Binding Patterns Research Articles

GeoNet enables the accurate prediction of protein-ligand binding sites through interpretable geometric deep learning.

The identification of protein binding residues is essential for understanding their functions invivo. However, it remains a computational challenge to accurately identify binding sites due to the lack of known residue binding patterns. Local residue spatial distribution and its interactive biophysical environment both determine binding patterns. Previous methods could not capture both information simultaneously, resulting in unsatisfactory performance. Here, we present GeoNet, an interpretable geometric deep learning model for predicting DNA, RNA, and protein binding sites by learning the latent residue binding patterns. GeoNet achieves this by introducing a coordinate-free geometric representation to characterize local residue distributions and generating an eigenspace to depict local interactive biophysical environments. Evaluation shows that GeoNet is superior compared to other leading predictors and it shows a strong interpretability of learned representations. We present three test cases, where interaction interfaces were successfully identified with GeoNet.

Development of Promising CDK5 Inhibitors Using Structure‐Based Pharmacophore Modeling, Molecular Docking, and Molecular Dynamics Approach

AbstractCancer is highlighted as one of the deadliest diseases globally, with CDK5 identified as a key enzyme in cancer progression. Despite its potential as a therapeutic target, developing CDK5 inhibitors has been challenging. We used multicomplex‐based pharmacophore modeling on CDK5 complexes, identifying hydrophobic groups, hydrogen bond donors, and acceptors as crucial inhibition features. Validated models were used for the virtual screening of drug‐like natural product databases. Thereafter, the screened candidates were selected to study their binding pattern and binding efficiency in the enzyme. Four molecules were shortlisted and analyzed for electrostatic potential (ESP) energy maps. Molecular dynamic simulations and free energy calculations on the docked complexes revealed stable behavior for all, with three (CNP0299652, CNP0362830, and CNP0009633) showing higher Poisson Boltzmann surface area continuum solvation (MM‐PBSA) binding scores than the reference. These candidates demonstrated drug‐like characteristics, crucial amino acid interactions, favorable electron potentials in ESP plots, stable dynamicigher free energy, highlighting their potential as CDK5 inhibitors.

Distinct H3K9me3 heterochromatin maintenance dynamics govern different gene programmes and repeats in pluripotent cells.

H3K9me3 heterochromatin, established by lysine methyltransferases (KMTs) and compacted by heterochromatin protein 1 (HP1) isoforms, represses alternative lineage genes and DNA repeats. Our understanding of H3K9me3 heterochromatin stability is presently limited to individual domains and DNA repeats. Here we engineered Suv39h2-knockout mouse embryonic stem cells to degrade remaining two H3K9me3 KMTs within 1 hour and found that both passive dilution and active removal contribute to H3K9me3 decay within 12-24 hours. We discovered four different H3K9me3 decay rates across the genome and chromatin features and transcription factor binding patterns that predict the stability classes. A 'binary switch' governs heterochromatin compaction, with HP1 rapidly dissociating from heterochromatin upon KMT depletion and a particular threshold level of HP1 limiting pioneer factor binding, chromatin opening and exit from pluripotency within 12 h. Unexpectedly, receding H3K9me3 domains unearth residual HP1β peaks enriched with heterochromatin-inducing proteins. Our findings reveal distinct H3K9me3 heterochromatin maintenance dynamics governing gene networks and repeats that together safeguard pluripotency.

Pharmacological blockade of a pioneer transcription factor.

Cancers frequently co-opt lineage-specific transcription factors (TFs) utilized in normal development to sustain proliferation. However, the effects of these TFs on tumor development depend considerably on where in the genome they bind. A new paper by Taylor and colleagues expands on previously developed diamidine compounds that obstruct the DNA binding sites of the pioneer TF PU.1 (SPI1) in acute myeloid leukemia (AML). Immobilization and sequencing of genomic DNA targeted by these compounds revealed that these inhibitors alter the genomic binding patterns of PU.1. The authors report that their strategy constrains the genomic binding preferences of PU.1, leading to redistribution of PU.1 to promoters and other gene-proximal regions with elevated G/C content. Here we discuss recent developments for targeting PU.1 in hematologic malignancies. We also explore the shared functional roles of PU.1 and SWI/SNF ATP-dependent chromatin remodeling complexes, which work together to sustain the enhancer landscape needed for tumor cell proliferation but also have key roles in non-tumor settings.

