We anticipate that this study will attract considerable attention among researchers in the relevant field, encouraging them to pursue advances in the development and application of fluorescent probes for the real-time monitoring of enzyme activity in live cells and in vivo models while ensuring excellent biocompatibility.

Ion mobility mass spectrometry unveils conformational effects of drug lead EPI-001 on the intrinsically disordered N-terminal domain of the androgen receptor.

Intrinsically disordered proteins (IDPs) are important drug targets as they are key actors within cell signaling networks. However, the conformational plasticity of IDPs renders them challenging to characterize, which is a bottleneck in developing small molecule drugs that bind to IDPs and modulate their behavior. In relation to this, ion mobility mass spectrometry (IM-MS) is a useful tool to investigate IDPs, as it can reveal their conformational preferences. It can also offer important insights in drug discovery, as it can measure binding stoichiometry and unveil conformational shifts of IDPs exerted by the binding of small drug-like molecules. Herein, we have used IM-MS to investigate the effect of drug lead EPI-001 on the disordered N-terminal domain of the androgen receptor (AR-NTD). Despite structural heterogeneity rendering the NTD a challenging region of the protein to drug, this domain harbors most, if not all, of the transcriptional activity. We quantify the stoichiometry of EPI-001 binding to various constructs corresponding to functional domains of AR-NTD and show that it binds to separate constructs containing transactivation unit (TAU)-1 and TAU-5, respectively, and that 1-2 molecules bind to a larger construct containing both sequences. We also identify a conformational shift upon EPI-001 binding to the TAU-5, and to a much lesser extent with TAU-1 containing constructs. This work provides novel insight on the interactions of EPI-001 with the AR-NTD, and the structural alterations that it exerts, and positions IM-MS as an informative tool that will enhance the tractability of IDPs, potentially leading to better therapies.

Comparison of Bacterial Intracellular and Secreted Proteins produced in Milk Versus Medium for Escherichia coli by Proteomic Analysis.

The growth and reproduction of microorganisms are dependent on nutrient supply. Here, Milk and LB media were utilized as nutrition sources for Escherichia coli, and the changes in bacterial and secretory proteins at 3 time points (3, 9, and 18 h) in the growth cycle were studied using a label-free proteomics technique. The findings revealed that the abundances of bacterial intracellular proteins inosine/xanthosine triphosphatase and universal stress protein F increase dramatically during the growth phase in milk and LB media. In terms of secretory proteins, RNase PH and tyrosine-tRNA ligase abundance increased dramatically, while outer membrane protein X and outer membrane protein C abundance decreased significantly from 3 to 18 h in both milk and LB conditions. Several bacterial intracellular and secretory proteins showed media-dependent changes, including hydrogenase-2 and s-adenosylmethionine synthase, which were only found in the LB medium. In contrast, DNA polymerase III subunit α and cold shock-like protein CspD (CspD) have been discovered only in milk. The 2 media shared the differential abundance of proteins involved in small molecule binding and small molecule metabolic process pathways. The differentially expressed intracellular proteins of E. coli cultured in milk were associated with membrane trafficking and signal transduction pathways. The findings improve our understanding of changes in E. coli bacterial intracellular proteins and secretory proteins in response to nutritional stimuli, as well as provide a new perspective and foundation for investigating its adaptive mechanisms in a variety of environments, potentially leading to better prevention and control strategies.

In silico Binding and Interactions of Known Antivirals to the Dimer Pocket of the SARS-CoV-2 Main Protease

The devastating COVID-19 pandemic began in December 2019, catalyzed by the emergence of the SARS-CoV-2 beta-coronavirus strain. This inflicted global havoc, infecting over 767 million individuals and claiming more than 6.9 million lives by the end of 2023. Despite accelerated vaccine approvals significantly curbing infection rates and fatalities, the persistent spread of COVID-19 cases has been driven by evolving SARS-CoV-2 variants. The risk of future pandemics due to viral mutations emphasizes the urgent need for more effective antiviral drugs to prevent resistance. In this study, we explored the potential binding of small molecules to the dimer site of SARS-CoV-2 main protease (Mpro). We used the DogSiteScore program to predict the druggable sites, and Autodock Vina to evaluate the binding affinities of known antivirals. The results revealed that most of the antivirals exhibit higher binding affinities to the dimer site compared to the catalytic site. Notably, indinavir, nelfinavir, lopinavir, grazoprevir, and dolutegravir are among the top binders, surpassing - 10 kcal/mol in the dimer site. Meanwhile, these antivirals exhibited affinities to the catalytic site that did not exceed -8.7 kcal/mol. These findings highlight the promising potential of the dimer site as an alternative target for developing specific COVID-19 inhibitors.

