S Chandrasekhar, K N N Prasad, S Balasaraswathy, M S Raghu, M K Prashanth, Fahd Alharethy, Byong-Hun Jeon
{"title":"A comprehensive multispectroscopic and molecular docking studies on the interaction of bioactive coumarins with bovine serum albumin.","authors":"S Chandrasekhar, K N N Prasad, S Balasaraswathy, M S Raghu, M K Prashanth, Fahd Alharethy, Byong-Hun Jeon","doi":"10.1080/07391102.2025.2490792","DOIUrl":"https://doi.org/10.1080/07391102.2025.2490792","url":null,"abstract":"<p><p>The investigation focused on the interaction between bovine serum albumin (BSA) and the biologically active coumarin derivatives 4-(5-amino-[1,3,4]thiadiazol-2-ylsulfanylmethyl)-7-methoxy-chrome-2-one (1) and 4-(5-amino-[1,3,4]thiadiazol-2-ylsulfanyl methyl)-7-methyl-chrome-2-one (2). Molecular docking approaches, synchronous fluorescence spectroscopy, UV-Vis spectroscopy, circular dichroism (CD) spectra and fluorescence spectroscopy were among the multispectroscopic methods used to study the interaction between BSA and coumarin derivatives. The examined coumarin compounds' interaction with BSA yielded a static quenching mechanism for fluorescence. Values for the binding constant (<i>K</i><sub>b</sub>) and quenching constant (<i>K</i><sub>q</sub>) for BSA-coumarin derivatives have been calculated using the Stern-Volmer equation. A change in the tryptophan residue of BSA was seen in its surroundings using synchronous fluorescence quenching investigations. The potential of the compounds under investigation to bind BSA was examined, and it was found that each compound had around one binding site. According to the free energy estimate, there is a spontaneous and very favorable binding interaction between BSA and test compounds. Using the Forster energy transfer theory, the binding average distance between BSA and the chemicals under investigation was found. In conjunction with the findings of CD spectral and fluorescence investigations, it shown that compound 2 has a higher affinity for BSA than compound 1. Molecular docking studies and spectroscopic experimental data are found to be in good agreement. The binding pocket for the development of the ligand-protein complex through hydrophobic and hydrogen bonding interactions was identified by the molecular docking investigation. Furthermore, the results of the Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) prediction and drug-likeness analysis demonstrated the medicinal chemistry characteristics and drug-likeness of these compounds.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-12"},"PeriodicalIF":2.7,"publicationDate":"2025-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144026314","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"<i>In silico</i> analysis of plumbagin's interaction with caspase 9: unveiling its potential as an anti-NSCLS agent.","authors":"Mohd Saeed, Samra Siddiqui, Munazzah Tasleem, Md Jahoor Alam, Saad Saeed Alqathani, Fevzi Bardakci, Nujud Almuzaini, Tarun Kumar Upadhyay, Rania Abdeen Hussain Abdalla, Farrukh Aqil","doi":"10.1080/07391102.2025.2487190","DOIUrl":"https://doi.org/10.1080/07391102.2025.2487190","url":null,"abstract":"<p><p>Lung cancer is one of the leading causes of cancer-related deaths worldwide. Non-Small Cell Lung Cancer (NSCLC) represents a predominant subset of lung cancer cases with a pressing need for innovative therapeutic strategies. Plumbagin, a naturally occurring naphthoquinone, has been investigated for its pharmacokinetic properties and potential anti-cancer effects, particularly against NSCLC. This study encompasses <i>in-silico</i> analysis of plumbagin's pharmacokinetic profile, its molecular interaction with the caspase-9 protein, and a subsequent molecular dynamic simulation to assess the stability of this interaction. Our findings demonstrate that plumbagin exhibits commendable drug-likeness properties in line with Lipinski's rule of five, Veber's criteria, and Ghose's criteria. Molecular docking results highlight its promising binding affinity to caspase-9 with a docking score of -5.3 kcal/mol. Molecular dynamic simulations further substantiate the stability of this protein-ligand complex. Collectively, these results emphasize plumbagin's potential as a caspase activator against NSCLC, emphasizing the need for in-depth biological studies to further validate these findings.