ASCL1 regulates and cooperates with FOXA2 to drive terminal neuroendocrine phenotype in prostate cancer.

Lineage plasticity mediates resistance to androgen receptor pathway inhibitors (ARPIs) and progression from adenocarcinoma to neuroendocrine prostate cancer (NEPC), a highly aggressive and poorly understood subtype. ASCL1 has emerged as a central regulator of the lineage plasticity driving neuroendocrine differentiation. Here, we showed that ASCL1 was reprogrammed in ARPI-induced transition to the terminal NEPC and identified that the ASCL1 binding pattern tailored the expression of lineage-determinant transcription factor combinations that underlying discrete terminal NEPC identity. Notably, we identified FOXA2 as a major co-factor of ASCL1 in terminal NEPC, which is highly expressed in ASCL1-driven NEPC. Mechanistically, FOXA2 and ASCL1 interacted and worked in concert to orchestrate terminal neuronal differentiation. We identified that Prospero-Related Homeobox 1 was a target of ASCL1 and FOXA2. Targeting prospero-related homeobox 1 abrogated neuroendocrine characteristics and led to a decrease in cell proliferation in vitro and tumor growth in vivo. Our findings provide insights into the molecular conduit underlying the interplay between different lineage-determinant transcription factors to support the neuroendocrine identity and nominate prospero-related homeobox 1 as a potential target in ASCL1 high NEPC.

Ribosomal A site binding pattern differs between Arm methyltransferases from clinical pathogens and a natural producer of aminoglycosides

The extensive use of aminoglycosides to treat bacterial infections has led to significant resistance, posing a global health threat. Recent clinical reports highlight high levels of aminoglycoside resistance due to Arm/Kam methyltransferases, which methylate specific nucleotides in 16S rRNA, preventing antibiotic binding to the ribosome. This study compared the ribosomal A site binding patterns of Arm methyltransferases from clinical pathogens (ArmA, RmtB, RmtC, and RmtD) with those of the Sgm methyltransferase from a natural aminoglycoside producer. We introduced single mutations near the G1405 nucleotide in helix 44 of 16S rRNA to assess their impact on the methylation ability of Arm methyltransferases in E. coli cells with homogeneous mutant ribosomes. We evaluated how these mutations affected bacterial viability in cells with mixed and homogeneous ribosome populations and determined the minimal inhibitory concentration of kanamycin to assess their impact on Arm enzyme activity. Notably, Sgm methyltransferase exhibited a distinct methylation pattern compared to Arm methyltransferases from clinical strains. Structural comparisons of Sgm, RmtB, and RmtC revealed different spatial orientations of key amino acids involved in ribosomal binding, highlighting evolutionary differences. This research enhances understanding of Arm methyltransferases and lays the groundwork for designing inhibitors to combat this potent form of antibiotic resistance.

Arylcarboxamide Derivatives as Promising HDAC8 Inhibitors: An Overview in Light of Structure-activity Relationship and Binding Mode of Interaction Analysis

Abstract: HDAC8 is associated with several disease conditions as well as various cancers of several organs and hematological malignancies. To counter such pathophysiological and disease conditions, inhibition of HDAC8 may be a promising approach for anticancer drug development. In this article, a detail of arylcarboxamide-based potential HDAC8 inhibitors has been outlined. Considering their binding pattern of interactions along with the chemical features, effective and selective novel HDAC8 inhibitors can be designed further. Therefore, modification of these compounds provides greater possibilities for the development of novel HDAC8 inhibitors. Nevertheless, structural modification of such arylcarboxamide derivatives may be able to produce potent dual-inhibitory compounds along with HDAC8 inhibition. Thus, this article is quite useful for exploring and identifying several possibilities for arylcarboxamide-based HDAC8 inhibitors. Moreover, it can be concluded that further study of the arylcarboxamide-based HDAC8 inhibitors can be effectively used for the treatment of different cancerous and non-cancerous diseases.

Two-Dimensional Covalent Organic Frameworks: Structural Insights across Different Length Scales and Their Impact on Photocatalytic Efficiency.

