Binding Affinity Research Articles

Assessing the Inhibitory Potential of Pregnenolone Sulfate on Pentraxin 3 in Diabetic Kidney Disease: A Molecular Docking and Simulation Study.

Diabetic Kidney Disease (DKD), a frequent consequence of diabetes, has substantial implications for both morbidity and mortality rates, prompting the exploration of new metabolic biomarkers due to limitations in current methods like creatinine and albumin measurements. Pentraxin 3 (PTX3) shows promise for assessing renal inflammation in DKD. This study investigates how DKD metabolites could influence PTX3 expression through molecular docking, ADMET profiling, and dynamic simulation. Network and pathway analyses were conducted to explore metabolite interactions with DKD genes and their contributions to DKD pathogenesis. Thirty-three DKD-associated metabolites were screened, using pentoxifylline (PEN) as a reference. The pharmacokinetic properties of these compounds were evaluated through molecular docking and ADMET profiling. Molecular dynamics simulations over 200 ns assessed the stability of PTX3 (apo), the PRE-PTX3 complex, and PEN-PTX3 across multiple parameters. Cytoscape identified 1082 nodes and 1381 edges linking metabolites with DKD genes. KEGG pathway analysis underscored PTX3's role in inflammation. Molecular docking revealed pregnenolone sulfate (PRE) with the highest binding affinity (-6.25 kcal/mol), followed by hydrocortisone (-6.03 kcal/mol) and 2-arachidonoylglycerol (-5.92 kcal/mol), compared to PEN (-5.35 kcal/mol). ADMET profiling selected PRE for dynamic simulation alongside PEN. Analysis of RMSD, RMSF, RG, SASA, H-bond, PCA, FEL, and MM-PBSA indicated stable complex behavior over time. Our findings suggest that increasing PRE levels could be beneficial in managing DKD, potentially through isolating PRE from fungal sources, synthesizing it as dietary supplements, or enhancing endogenous PRE synthesis within the body.

Anticancer Potential of Quercetin on Oral Squamous Cell Carcinoma: A Scoping Review and Molecular Docking.

Oral squamous cell carcinoma (OSCC) is a type of cancer that has a low survival rate and high recurrence and metastasis rates. To date, there is still no effective treatment for OSCC. Various types of cancer, including OSCC, have reported quercetin to act as an anticancer agent, but there is no clear research data on how it may affect OSCC. To determine the anticancer potential of quercetin in OSCC, we conducted a scoping review, and to determine the interaction of quercetin with one of the proteins that plays a role in carcinogenesis, namely, BCL-2, we conducted molecular docking. The scoping review process was conducted based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews. The scoping review was searched by collecting articles related to the research topic in Google Scholar, PubMed, ScienceDirect, Cochrane, and EBSCOhost databases. All of the literature records found during the search were imported into the Mendeley software to remove duplication. Nine studies were generated after the titles and abstracts were reviewed according to the inclusion and exclusion criteria. After the full-text screening, no studies were excluded, leaving nine publications determined to be eligible for inclusion in the scoping review. Quercetin showed effects on inhibiting cancer invasion, migration, proliferation, and many protein expressions, as well as increasing cell apoptosis. Molecular docking was done for quercetin and BCl-2 protein. Doxorubicin was utilized as a comparison ligand. The in silico study was utilized using AutoDock Vina, AutoDock Tools 1.5.6, Biovia Discovery Studio 2021, and PyMol. Molecular docking indicated quercetin has a strong binding affinity with BCl-2 protein (ΔG -7.2 kcal/mol). Both scoping review and molecular docking revealed that quercetin is a promising candidate for anticancer agent.