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-11"},"PeriodicalIF":2.7,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144019101","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Molecular dynamics simulations reveal R399Q mutation disrupts XRCC1-polβ interaction, potentially impairing DNA base excision repair pathway.","authors":"Nabajyoti Goswami, Rupam Dutta, Rene Barbie Browne, Probodh Borah, Saurov Mahanta, Subhash Medhi","doi":"10.1080/07391102.2025.2481591","DOIUrl":"https://doi.org/10.1080/07391102.2025.2481591","url":null,"abstract":"<p><p>Mutations in XRCC1 can disrupt essential protein-protein interactions required for DNA base excision repair, potentially leading to genomic instability and increased cancer risk. This study employs large-scale molecular dynamics simulations to investigate the structural and functional consequences of the R399Q mutation on interactions with DNA ligase IIIα and DNA polymerase β. The results reveal that while the mutant protein retains a stable interaction with DNA ligase IIIα, key residues such as Gly 511, Glu 538, Arg 564, Thr 567 and Ala 568, which form critical hydrogen bonds, exhibit subtle rearrangements. In contrast, binding to DNA polymerase β is significantly destabilized, disrupting key interactions involving Glu 85, Ser 92, Arg 109 and Gly 556. Free energy calculations confirm a substantial reduction in binding affinity between the mutant protein and DNA polymerase β, suggesting an impaired repair efficiency. Unlike previous studies that relied on static structural models or biochemical characterizations, this research provides dynamic, atomic-level insights into how the mutation alters protein stability and interactions over biologically relevant timescales. These findings reconcile conflicting experimental observations and establish a computational framework for understanding mutation-driven defects in DNA repair. Interestingly, the data generated by these extensive simulations resemble empirical findings regarding XRCC1's interactions with BER enzymes. The study thus provides valuable insights into how the R399Q mutation impairs XRCC1's interactions with key DNA repair enzymes, potentially leading to defects in the DNA repair pathway and offering a computational perspective that aligns with experimental observations.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-22"},"PeriodicalIF":2.7,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144020210","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chen Zhang, Guoqiang Song, Wanhui Di, Ying Gao, Shan Chang, Zhou Chen, Long Tang, Ren Kong
{"title":"Identify natural compounds as novel phosphodiesterase-2A inhibitors.","authors":"Chen Zhang, Guoqiang Song, Wanhui Di, Ying Gao, Shan Chang, Zhou Chen, Long Tang, Ren Kong","doi":"10.1080/07391102.2025.2487193","DOIUrl":"https://doi.org/10.1080/07391102.2025.2487193","url":null,"abstract":"<p><p>Phosphodiesterase-2A (PDE2A) is a potential therapeutic target for the treatment of ganglion dysfunction-related diseases such as Alzheimer's disease, schizophrenia, cognitive impairment, anxiety, and depression. However, most current PDE2A inhibitors have moderate selectivity compared to other PDEs. In this study, we described the discovery of 6 novel PDE2A inhibitors by bioassays, molecular docking, and molecular dynamics simulations. Six molecules out of 2592 compounds from the L6000-Natural Compound Library inhibited PDE2A with affinity ranging from 4.03 to 39.84 μM. Selective experiments were carried out on PDE4D, PDE5A, PDE9A, and PDE10A, among which 5-5H and 16-2H exhibited good dual inhibition against both PDE2A and PDE4D. Their IC<sub>50</sub> values for PDE2A were 4.03 and 9.08 μM, respectively, and for PDE4D they were 3.89 and 10.96 μM, respectively. Molecular docking and molecular dynamics simulation were used to explore the binding modes of active compounds with PDE2A. It is shown that in addition to the common interactions with Gln859 and Phe862 of PDE2A, 6 molecules formed extra hydrogen bonds with Ile826 and Leu809. These molecules may serve as starting points for further optimization of selective PDE2A inhibitors.