ConspectusCovalent organic frameworks (COFs) are a rapidly emerging class of crystalline porous polymers, characterized by their highly defined, predictable, and tunable structure, porosity, and properties. COFs can form both two-dimensional (2D) and three-dimensional (3D) architectures, each with unique characteristics and potential applications. 2D COFs have attracted particular interest due to their favorable structural and optoelectronic properties. They can be equipped with a range of different functional moieties in their backbone, ranging from acidic to basic, from hydrophilic to hydrophobic, and from metal-coordinating to redox-active functions. In addition, their crystallinity, high specific surface area, and remarkable thermal and chemical stability make them attractive for a variety of applications, including gas separation, catalysis, energy storage, and optoelectronics.This Account provides a detailed overview of our recent efforts to synthesize and apply 2D COFs. First, various synthesis routes are discussed, focusing on methods that involve reversible and irreversible linkage reactions. Reversible reactions, such as imine or boronate ester formation, are advantageous for producing highly crystalline COFs because they allow for error correction during synthesis. In contrast, irreversible reactions, such as carbon-carbon or carbon-nitrogen bond formation, yield COFs with greater chemical stability, although controlling crystallinity can be more challenging. Our group has contributed significantly to refining these methods to balance crystallinity and stability, enhancing the performance of the resulting 2D COFs.In addition to different binding patterns, we have also developed strategies to control the micro- and macromorphologies of COFs, which is crucial for optimizing their properties for specific applications. For example, we have explored the synthesis of hierarchical porous COFs by using templating techniques or by forming composites with other functional materials. These strategies enable us to fine-tune the porosity and surface properties of COFs, thereby improving their performance in applications like catalysis. Hierarchical structures in particular enhance photocatalytic efficiency by providing a larger surface area for light absorption and facilitating the transport of photogenerated charge carriers.We further examine the practical applications of 2D COFs, with a primary focus on photocatalysis. Photocatalysis uses light to enable or accelerate chemical reactions, and 2D COFs are ideal for this purpose due to their tunable band gaps and large surface areas. Our research has shown that 2D COFs are highly versatile photocatalysts that can effectively catalyze reactions such as water splitting, carbon dioxide reduction, hydrogen peroxide formation, and cross-coupling reactions. By exploiting the unique properties of 2D COFs, we have achieved significant improvement in many photocatalytic reactions.With this comprehensive overview, we aim to contribute to the further development and understanding of 2D COFs and encourage further research and innovation in this promising field.

In-vitro and in-silico studies based discovery of 2-aryl-N-(4-morpholinophenyl)thiazol-4-amines as promising DNA gyrase inhibitors

Background: DNA gyrase is an important enzyme for the survival of bacteria. Many DNA gyrase inhibitors are in clinical practice. However, these inhibitors also encompass certain toxic and drug/food interactions. This warrants the development of a new template as DNA gyrase inhibitors. Therefore, this study aimed to deliver morpholine-based thiazoles (5a-5l) as safer DNA gyrase inhibitors.Methods: The 5a-5l were prepared by reacting compound 3 with various aryl thioamides. The structures of 5a-5l were ascertained by their spectral records. The 5a-5l were subjected to their antibacterial activity potential (serial plate dilution method), DNA gyrase inhibiting activity, and toxicity analysis (MTT assay) against HepG2 & Vero cell lines. The in-silico studies (pharmacokinetic parameters and molecular docking) of 5a-5l were likewise performed.Results: It was surprisingly observed that the MIC values of 5a-5l were equal to the MIC values of ciprofloxacin (12.5 µg/ml) against the tested bacteria, whereas the DNA gyrase inhibitory activity (IC50 in µg/ml) of 5h (3.52), 5g (3.76), 5f (3.88), 5e (4.08), 5l (4.11), 5b (4.28), 5k (4.28), 5i (4.30), and 5d (4.32) was equal/better than ciprofloxacin (4.32). The MTT assay also implied the non-cytotoxic nature of 5a-5l against HepG2 & Vero cell lines up to 200 µg/ml concentration. The docking outcomes indicated a similar binding pattern of 5a-5l and ciprofloxacin at the active site of DNA gyrase, wherein 5a-5l displayed a better binding affinity for the active site. The in-silico toxicity data employing the ProTox-II web server indicated no hepatotoxicity, carcinogenicity, immunotoxicity, mutagenicity, or cytotoxic effect of 5a-5l. Also, the SwissADME software supported the drug-likeliness properties and high gastrointestinal absorption of 5a-5l.Conclusion: Compounds 5h, 5g, 5f, 5e, 5l, 5b, 5k, 5i, and 5d are potent DNA gyrase inhibitors with promising safety profiles.Keywords: Discovery; Morpholine; Thiazole; DNA gyrase; MTT assay; Docking