Computational Workflow to Design Novel Vaccine Candidates and Small-Molecule Therapeutics for Schistosomiasis

Human schistosomiasis, caused by the Schistosoma trematode, is a neglected parasitic disease affecting over 250 million people worldwide. There is no vaccine, and the single available drug is threatened by drug resistance. This study presents a computational approach to designing multiepitope vaccines (MEVs) targeting the cercarial (CMEV) and schistosomular (SMEV) stages of schistosomes, and identifies potential schistosomicidal compounds from the Medicine for Malaria Ventures (MMV) and SuperNatural Database (SND) libraries. The designed vaccines (CMEV and SMEV) are engineered to provoke robust immune responses by incorporating a blend of T- and B-cell epitopes. Structural and immunoinformatics evaluations predicted robust interactions of CMEV and SMEV with key immune receptors and prolonged immune responses. In addition, molecular docking identified several compounds from the MMV and SND libraries with strong binding affinities to vital Schistosoma cathepsin proteases, indicating their potential as schistosomicidal agents. Our findings contribute to the potential development of effective vaccines and drugs against schistosomiasis.

In silico and in vitro evaluation of compounds from Methanol whole extracts of Solanum aculeastrum Dunal berries against benign prostatic hyperplasia and prostate cancer

Background: This study evaluated anti-prostate potentials of compounds from methanol extract of Solanum aculeastrum Dunal berries (MESADB) against benign prostatic hyperplasia (BPH) and prostate cancer (PC). Methods: We used Swiss ADME and pKCSM tools to select drug-like candidates from MESADB. DisGeNET and related databases were used to identify targets for compounds of MESADB, BPH and PC. Molecular roles, biological processes, cellular components involved, and crucial pathways associated with biological processes of gene enrichment were obtained using Gene Ontology (GO) & Kyoto Encyclopedia of Genes and Genomes (KEGG), respectively. Docking was achieved using VINA tool. Antiproliferative and gene expression profiling were determined using 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide (MTT) bioassay, and RT-qPCR respectively, and data analyzed using Graph Pad Prism (version 8.4). Results: Three ideal drug-like candidates [Undecane; D-Arabinitol; and 9-Oxabicyclo [3.3.1] nonan-2-one,6-hydroxy-] were identified. Key targets included TLR4, PTGS2, STAT3, ESR1, MTOR, SRC, MMP9, HDAC1, AKT1 and EGFR. GO analysis revealed key targets were mainly enriched in 601 biological processes (BP), 53 molecular function (MF) and 24 cellular components (CC) terms (p < 0.05). KEGG analysis presented pathways for cancer, pathway of proteoglycans in cancer, amongst others. Docking revealed [D-Arabinitol; and 9-Oxabicyclo [3.3.1] nonan-2-one,6-hydroxy-] demonstrated high binding affinity with PTGS2 and EGFR. MESADB significantly (p < 0.0001) inhibited growth of DU-145 cells with IC50 value and selectivity index of 5.11μg/ml and 14.84, respectively, while sparing Vero CCL-81 cells. There were significant (p < 0.0001) downregulations of EGFR, PTGS2 and BCL-2, in treated DU-145 cells compared to control. Conclusion: MESADB possesses antiprostate potentials.

Design, synthesis, in vitro and in silico studies of novel piperidine derived thiosemicarbazones as inhibitors of dihydrofolate reductase.

Dihydrofolate reductase (DHFR), an essential enzyme in folate metabolism, presents a promising target for drug development against various diseases, including cancer and tuberculosis. Herein, we present an integrated approach combining in vitro biochemical assays with in silico molecular docking analysis to evaluate the inhibitory potential of 4-piperidine-based thiosemicarbazones 5(a-s) against DHFR. In our in vitro study, a novel series of 4-piperidine-based thiosemicarbazones 5(a-s) were assessed for their inhibitory activity against DHFR enzyme. The synthesized compounds 5(a-s) exhibited potent inhibition with IC50 values in the range of 13.70 ± 0.25 µM to 47.30 ± 0.86 µM. Among all the derivatives 5p displayed highest inhibitory activity. Simultaneously, in silico analysis were performed and compared with standard drug (Methotrexate) to predict the binding affinity and interaction pattern of synthesized compounds with DHFR active site. SAR analysis was done to elucidate how structural modifications impact compound's biological activity, guiding the rational design of potent and selective drug candidates for targeted diseases. These findings may provide a comprehensive assessment of 4-piperdine-based thiosemicarbazones as DHFR inhibitors and contribute to the development of novel therapeutics targeting DHFR-associated diseases.