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-10"},"PeriodicalIF":2.7,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144009339","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Designing new pharmaceutical derivatives for potential inhibition of human immunodeficiency virus protease enzyme inhibition; a comprehensive <i>in silico</i> study.","authors":"Mehdi Yoosefian","doi":"10.1080/07391102.2025.2490791","DOIUrl":"https://doi.org/10.1080/07391102.2025.2490791","url":null,"abstract":"<p><p>In the ongoing effort to address viral diseases, the utilization of enzyme inhibitors targeting viral enzymes has emerged as a notable and effective strategy. The prevalence of hazardous and potentially fatal viral infections, such as Acquired Immunodeficiency Syndrome (AIDS), emphasizes the importance of exploring these inhibitors to advance healthcare solutions. This study conducts a comprehensive examination of the interaction between Indinavir and HIV protease, evaluating the functional efficacy of designed analogs based on Indinavir using docking tools. Quantum mechanics calculations are used for precise analysis of the structural and molecular properties of each designed analog. Additionally, ADMET studies for these compounds are examined to increase the evaluation of potential side effects and physicochemical properties. Molecular dynamics simulations are performed to deepen understanding and evaluate the inhibitory potential of these compounds on the protease enzyme. In conclusion, this comprehensive approach, integrating quantum mechanics calculations, ADMET screening, molecular docking, and molecular dynamics aims to enhance results in the development of antiviral candidates and refinement of existing drugs. Results introduce Lig12 as a designed compound that shows higher enzyme inhibition ability compared to Indinavir. This study emphasizes the importance of innovative drug design approaches in addressing the evolving challenges posed by viral infections. However, it is imperative to acknowledge the necessity for further experimental validations to verify the current findings and ensure their relevance.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-22"},"PeriodicalIF":2.7,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144012726","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mohammad H Alqarni, Aftab Alam, Mishary Saad Al Oraby, Ahmed I Foudah
{"title":"Identification of potential therapeutics by targeting AcrB protein from AcrAB-TolC multidrug efflux pump of <i>Escherichia coli</i>: an in-silico exploration.","authors":"Mohammad H Alqarni, Aftab Alam, Mishary Saad Al Oraby, Ahmed I Foudah","doi":"10.1080/07391102.2025.2487203","DOIUrl":"https://doi.org/10.1080/07391102.2025.2487203","url":null,"abstract":"<p><p>Antibiotic resistance, a critical global health concern, arises as bacteria and other microbes evolve to resist drugs. The AcrB protein, a key component of the AcrAB-TolC multidrug efflux pump in <i>Escherichia coli</i>, plays a significant role in antibiotic resistance and presents an opportunity for new drug development. Inhibiting this pump has the potential to reverse antibiotic resistance and restore drug efficacy. This study explores potential molecules that target the AcrB protein as a novel therapeutic strategy against multidrug-resistant (MDR) Gram-negative bacteria, utilizing <i>in-silico</i> techniques. The initial step in the selection of ligands involved gathering compounds from the PubChem database that are structurally similar to erythromycin A, with a cutoff score of 80 or higher in the similarity search. Stringent drug-likeness criteria were applied, yielding 111 compounds that share structural similarities with erythromycin A. Virtual screening against the target protein identified 72 compounds with promising docking scores between -6.13 and -3.06 kcal/mol using the MtiOpenScreen web server. Subsequently, four compounds (CID:102055530, CID:101369593, CID:139312504, and CID:143044924), along with the control compound (erythromycin A), were selected for further analysis. These analyses included re-docking, molecular dynamics simulations, free binding energy calculations, and PCA-based free energy landscape investigation. The findings suggest that the identified compounds could serve as foundations for developing new inhibitors targeting the AcrB protein, offering a promising strategy to counteract bacterial resistance. This research supports the need for further experimental validation to confirm these <i>in-silico</i> predictions and to potentially advance these compounds through the drug development process.