Evaluation of a multiplexed immunoassay for assessing long-term humoral immunity Orthopoxviruses

BackgroundThe 2022 Monkeypox virus (MPXV) global outbreak boosted development of multiple serological assays to aid understanding of Mpox immunology. ObjectivesThe study aimed to assess a multiplexed solid-phase electrochemiluminescence immunoassay (Meso Scale Discovery (MSD)) for simultaneous detection of antibodies against MPXV, including A35, E8 and M1 antigens, along with corresponding Vaccina Virus (VACV) homologues and demonstrate its accuracy in assessing antibody titres post-vaccination and infection. MethodsAssay performance was assessed for simultaneous detection of antibodies against MPXV and corresponding VACV antigens. Sensitivity and specificity were evaluated with paediatric negatives (n = 215), pre- and post-IMVANEX vaccinated (n = 80), and MPXV (Clade IIb, n = 39) infected serum samples. ResultsThe assay demonstrated high specificity (75.68 % (CI: 69.01–81.29) - 95.98 % (CI:92.54–97.87)) and sensitivity (62.11 % (CI:52.06–71.21) - 98.59 % (CI:92.44 %–99.93 %)) depending on the Orthopoxvirus antigen. Preferential binding was observed between MPXV-infected individuals and MPXV antigens, while vaccinated individuals exhibited increased binding to VACV antigens. These results highlight differential binding patterns between antigen homologues in related viruses. ConclusionOverall, this assay demonstrates high sensitivities in detecting antibodies for multiple relevant MPXV and VACV antigens post-infection and post-vaccination, indicating its utility in understanding immune responses to Orthopoxviruses in current and future outbreaks and evaluating the immunogenicity of new-generation Mpox-specific vaccinations.

The mouse monoclonal antibody 4E3 is specific for the G1m17 allotype of human IgG1

Allotype is an amino acid variation within the immunoglobulin isotypes. Four allotypes have been described for human IgG1 and two of them (G1m3 and G1m17) are located at position 214 in the CH1 region of the gamma chain. Various diseases have been associated with allotype expression, making the allotype research an interesting field in immunology. However, allotype-specific reagents are rare. In the present study the specificity of a widely used and commercially available IgG1-specific monoclonal antibody named 4E3, described as binding to the hinge region of IgG1, was evaluated. Using the ImmunoCAP™ assay technology, surprisingly no IgG1 was measured in 13 of 23 human serum and plasma samples when 4E3 was used in an antibody-enzyme conjugate as detection reagent. Further evaluation of 4E3 using eight IgG1 myeloma paraproteins revealed that 4E3 did not bind to three of them. No association was seen between the binding pattern and myeloma light chain glycosylation or the kappa or light chain use. By comparing the myeloma paraprotein binding patterns of 4E3 and TM14 (a monoclonal antibody with known G1m3 specificity), it was indicated that 4E3 only bound to myeloma paraproteins expressing the G1m17 allotype. This was confirmed using recombinant human antibodies expressing either the G1m3 or G1m17 allotype. The G1m17 bias of 4E3 seen using ImmunoCAP was also observed in microtiter plate-based enzyme-linked immunosorbent assays. The antibody 4E3 has a G1m17 bias limiting its use in assays to measure IgG1 antibodies. However, it may be a valuable allotype-specific reagent.

Adsorption of Proteins onto Nitrocellulose Membranes from a Flowing Solution – Theory and Experiment

Some analytical laboratory procedures involve passing the sample through a porous polymer membrane. In this process, the analyte binds to the surface of the membrane modified with a specific receptor layer and is then detected using optical or electrochemical signals. This paper presents an experimental and theoretical analysis of the binding patterns of the analyte to nitrocellulose membranes. Two cases are considered: specific binding of the analyte to antibodies immobilized on the membrane and non-specific adsorption of the analyte. It is shown that increasing the volume of the sample passed through the membrane leads to an increase in the amount of adsorbed analyte, and this can generally be used to improve the sensitivity of biosensors.