Effects of Dapagliflozin in Combination with Hydrochlorothiazide on Cardiac Remodeling in Rats with Heart Failure After Myocardial Infarction.

In addition to its antihypertensive and diuretic effects, hydrochlorothiazide also demonstrates additional cardioprotective properties; however, the existence of a synergistic interaction between dapagliflozin and hydrochlorothiazide remains unclear.To establish a rat model of heart failure for investigating the effects and mechanisms of dapagliflozin in combination with hydrochlorothiazide during early intervention, H9c2 cells were cultured to validate their in vitro efficacy. The combination group exhibits a synergistic improvement in hemodynamics, ejection fraction, and a reduction in plasma B-type natriuretic peptide concentration. This combination effectively decreases collagen volume fraction and the expression of collagen I and III, p47phox, p67phox, NF-κB p65, Bax, and caspase-3. The combination group demonstrates a synergistic effect in enhancing cardiac function, attenuating oxidative stress and inflammation. The in vitro effects of the combination were demonstrated in H9c2 cardiomyocytes. In addition, the combination exhibits a more pronounced inhibitory effect on NHE1 expression. The expression of NHE1 in H9c2 cells is inhibited by hydrochlorothiazide, thereby alleviating the consequences of NHE1 overexpression. The results of molecular docking and kinetic simulations indicate a strong binding affinity (-6.1 kcal/mol) between hydrochlorothiazide and NHE1, resulting in the formation of a stable conformation. This may elucidate the underlying mechanism responsible for the synergistic effects of drugs.The combination of dapagliflozin and hydrochlorothiazide has synergistic effects on improving cardiac function, oxidative stress, and inflammation in rats with heart failure. Hydrochlorothiazide binds to and inhibits the expression of NHE1, thereby enhancing dapagliflozin's inhibitory effect on NHE activity. This mechanism potentially elucidates its enhanced cardioprotective effects.

Phytol exerts sedative-like effects and modulates the diazepam and flumazenil’s action, possibly through the GABAA receptor interaction pathway

This study aimed at the evaluation of the sedative effect of phytol (PHY) with possible molecular mechanisms through in vivo and in silico studies. For this, adult male mice were randomly divided into six individual groups, namely control (vehicle), two standards (DZP: diazepam at 2 m/kg, FLU: flumazenil at 0.1 mg/kg), three test groups (PHY at 25, 50, and 75 mg/kg), and three combined groups with the DZP-2 and/or FLU-0.1 with PHY-75 mg/kg. After thirty minutes, each animal was treated with thiopental sodium (TS) at 40 mg/kg to produce sedation and observed for latency and duration of sleep up to 4 h. In silico studies were performed with the 6X3X protein of the GABAA receptor α1 and β2 subunits. The results demonstrate that PHY dose-dependently enhanced sleep duration in animals. However, it produced an insignificant sleep duration compared to the control and standard groups. It also significantly (p < 0.05) decreased the latency and increased the duration of sleep with DZP-2, while reducing these parameters with FLU-0.1. In in silico studies, DZP and FLU exhibited binding affinities with 6X3X by −6.8 and −6.9 kcal/mol, respectively, while PHY exhibited −6.9 kcal/mol. Taken together, PHY may exert a sedative-like effect in TS-induced sleeping mice and modulate the effects of DZP and FLU, possibly through interacting with the 6X3X protein of the GABAA receptor. PHY may be one of the good candidates for the management of sleep disturbances, such as insomnia.

Differential expression of ST6GALNAC1 and ST6GALNAC2 and their clinical relevance to colorectal cancer progression.