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-16"},"PeriodicalIF":2.7,"publicationDate":"2025-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143965819","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Polyoxometalates as effective inhibitors of insulin amyloid fibrils: a promising therapeutic avenue.","authors":"Ashim Jyoti Bharati, Ritu Zende, Manash Jyoti Deka, Kaberi Kalita, Somenath Garai, Mounish Reddy Mannem, Kamatchi Sankaranarayanan","doi":"10.1080/07391102.2025.2487192","DOIUrl":"https://doi.org/10.1080/07391102.2025.2487192","url":null,"abstract":"<p><p>Insulin is listed on the WHO model list of essential medicines for a basic healthcare system. Due to its usage at regular intervals on diabetic patients, a disease condition called injection amyloidosis exists due to the propensity of insulin to form fibrils. Hence, it is essential to understand the aggregation of the protein insulin and understand the role of fibrillation of the protein insulin and possible inhibition. In this particular investigation, insulin fibrils were produced in a controlled environment. The study focused on exploring the potential of a special class of inorganic nanomaterials known as polyoxometalates (POMs) to inhibit the formation of these insulin amyloid fibrils. Four specific POMs-phosphomolybdic acid (PMA), silicomolybdic acid (SMA), tungstosilicic acid (TSA), and phosphotungstic acid (PTA)-were selected for assessing the inhibition of fibril formation by POMs using the Thioflavin T (ThT) assay. The molecular docking study also shows the binding sites of POMs with insulin. The results provided promising insights into the inhibitory effects of POMs on insulin amyloid fibrils. This investigation opens up potential avenues for exploring the application of Keggin POMs in the context of neurodegeneration.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-8"},"PeriodicalIF":2.7,"publicationDate":"2025-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143965783","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Study on behavior intermolecular force and binding mechanism interaction between bovine hemoglobin and cyanocobalamin by using of spectroscopic and molecular docking methods.","authors":"Marzieh Rahimi Ratky, Hamid Dezhampanah","doi":"10.1080/07391102.2025.2487711","DOIUrl":"https://doi.org/10.1080/07391102.2025.2487711","url":null,"abstract":"<p><p>In this study, fluorescence, synchronous fluorescence, fluorescence resonance energy transfer (FRET), Fourier transform infrared (FT-IR) and molecular docking methods were employed to investigate the binding mechanism between bovine hemoglobin (BHb) and vitamin B12 (cyanocobalamin). Since BHb shares 90% sequence similarity with human hemoglobin investigating its interactions with small molecules is highly relevant. Fluorescence data analysis under varying temperatures indicated that the complex formation between vitamin B12 and BHb is stationary with ground-state complex formation. Thermodynamic investigation indicated hydrogen bonding and hydrophobic interactions in negative changes in enthalpy and entropy during the process of binding. Förster resonance energy transfer analysis determined the binding distance of vitamin B12 with BHb tryptophan residues as 3.11 nm. FT-IR spectroscopy, synchronous fluorescence and UV-visible examinations revealed that vitamin B12 may induce structural modification in BHb. Additionally, molecular docking simulations provided information about binding interactions and validated the spectroscopic findings.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-11"},"PeriodicalIF":2.7,"publicationDate":"2025-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144020221","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jinal M Thakor, Unnati V Panchal, Dhaval Patel, Slawomir Filipek, Urszula Orzeł, Ramasamy Paulmurugan, Katja Hanack, Dorian Liepmann, Venkatesan Renugopalakrishnan, Chaitanya G Joshi, Madhvi Joshi