Structure of blood cell-specific tubulin and demonstration of dimer spacing compaction in a single protofilament.

Microtubule (MT) function plasticity originates from its composition of α- and β-tubulin isotypes and the post-translational modifications of both subunits. Aspects such as MT assembly dynamics, structure, and anticancer drug binding can be modulated by αβ-tubulin heterogeneity. However, the exact molecular mechanism regulating these aspects is only partially understood. A recent insight is the discovery of expansion and compaction of the MT lattice, which can occur via fine modulation of dimer longitudinal spacing mediated by GTP hydrolysis, taxol binding, protein binding, or isotype composition. Here, we report the first structure of the blood cell-specific α1/β1-tubulin isolated from the marginal band of chicken erythrocytes (ChET) determined to a resolution of 3.2 Å by cryo-EM. We show that ChET rings induced with Cryptophycin-52 (Cp-52) are smaller in diameter than HeLa tubulin (HeLaT) rings induced with Cp-52 and composed of the same number of heterodimers. We observe compacted interdimer and intradimer curved protofilament interfaces, characterized by shorter distances between ChET subunits and accompanied by conformational changes in the β-tubulin subunit. The compacted ChET interdimer interface brings more residues near the Cp-52 binding site. We measured the Cp-52 apparent binding affinities of ChET and HeLaT by mass photometry, observing small differences, and detected the intermediates of the ring assembly reaction. These findings demonstrate that compaction/expansion of dimer spacing can occur in a single protofilament context and that the subtle structural differences between tubulin isotypes can modulate tubulin small molecule binding.

Binding Molecules in Tick Saliva for Targeting Host Cytokines, Chemokines, and Beyond.

Ticks have coevolved with their hosts over millions of years, developing the ability to evade hemostatic, inflammatory, and immunological responses. Salivary molecules from these vectors bind to cytokines, chemokines, antibodies, complement system proteins, vasodilators, and molecules involved in coagulation and platelet aggregation, among others, inhibiting or blocking their activities. Initially studied to understand the complexities of tick-host interactions, these molecules have been more recently recognized for their potential clinical applications. Their ability to bind to soluble molecules and modulate important physiological systems, such as immunity, hemostasis, and coagulation, positions them as promising candidates for future therapeutic development. This review aims to identify the binding molecules present in tick saliva, determine their primary targets, and explore the tick species involved in these processes. By associating the binding molecules, the molecules to which they bind, and the effect caused, the review provides a basis for understanding how these molecules can contribute to possible future advances in clinical applications.

A structure-based mechanism for initiation of AP-3 coated vesicle formation

Adaptor protein complex-3 (AP-3) mediates cargo sorting from endosomes to lysosomes and lysosome-related organelles. Recently, it was shown that AP-3 adopts a constitutively open conformation compared to the related AP-1 and AP-2 coat complexes, which are inactive until undergoing large conformational changes upon membrane recruitment. How AP-3 is regulated is therefore an open question. To understand the mechanism of AP-3 membrane recruitment and activation, we reconstituted human AP-3 and determined multiple structures in the soluble and membrane-bound states using electron cryo-microscopy. Similar to yeast AP-3, human AP-3 is in a constitutively open conformation. To reconstitute AP-3 activation by adenosine di-phosphate (ADP)-ribosylation factor 1 (Arf1), a small guanosine tri-phosphate (GTP)ase, we used lipid nanodiscs to build Arf1-AP-3 complexes on membranes and determined three structures showing the stepwise conformational changes required for formation of AP-3 coated vesicles. First, membrane recruitment is driven by one of two predicted Arf1 binding sites, which flexibly tethers AP-3 to the membrane. Second, cargo binding causes AP-3 to adopt a fixed position and rigidifies the complex, which stabilizes binding for a second Arf1 molecule. Finally, binding of the second Arf1 molecule provides the template for AP-3 dimerization, providing a glimpse into the first step of coat polymerization. We propose coat polymerization only occurs after cargo engagement, thereby linking cargo sorting with assembly of higher-order coat structures. Additionally, we provide evidence for two amphipathic helices in AP-3, suggesting that AP-3 contributes to membrane deformation during coat assembly. In total, these data provide evidence for the first stages of AP-3-mediated vesicle coat assembly.

Modes of Binding of Small Molecules Dictate the Interruption of RBD-ACE2 Complex of SARS-CoV-2.