Colorectal cancer (CRC) has become a significant global health concern and ranks among the leading causes of morbidity and mortality worldwide. Due to its malignant nature, current immunotherapeutic treatments are used to tackle this issue. However, not all patients respond positively to treatment, thereby limiting clinical effectiveness and requiring the identification of novel therapeutic targets to optimise current strategies. The putative ligand of Siglec-15, Sialyl-Tn (STn), is associated with tumour progression and is synthesised by the sialyltransferases ST6GALNAC1 and ST6GALNAC2. However, the deregulation of both sialyltransferases within the literature remain limited, and the involvement of microRNAs (miRNAs) in STn production require further elucidation. Here, we identified miRNAs involved in the regulation of ST6GALNAC1 via a computational approach and further analysis of miRNA binding sites were determined. In silico tools predicted miR-21, miR-30e and miR-26b to regulate the ST6GALNAC1 gene, all of which had shown significant upregulated expression in the tumour cohort. Moreover, each miRNA displayed a high binding affinity towards the seed region of ST6GALNAC1. Additionally, enrichment analysis outlined pathways associated with several cancer hallmarks, including epithelial to mesenchymal transition (EMT) and MYC targets associated with tumour progression. Furthermore, our in silico findings demonstrated that the ST6GALNAC1 expression profile was significantly downregulated in CRC tumours, and its low expression correlated with poor survival outcomes when compared with patient survival data. In comparison to its counterpart, there were no significant differences in the expression of ST6GALNAC2 between normal and malignant tissues, which was further evidenced in our immunohistochemistry analysis. Immunohistochemistry staining highlighted significantly higher expression was more prevalent in normal human tissues with regard to ST6GALNAC1. In conclusion, the integrated in silico analysis highlighted that STn production is not reliant on deregulated sialyltransferase expression in CRC, and ST6GALNAC1 expression is regulated by several oncomirs. We proposed the involvement of other sialyltransferases in the production of the STn antigen and CRC progression via the Siglec-15/Sia axis.

&lt;i&gt;In silico&lt;/i&gt; Pharmacokinetic, Molecular Docking and Molecular Dynamics Simulation Studies of Phytochemicals isolated from &lt;i&gt;Cascabela thevetia&lt;/i&gt; as Potential Anticancer Agents

Cascabela thevetia generally recognized as yellow oleander, Lippold or lucky nut (in English) and Peeli Kaner (in Hindi), is Indigenous to Central America and Mexico and widely distributed in the Indian subcontinent as well, is a medicinally important herb that has long been employed to treat disorders like ulcers, scabies, haemorrhoids, and tumour dissolution. Seven Cardenolides (Compounds 1-7) isolated from fruits of Cascabela thevetia are selected as ligands for in silico pharmacokinetic (ADME properties) and drug-likeness studies via the Swiss ADME online server. Further, molecular docking studies were accomplished for the selected ligands via the Auto Dock Vina module of PyRx to explore the receptor-ligand interaction with β-tubulin (a potential target for anticancer drugs, PDB ID: 1SA0), to find out potential therapeutic ligands for cancer chemotherapy. From the studies performed it was found that most of the ligands (compounds) have the capability of good binding affinity with the receptor, β-tubulin, good drug-likeness and ADME properties among which compounds 3, 6 and 7 are the best drug candidates because they followed the Lipinski rule of 5 with 0 violation and also have good binding affinities (-8.3, -8.0 and -7.9 kcal/mol respectively) against the target protein. Hence, compounds 3, 6 and 7 can be developed as novel therapeutic agents in cancer chemotherapy. Further, a Molecular Dynamics (MD) simulation study of best-docked ligand 3 was performed to establish its stability and validate molecular docking results. Based on simulation results, it may be stated that ligand 3 was firmly attached to the receptor protein during MD simulation since none of the conformations of the receptor-ligand complex were unstable, and no folding or unfolding of the complex took place. Therefore, compound 3 can be considered a good inhibitor of β-tubulin after validation of various parameters of drug discovery.