Discovery, recognized antigenic structures, and evolution of cross-serotype broadly neutralizing antibodies from porcine B-cell repertoires against foot-and-mouth disease virus.

It is a great challenge to isolate the broadly neutralizing antibodies (bnAbs) against foot-and-mouth disease virus (FMDV) due to its existence as seven distinct serotypes without cross-protection. Here, by vaccination of pig with FMDV serotype O and A whole virus antigens, we obtained 10 bnAbs against serotypes O, A and/or Asia1 by dissecting 216 common clonotypes of two serotype O and A specific porcine B-cell receptor (BCR) gene repertoires containing total 12720 B cell clones, indicating the induction of cross-serotype bnAbs after sequential vaccination with serotypes O and A antigens. The majority of porcine bnAbs (9/10) were derived from terminally differentiated B cells of different clonal lineages, which convergently targeted the conserved "RGDL" motif on structural protein VP1 of FMDV by mimicking receptor recognition to inhibit viral attachment to cells. Cryo-EM complex structures revealed that the other bnAb pOA-2 specifically targets a novel inter-pentamer antigen structure surrounding the viral three-fold axis, with a highly conserved determinant at residue 68 on VP2. This unique binding pattern enabled cross-serotype neutralization by destabilizing the viral particle. The evolutionary analysis of pOA-2 demonstrated its origin from an intermediate B-cell, emphasizing the crucial role of somatic hypermutations (SHMs) in balancing the breadth and potency of neutralization. However, excessive SHMs may deviate from the trajectory of broad neutralization. This study provides a strategy to uncover bnAbs against highly mutable pathogens and the cross-serotype antigenic structures to explore broadly protective FMDV vaccine.

A novel investigation of NANOG and POU5F1 associations in the pluripotent characterization of ES-like and epiblast cells

The transcription factors NANOG and POU5F1 (OCT4) play crucial roles in maintaining pluripotency in embryonic stem (ES) cells. While their functions have been well-studied, the specific interactions between NANOG and POU5F1 and their combined effects on pluripotency in ES-like and Epiblast cells remain less understood. Understanding these associations is vital for refining pluripotent stem cell characterization and advancing regenerative medicine. In this matter, we investigated the associations between NANOG and POU5F1 in maintaining pluripotency in ES-like and Epiblast cells and how these interactions contribute to the distinct pluripotent states of these cells. In the present paper, we examined the pattern of NANOG expression by the immunocytochemical method in embryonic stem-like (ES-like) cells and compared it with its expression pattern in embryonic stem cells (ESCs). Similarly, we examined the expression pattern of POU5F1 in ES-like cells, ESCs, and epiblast cells and compared the expression pattern of these two genes with each other. On the other hand, using Fluidigm Biomark system analysis, we compared the amount of NANOG mRNA in these three cell lines and differentiated and undifferentiated Spermatogonial stem cells in several passages. Microscopic observations indicated the cytoplasmic expression of NANOG in the considered cells; moreover, they showed a similar expression pattern of NANOG with POU5F1 in the experimented cells. It has also been suggested that the more limited the cell’s pluripotency, the lower the expression of these two genes. However, the decrease in NANOG expression is less than that of POU5F1. Fluidigm real-time RT-PCR analysis also confirmed these results. During the experimental process, protein-protein (PPI) network analysis shows a significant association of NANOG with other stem cell proteins, such as POU5F1. Our findings reveal distinct yet overlapping roles of NANOG and POU5F1 in maintaining pluripotency in ES-like and Epiblast cells. The differential binding patterns and functional interactions between these factors underscore the complexity of pluripotency regulation in different stem cell states. This study provides new insights into the molecular mechanisms governing pluripotency and highlights potential targets for enhancing stem cell-based therapies.

From unbound to bound states: Ab initio molecular dynamics of ammonia clusters with an excess electron.