The spike protein is a vital target for therapeutic advancement to inhibit viral entrance. Given that the connection between Spike and ACE2 constitutes the initial phase of SARS-CoV-2 pathogenesis, obstructing this interaction presents a promising therapeutic approach. This work aims to find compounds from DrugBank that can modulate the stability of the spike RBD-ACE2 protein-protein complex. Employing a therapeutic repurposing strategy, we conducted molecular docking of over 9000 DrugBank compounds against the Spike RBD-ACE2 complex, on ten variants, including the wild-type. We also evaluated the intricate stability of the RBD-ACE2 proteins by molecular dynamics simulations, hydrogen bond analysis, RMSD analysis, radius of gyration analysis, and the QM-MM approach. We assessed the efficacy of the top ten candidates for each variant as an inhibitor. Our findings demonstrated for the first time that DrugBank small molecules can interact in three distinct modalities inside the extensive protein-protein interface of RBD and ACE2 complexes. The top ten analyses identified specific DrugBank candidates for each variant and molecules capable of binding to multiple variants. This comprehensive computational technique enables the screening and forecasting of hits for any big and shallow protein-protein interface drug targets.

An integrated machine learning approach delineates an entropic expansion mechanism for the binding of a small molecule to α-synuclein

The mis-folding and aggregation of intrinsically disordered proteins (IDPs) such as α-synuclein (αS) underlie the pathogenesis of various neurodegenerative disorders. However, targeting αS with small molecules faces challenges due to the lack of defined ligand-binding pockets in its disordered structure. Here, we implement a deep artificial neural network-based machine learning approach, which is able to statistically distinguish the fuzzy ensemble of conformational substates of αS in neat water from those in aqueous fasudil (small molecule of interest) solution. In particular, the presence of fasudil in the solvent either modulates pre-existing states of αS or gives rise to new conformational states of αS, akin to an ensemble-expansion mechanism. The ensembles display strong conformation-dependence in residue-wise interaction with the small molecule. A thermodynamic analysis indicates that small-molecule modulates the structural repertoire of αS by tuning protein backbone entropy, however entropy of the water remains unperturbed. Together, this study sheds light on the intricate interplay between small molecules and IDPs, offering insights into entropic modulation and ensemble expansion as key biophysical mechanisms driving potential therapeutics.

Synthesis and Study of the Complex Compound of Isonicotinamide with Zinc Nitrate

A complex compound of zinc nitrate with isonicotinamide was synthesized. The advantages of the mechanochemical (solid-phase) method, the optimal conditions of synthesis are presented IR- and 1Н NMRspectroscopic analysis provide information about ligands and the complex compound formed on their basis, the nature of the bond, central atom surrounding, polyhedra, valence and deformation vibrations, shifts in proton signals. Crystallographic data of the complex compound were obtained using a Malvern Panalytical Empyrean diffractometer. Analysis of the obtained results was carried out using FULLPROF and VESTA programs. When the lengths and angles of the valence bonds were analyzed using the MOGUL program adapted to the MERCURY complex, it was found that there were no bonds and angles with non-standard values between them. The state of the central atomic spatial structure, hybridization, binding of the isonicotinamide molecule and the nitric acid residue to the zinc atom were studied. Based on the data obtained, it was concluded.

Applications of Surface Plasmon Resonance for Advanced Studies Involving Nucleic Acids

Surface plasmon resonance (SPR) is increasingly recognized as one of the most widely used techniques for studying nucleic acid interactions. The main advantage of SPR is its ability to measure the binding affinities and association/dissociation kinetics of complexes in real-time, in a label-free environment, and using relatively small quantities of materials. The method is based on the immobilization of one of the binding partners, ligand, on a dedicated sensor surface. Immobilization is followed by the injection of the other partner, analyte, over the surface containing the ligand. The binding is monitored by subsequent changes in the refractive index of the medium close to the sensor surface upon injection of the analyte. In the field of Nucleic Acid, SPR has been intensively used in the study of various artificial and naturally occurring RNA/DNA molecules interaction with large molecular weight mass proteins and small organic molecules because of its ability to detect highly dynamic complexes that are difficult to investigate using other techniques. This mini review aims to provide a short guideline for setting up SPR experiments to identify nucleic acid complexes and assess their binding affinity or kinetics. It covers protocols for (i) nucleic acid immobilization methods, including biotin-streptavidin, metal ion-based affinity, and amine coupling, (ii) analyte-binding analysis, (iii) affinity and kinetic measurements, and (iv) data interpretation. Determining the affinity and kinetics of nucleic acid interactions through SPR is essential for gaining insights into molecular-level binding mechanisms, thus supporting advancements in nucleic acid nanotechnology. The review also highlights the various sections of SPR applications in nucleic acid research, including nucleic acid-probe immobilization, interactions with biomolecules, aptamer studies, and small molecule binding, concluding with perspectives on future developments in the field.