Investigating the potential impact of ELF3-associated SNPs on chondrocyte inflammation

Objective: Chondrocyte inflammation is a critical factor in degenerative joint diseases, such as osteoarthritis (OA), significantly impairing quality of life through chronic pain and limited mobility. Genetic predisposition is recognized as a critical factor in the progression of chondrocyte inflammation and OA, with particular focus on the role of genetic variants in the expression and regulation of inflammatory mediators. This study aimed to obtain information about the potential roles of a few genes containing ELF3-associated SNPs in the pathogenesis of chondrocyte inflammation. Materials and Methods: GVAT Database was used to select top candidate SNPs associated with ELF3, a cardinal transcription factor in chondrocyte inflammation. Inflammation was induced by IL-1β treatment in differentiated chondrocytes to analyze gene expression patterns. Transcriptome analysis was done by RNA sequencing. Results: The most important SNPs that could potentially affect the binding affinity of ELF3 transcription factor were analyzed. As a result of the analysis, 52% of ELF3-associated SNPs were found in protein-coding regions, 40% in gene-free intergenic regions, and 8% in non-coding RNA sequences. Some of these SNPs are located in regulatory regions (enhancers). A significant increase in expression levels in the ELF3 gene was detected after IL-1β administration, indicating that IL-1β promotes the activity of this transcription factor. mRNA expressions of TLN2, BABAM2, PEPD, and NUDT5 were also increased after IL-1β stimulation. Conclusion: The presence of ELF3-associated SNPs in the enhancer sequences of TLN2 and BABAM2 genes, in addition to the increased expression of these two genes upon IL-1β stimulation, suggested that TLN2 and BABAM2 genes may be associated with the severity of chondrocyte inflammation and OA.

The bioassay tests and mass spectrometry for evaluation of xenoestrogens in tuna fish

Exposure to xenoestrogens through food is a significant concern. These compounds have estrogen-like activity and lead to cell proliferation. In this study, MCF-7 cells were utilized for bioassay tests and evaluation of cell proliferation of extracts prepared from canned tuna fish. First, a pre-screening using the MTT test was done with the solid and liquid parts of the canned tuna fish. It was observed that the proliferation of cells in the solid part of canned tuna cans actually occurs in tuna meat. Therefore, this portion of canned tuna fish was selected for further studies. The binding affinity with ERα and ERβ receptors was determined through RT-qPCR, and the extract was analyzed via mass spectrometry to identify estrogenic components. The study revealed an increased cell proliferation rate upon treatment with the canned tuna fish extract. 17β-estradiol was considered as positive control. The cell proliferation rate ranged from 27 % to 36.6 % compared to 17β-estradiol. Both ERα and ERβ receptors of MCF-7 cells were stimulated almost equally in the sample extract group. Mass spectrometry analysis identified bisphenol A(BPA) and other estrogenic compounds such as phytoestrogens, phthalates, polychlorinated biphenyls, natural and synthetic estrogen hormones. Our findings emphasize the necessity of using a combination of bioassay tests and analytical methods to carefully manage and evaluate the combined estrogenic effects of components in food samples.

Fabrication of a Heptapeptide-Modified Poly(glycidyl Methac-Rylate) Nanosphere for Oriented Antibody Immobilization and Immunoassay

Oriented antibody immobilization has been widely employed in immunoassays and immunodiagnoses due to its efficacy in identifying target antigens. Herein, a heptapeptide ligand, HWRGWVC (HC7), was coupled to poly(glycidyl methacrylate) (PGMA) nanospheres (PGMA-HC7). The antibody immobilization behavior and antigen recognition performance were investigated and compared with those on PGMA nanospheres by nonspecific adsorption and covalent coupling via carbodiimide chemistry. The antibodies tested included bovine, rabbit, and human immunoglobulin G (IgG), while the antigens included horseradish peroxidase (HRP) and β-2-Microglobulin (β2-MG). The nanospheres were characterized using zeta potential and particle size analyzers, scanning electron microscopy, transmission electron microscopy, Fourier transform infrared spectroscopy, and reversed-phase chromatography, proving each synthesis step was succeeded. Isothermal titration calorimetry assay demonstrated the strong affinity interaction between IgG and PGMA-HC7. Notably, PGMA-HC7 achieved rapid and extremely high IgG adsorption capacity (~3 mg/mg) within 5 min via a specific recognition via HC7 without nonspecific interactions. Moreover, the activities of immobilized anti-HRP and anti-β2-MG antibodies obtained via affinity binding were 1.5-fold and 2-fold higher than those of their covalent coupling counterparts. Further, the oriented-immobilized anti-β2-MG antibody on PGMA-HC7 exhibited excellent performance in antigen recognition with a linear detection range of 0–5.3 μg/mL, proving its great potential in immunoassay applications.