Ab initio molecular dynamics simulations of negatively charged clusters of 2-48 ammonia molecules were performed to elucidate the electronic stability of the excess electron as a function of cluster size. We show that while the electronic stability of finite temperature clusters increases with cluster size, as few as 5-7 ammonia molecules can bind an excess electron, reaching a vertical binding energy slightly less than half of the bulk value for the largest system studied. These results, which are in agreement with previous studies wherever available, allowed us to analyze the excess electron binding patterns in terms of its radius of gyration and shape anisotropy and provide a qualitative interpretation based on a particle-in-a-spherical-well model.

The development of single-domain VHH nanobodies that target the Candida albicans cell surface.

Candida albicans causes life-threatening invasive infections that are hard to diagnose and treat, with drug resistance leading to treatment failure. The goal of this study was to develop VHH (single variable domain on a heavy chain) nanobodies to detect drug-resistant infections. Llamas were immunized with a mixture of heat killed and fixed C. albicans cells of different morphologies. Llama lymphocyte RNA was used to generate phage display libraries that were tested for binding to C. albicans cells or cell wall fractions, and single antibody domains were isolated. The libraries were panned against echinocandin-resistant C. albicans isolates and counter-selected against echinocandin-susceptible isolates with the aim of isolating binding domains specific for antigens on drug-resistant cells. Thirty diverse VHH nanobodies were selected, and binding characteristics were assessed via dose-response ELISA. Binding was tested against a variety of C. albicans isolates and other Candida species, indicating that the VHHs were specific for C. albicans. The VHH nanobodies were sorted into four distinct groups based on their binding patterns. Two of the groups bound preferentially to the yeast cell poles and hyphae, respectively. Nanobody binding to C. albicans deletion mutants was tested by fluorescence microscopy and ELISA to identify the antigen targets. VHH19 nanobody, belonging to the largest group, recognized the Als4 adhesin. VHH14 antibody in the hyphae-specific group recognized Als3. None of the isolated VHH nanobodies was selective for drug-resistant clinical isolates. Our data indicate that this approach can generate valuable single-domain antibodies specific to C. albicans proteins.IMPORTANCEThe human fungal pathogen Candida albicans causes a range of diseases from superficial mucosal infections such as oral and vaginal thrush to life-threatening, systemic infections. Accurate and rapid diagnosis of these infections remains challenging, and currently, there are no rapid ways to diagnose drug-resistant infections without performing drug susceptibility testing from blood culture, which can take several days. In this proof-of-concept study, we have generated a diverse set of single domain VHH antibodies (nanobodies) from llamas that recognize and bind specifically to C. albicans cell surface. The nanobodies were classified into four groups based on their binding patterns, for example, cell poles or hyphae. Specific nanobodies were verified as recognizing the important adhesin Als4 or the hyphae associated invasin Als3, respectively. The data validate the approach that small VHH antibody domains hold future promise for diagnostic applications and as probes to study the fungal cell surface.

FTIR, 1H-/13C-NMR spectral characterization, antimicrobial, anticancer, antioxidant, anti-inflammatory, PASS, SAR, and in silico properties of methyl α-D-glucopyranoside derivatives

A novel series of biologically active derivatives based on methyl α-D-glucopyranoside (MGP) has been developed, comprising 6-O-monosubstituted MGP derivatives obtained from methyl α-D-glucopyranoside. These derivatives were transformed into 2,3,4-tri-O-acyl MGP derivatives, incorporating diverse functionalities within a single molecular framework, aimed at producing new products for antimicrobial studies. All synthesized compounds were identified through spectral analyses (FTIR, 1H-NMR, and 13C-NMR) and elemental analysis. Antimicrobial in vitro testing revealed that these MGP derivatives have notable efficacy against various pathogenic microorganisms, along with the prediction of activity spectra for substances (PASS). Compounds 2 and 7 exhibited the highest inhibitory activity against Bacillus subtilis and Escherichia coli, with minimum inhibitory concentration (MIC) values ranging from 0.25 to 64.0 µg/mL and minimum bactericidal concentration (MBC) values ranging from 8.0 to 128.0 µg/mL. Moreover, these compounds demonstrated significant antioxidant properties compared with those of standard antioxidants according to the results of the DPPH free radical scavenging assay. An evaluation of the growth and proliferation of Ehrlich ascites carcinoma (EAC) cells revealed moderate cell growth inhibition by compounds 5 and 6, with IC50 values of 5958.54 and 5437.17 µg/mL, respectively, as determined via an MTT colorimetric assay. An analysis of the structure-activity relationship (SAR) revealed that the combination of the (p-CH3.C6H4CO-) and halo-aromatic [3-Cl.C6H4CO-] chains with sugar had the highest efficiency in pathogens. Molecular docking studies using AutoDock Vina highlighted compound 7 as a promising inhibitor of the carbapenemase, OmpF, and HmoB proteins, with binding energies of -11.53 kcal/mol, -2.26 kcal/mol, and -30.75 kcal/mol, respectively. A 100-ns molecular dynamics simulation study demonstrated the validity of stable conformation and binding patterns in a stimulating environment. Pharmacokinetic characterization and ADMET predictions indicated favorable drug-like properties. These substantial in vitro and in silico studies demonstrate the importance of additional investigations to confirm the efficacy of MGP derivatives as antimicrobial agents.