{"title":"Cross-variant immune shield: computational multiepitope vaccine design against B.617.2 to Omicron sub-lineages in SARS-CoV-2.","authors":"Jinal M Thakor, Unnati V Panchal, Dhaval Patel, Slawomir Filipek, Urszula Orzeł, Ramasamy Paulmurugan, Katja Hanack, Dorian Liepmann, Venkatesan Renugopalakrishnan, Chaitanya G Joshi, Madhvi Joshi","doi":"10.1080/07391102.2025.2487196","DOIUrl":"https://doi.org/10.1080/07391102.2025.2487196","url":null,"abstract":"<p><p>The COVID-19 pandemic had a profound impact on global health. This study focuses on an in-depth analysis of the structural proteins (Spike (S), Nucleocapsid (N), Membrane (M), and Envelope (E) protein) of SARS-CoV-2 and its variants, aiming to develop a multiepitope vaccine construct that targets the virus independently of its variants. The analysis began by examining genetic variations in viral proteins relative to the reference strain Wuhan-Hu2, particularly in the S, M, N, and E proteins. T-cell epitope predictions for MHC Class-I and Class-II binding were conducted, shedding light on potential cytotoxic and helper T lymphocyte recognition. Identification of linear B-cell epitopes laid the groundwork for antibody-based humoral immune responses. The safety and efficacy of these epitopes were assessed for antigenicity, allergenicity, toxicity, immunogenicity, and conservancy. Population coverage analysis indicated promising global effectiveness of the designed vaccine construct. By incorporating 28 epitopes, we validated that was designed vaccine construct for stability through structural analysis. Molecular dynamics simulations and docking studies revealed its robust interaction with Toll-like receptor 4 (TLR4). Immune simulation studies suggested that the vaccine construct could induce a potent immune response by enhancing antibody titers, B-cell proliferation, memory cell development, and activation of T cells and natural killer cells upon administration. This comprehensive approach offers a promising multiepitope vaccine against SARS-CoV-2, with the potential for broad global coverage and strong immunogenicity. Further experimental validation holds the prospect of introducing a novel candidate vaccine to aid in the ongoing battle against the COVID-19 pandemic.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-20"},"PeriodicalIF":2.7,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143811557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Computational insights of deucravacitinib's selectivity for TYK2 pseudokinase vs. JAK kinase domain via molecular modeling studies.","authors":"Manish Ramchandani, Amit Kumar Goyal","doi":"10.1080/07391102.2025.2484663","DOIUrl":"https://doi.org/10.1080/07391102.2025.2484663","url":null,"abstract":"<p><p>Deucravacitinib (Sotyktu) stands out as a novel and highly specific oral inhibitor targeting tyrosine kinase 2 (TYK2). Its mechanism of action involves an allosteric binding, to catalytically inactive pseudokinase domain of TYK2, this stabilizes an inhibitory contact between the catalytic and regulatory domains. This inhibition of Janus kinase (JAK) is associated with suppression of cytokine signaling using diverse molecules defining wide importance in current research. In our recent investigation, we examined the selectivity of the TYK2JH2 inhibitor, deucravacitinib, against four JAK kinases (JAK1, JAK2, JAK3, TYK2) and TYK2 pseudokinases utilizing a merged approach involving molecular docking, molecular dynamics analysis (300 ns), and binding free energy calculation through the molecular mechanics Poisson - Boltzmann surface area (MM-PBSA) scheme. The results obtained indicate that deucravacitinib effectively interacts with the ATP-binding site of four JAK kinases and TYK2 pseudokinase through hydrogen bond formation, electrostatic attraction, and notably, van der Waals interaction. We found the calculated binding affinity demonstrates a reduction in the TYK2JH2-deucravacitinib complex due to an increased favorable intermolecular electrostatic contribution. Consequently, deucravacitinib exhibits greater selectivity for the TYK2 pseudokinase domain compared to the other four JAKs. Moreover, the interaction with DPG motif residues and the hinge region contributed to the stabilization of deucravacitinib through robustly formed hydrogen bonds. The interaction with the hydrophobic catalytic region caused the ATP-binding site to adopt a closed conformation, thereby minimizing protein movement at the glycine loop of the JAK pseudokinase protein. In summary, our study holds significant potential for informing the strategic design of TYK2 inhibitors with enhanced affinity.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-15"},"PeriodicalIF":2.7,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143811553","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}