Analytical Insights into Methods for Measuring Ischemia-Modified Albumin

Ischemia-modified albumin (IMA) has emerged as a pivotal biomarker for the early detection of ischemic conditions, particularly myocardial ischemia, where timely diagnosis is crucial for effective intervention. This review provides an overview of the analytical methods for assessment of IMA, including Albumin Cobalt Binding (ACB), Albumin Copper Binding (ACuB), Enzyme-Linked Immunosorbent Assay (ELISA), new techniques such as liquid crystal biosensors (LCB), quantum dot coupled X-ray fluorescence spectroscopy (Q-XRF), mass spectrometry (MS), and electron paramagnetic resonance (EPR) spectroscopy. Each method was thoroughly examined for its analytical performance in terms of sensitivity, specificity, and feasibility. The ACB assay is the most readily implementable method in clinical laboratories for its cost-effectiveness and operational simplicity. On the other hand, the ACuB assay exhibits enhanced sensitivity and specificity, driven by the superior binding affinity of copper to IMA. Furthermore, nanoparticle-enhanced immunoassays and liquid crystal biosensors, while more resource-intensive, significantly improve the analytical sensitivity and specificity of IMA detection, enabling earlier and more accurate identification of ischemic events. Additionally, different biological matrices, such as serum, saliva, and urine, were reviewed to identify the most suitable for accurate measurements in clinical application. Although serum was considered the gold standard, non-invasive matrices such as saliva and urine are becoming increasingly feasible due to advances in technology. This review underscores the role of IMA in clinical diagnostics and suggests how advanced analytical techniques have the potential to significantly enhance patient outcomes in ischemic disease management.

Uncovering Intermolecular Interactions Driving the Liquid-Liquid Phase Separation of the TDP-43 Low-Complexity Domain via Atomistic Dimerization Simulations.

Liquid-liquid phase separation (LLPS) of transactive response DNA-binding protein of 43 kDa (TDP-43), which exerts multiple functions in the splicing, trafficking, and stabilization of RNA, mediates the formation of membraneless condensates with crucial physiological roles, while its aberrant LLPS is linked to multiple neurodegenerative diseases. However, due to the heterogeneous and dynamic nature of LLPS, major gaps remain in understanding the precise intermolecular interactions driving LLPS and how specific mutations alter LLPS dynamics. Here, we investigated the molecular mechanisms underlying the LLPS of the TDP-43 low-complexity domain (LCD) by simulating the dimerization process using all-atom discrete molecular dynamics with microsecond-long simulations. Our results showed that the TDP-43 LCD was intrinsically disordered, with helical structures consistent with prior nuclear magnetic resonance studies. Phase separation propensity was assessed by simulating the dimerization of the TDP-43 LCD and four mutants, showing that A321G, W334G, and M337V inhibited self-association, while G335D promoted it, fully consistent with experimental reports. During the dimerization process, two peptides experienced both elastic and nonelastic collisions, and the self-associated dimer featured both high- and low-contact states. These results suggested that the dimerization process of the TDP-43 LCD was accordingly dynamic and heterogeneous. Additionally, we identified crucial regions containing hydrophobic clusters and aromatic residues in the N-terminus, central region, and C-terminus that were essential for the self-association of the TDP-43 LCD. These residues with high binding affinities can act as stickers to form peptide networks in LLPS. Together, our simulation provides a comprehensive picture of the intermolecular interactions driving the phase separation of the TDP-43 LCD, offering insights into both physiological functions and pathological mechanisms.