Molecular Docking and Molecular Dynamics Simulations of the Urease Inhibitory Activity of 2,3‐Dihydroxybenzohydrazide Derivatives

AbstractThis investigation focuses on a suite of 2,3‐dihydroxybenzoyl hydrazine derivative ligands, examining their viability as urease activity inhibitors and delving into their operative mechanisms. Utilizing molecular docking approaches, the binding patterns and interactive loci of 2,3‐dihydroxybenzoyl hydrazine derivatives with urease were elucidated. The origin of the binding forces between the ligands and urease, along with pertinent descriptors, were scrutinized through an amalgamation of density functional theory calculations and molecular dynamics simulations. The findings indicate that the HOMO‐LUMO energy gap, the dipole moment, and the electrostatic potential serve as robust descriptors of the inhibitory activity exhibited by 2,3‐dihydroxybenzoyl hydrazine derivative ligands against urease. The ligand designated BH‐k emerged as the most efficacious urease inhibitor, with critical hydrogen bonds forming between it and the residues His409, Ala636, and Asp633, in addition to hydrophobic interactions with Arg439. The design of ligands capable of establishing additional hydrogen bonds constitutes an effective strategy to amplify inhibitory efficacy. The results of this research aspire to lay a theoretical foundation for the advancement of novel urease inhibitor designs to counteract health issues emanating from aberrant urease activity.

ANTIPASTI: Interpretable prediction of antibody binding affinity exploiting normal modes and deep learning.

The high binding affinity of antibodies toward their cognate targets is key to eliciting effective immune responses, as well as to the use of antibodies as research and therapeutic tools. Here, we propose ANTIPASTI, a convolutional neural network model that achieves state-of-the-art performance in the prediction of antibody binding affinity using as input a representation of antibody-antigen structures in terms of normal mode correlation maps derived from elastic network models. This representation captures not only structural features but energetic patterns of local and global residue fluctuations. The learnt representations are interpretable: they reveal similarities of binding patterns among antibodies targeting the same antigen type, and can be used to quantify the importance of antibody regions contributing to binding affinity. Our results show the importance of the antigen imprint in the normal mode landscape, and the dominance of cooperative effects and long-range correlations between antibody regions to determine binding affinity.

Beyond RNA binding domains: determinants of protein-RNA binding.

RNA binding proteins (RBPs) are composed of RNA binding domains (RBDs) often linked via intrinsically disordered regions (IDRs). Structural and biochemical analysis have shown that disordered linkers contribute to RNA binding by orienting the adjacent RBDs and also characterized certain disordered repeats that directly contact the RNA. However, the relative contribution of IDRs and predicted RBDs to the in-vivo binding pattern is poorly explored. Here, we upscaled the RNA tagging method to map the transcriptome-wide binding of sixteen RBPs in budding yeast. We then performed extensive sequence mutations to distinguish binding determinants within predicted RBDs and the surrounding IDRs in eight of these. The majority of the predicted RBDs tested were not individually essential for mRNA binding, while multiple IDRs that lacked predicted RNA binding potential appeared essential for binding affinity or specificity. Our results provide new insights into the function of poorly studied RBPs and emphasize the complex and distributed encoding of RBP-RNA interaction in-vivo.