Expanded Gene Regulatory Network Reveals Potential Light-Responsive Transcription Factors and Target Genes in Cordyceps militaris

Cordyceps militaris, a fungus widely used in traditional Chinese medicine and pharmacology, is recognized for its abundant bioactive compounds, including cordycepin and carotenoids. The growth, development, and metabolite production in various fungi are influenced by the complex interactions between regulatory cascades and light-signaling pathways. However, the mechanisms of gene regulation in response to light exposure in C. militaris remain largely unexplored. This study aimed to identify light-responsive genes and potential transcription factors (TFs) in C. militaris through an integrative transcriptome analysis. To achieve this, we reconstructed an expanded gene regulatory network (eGRN) comprising 507 TFs and 8662 regulated genes using both interolog-based and homolog-based methods to build the protein–protein interaction network. Aspergillus nidulans and Neurospora crassa were chosen as templates due to their relevance as fungal models and the extensive study of their light-responsive mechanisms. By utilizing the eGRN as a framework for comparing transcriptomic responses between light-exposure and dark conditions, we identified five key TFs—homeobox TF (CCM_07504), FlbC (CCM_04849), FlbB (CCM_01128), C6 zinc finger TF (CCM_05172), and mcrA (CCM_06477)—along with ten regulated genes within the light-responsive subnetwork. These TFs and regulated genes are likely crucial for the growth, development, and secondary metabolite production in C. militaris. Moreover, molecular docking analysis revealed that two novel TFs, CCM_05727 and CCM_06992, exhibit strong binding affinities and favorable docking scores with the primary light-responsive protein CmWC-1, suggesting their potential roles in light signaling pathways. This information provides an important functional interactive network for future studies on global transcriptional regulation in C. militaris and related fungi.

Guest‐Induced “Breathing‐Helical” Dynamic System of a Porphyrinic Metallo‐Organic Cage for Advanced Conformational Manipulation

Host‐guest dynamic systems in coordination‐driven metallo‐organic cages have gained significant attentions since their promising applications in chiral separation, drug delivery, and catalytical fields. To maximize guest‐binding affinity, hosts adopting multiple conformations are widely investigated on their structural flexibility for guest accommodation. In this study, a novel metallo‐organic cage S with breathing inner cavity and freely twisted side chains was proposed. Single‐crystal X‐ray diffraction analyses depicted a characteristic “breathing‐helical” dynamic system on the semiflexible framework, which led to an unprecedent co‐crystallisation of racemic and symmetric conformations via the encapsulation locking of C70 guests. By taking advantages of the high binding affinity, selective extraction of C70 was realized. This research provides new ideas for the modification on the helicities of metallo‐organic cages, which could pave a new way for advanced conformational manipulation of supramolecular host systems.

Guest-Induced "Breathing-Helical" Dynamic System of a Porphyrinic Metallo-Organic Cage for Advanced Conformational Manipulation.

Host-guest dynamic systems in coordination-driven metallo-organic cages have gained significant attentions since their promising applications in chiral separation, drug delivery, and catalytical fields. To maximize guest-binding affinity, hosts adopting multiple conformations are widely investigated on their structural flexibility for guest accommodation. In this study, a novel metallo-organic cage S with breathing inner cavity and freely twisted side chains was proposed. Single-crystal X-ray diffraction analyses depicted a characteristic "breathing-helical" dynamic system on the semiflexible framework, which led to an unprecedent co-crystallisation of racemic and symmetric conformations via the encapsulation locking of C70 guests. By taking advantages of the high binding affinity, selective extraction of C70 was realized. This research provides new ideas for the modification on the helicities of metallo-organic cages, which could pave a new way for advanced conformational manipulation of supramolecular host systems.

Revolutionizing Molecular Design for Innovative Therapeutic Applications through Artificial Intelligence

The field of computational protein engineering has been transformed by recent advancements in machine learning, artificial intelligence, and molecular modeling, enabling the design of proteins with unprecedented precision and functionality. Computational methods now play a crucial role in enhancing the stability, activity, and specificity of proteins for diverse applications in biotechnology and medicine. Techniques such as deep learning, reinforcement learning, and transfer learning have dramatically improved protein structure prediction, optimization of binding affinities, and enzyme design. These innovations have streamlined the process of protein engineering by allowing the rapid generation of targeted libraries, reducing experimental sampling, and enabling the rational design of proteins with tailored properties. Furthermore, the integration of computational approaches with high-throughput experimental techniques has facilitated the development of multifunctional proteins and novel therapeutics. However, challenges remain in bridging the gap between computational predictions and experimental validation and in addressing ethical concerns related to AI-driven protein design. This review provides a comprehensive overview of the current state and future directions of computational methods in protein engineering, emphasizing their transformative potential in creating next-generation biologics and advancing synthetic biology.

Expression analysis, molecular docking and molecular dynamics simulations to identify potential BTK inhibitors: strategy for targeting pan-cancer

ABSTRACT Bruton's Tyrosine Kinase (BTK), a soluble tyrosine kinase plays an essential role in the growth, development, and signalling of B cells. It is a non-receptor kinase that is crucial for leukemic cell survival, proliferation, and oncogenic signalling in many B cell malignancies. The enhanced metastasis caused by BTK expression may be reduced by BTK inhibitors, which also have powerful therapeutic effects. The goal of the study is to identify potential inhibitors which have good binding affinity with BTK. The current study also aims to investigate the expression pattern and the prognostic significance of BTK across all cancer types. Interestingly, it was found that BTK was highly overexpressed in numerous cancer types including; clear cell renal carcinoma, glioblastoma, head and neck, liver and breast cancer. BTK was found to reduce the relapse-free and overall survival rate. Furthermore, using in silico approach two structural analogues of Pirtobrutinib namely; 163207918 and 129269825 that bind to BTK with higher affinity were identified. Using drug-likeness analysis the therapeutic possibility of screened Pirtobrutinib analogues were evaluated. The Molecular docking and dynamic analysis revealed that the new Pirtobrutinib analogues could be potent inhibitors with higher binding affinity and stability in comparison with the parent compound. In conclusion, after preclinical and clinical research, the identified analogues may open the door for their prospective use in cancer therapy.

Comparative studies on the interaction of casticin with five digestive enzymes using multi-spectroscopic methods, enzyme activities, and computational simulations

Casticin, which belongs to the flavonoid class, has been studied extensively due to its interesting biological activities. α-Amylase, trypsin, α-chymotrypsin, pepsin and lipase are common digestive enzymes with important physiological functions. In this study, the interactions of casticin with α-amylase, trypsin, α-chymotrypsin, pepsin and lipase were investigated by spectroscopy, enzymology and computational simulations. It has been shown that casticin binds to five digestive enzymes to form casticin-enzyme complexes with weak quenching ability, binding affinity and inhibitory activity. It is elucidated that casticin has different effects on the quenching constants, binding constants, number of binding sites, thermodynamic parameters, conformational microenvironment, secondary structure and binding stability of digestive enzymes. The interactions between casticin and α-amylase, trypsin, α-chymotrypsin, pepsin and lipase are a spontaneous exothermic process driven by enthalpy and entropy, and the binding forces are hydrogen bonds, van der Waals forces and hydrophobic interactions. Computational simulations, including molecular docking and molecular dynamics simulations, were employed to predict the binding model of casticin to these digestive enzymes. In summary, our research provides a theoretical guidance for exploring the role of casticin in pharmacology and biochemistry, which contributes to the understanding of the binding mechanism of casticin to digestive enzymes and its biological activity in vivo.