In silico pharmacology最新文献

{"title":"Antiproliferative activity of <i>Xylopia aethiopica</i> extracts and molecular docking studies of their main phytochemicals.","authors":"T T Alawode, E O Odokwo, M Leoma, O O Oderinlo, G R Nyemba, C Davison, M P Ngoepe, J A de la Mare, T Tshiwawa","doi":"10.1007/s40203-026-00633-4","DOIUrl":"https://doi.org/10.1007/s40203-026-00633-4","url":null,"abstract":"<p><p><i>Xylopia aethiopica</i> (African pepper) is an intriguing medicinal plant which grows abundantly in West Africa and demonstrates a variety of pharmacological properties. This study assesses the cytotoxic activity of hexane, ethyl acetate and methanol extracts of the fruits and root of the plant against HCC-70, MCF-7, and MCF12A cell lines. The ethyl acetate fraction of the root had the strongest cytotoxic activity against HCC-70, a highly aggressive Triple-Negative Breast Cancer (TNBC) cell line, with an IC₅₀ of 19.96 µg/mL. The hexane extract of the fruit had an IC₅₀ value of 30.39 µg/mL against MCF-7. The cytotoxic effects observed could be attributed to a wide spectrum of phytochemicals in the extracts. Using the fingerprint pattern from the ¹³C-NMR of the extracts, seven compounds belonging to two classes (i.e., kaurene and trachylobane-type diterpenoids and aporphine-type alkaloids) were annotated from the extracts. Furthermore, these compounds were assessed in silico on several important tumour cell-associated proteins. Two compounds showcased excellent binding interactions across all the proteins investigated and displayed a favourable ADMET profile. N-methylnordomesticine and N-methyllaurotetanine are excellent leads for further medicinal chemistry development.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s40203-026-00633-4.</p>","PeriodicalId":94038,"journal":{"name":"In silico pharmacology","volume":"14 2","pages":"128"},"PeriodicalIF":0.0,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13125549/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147825090","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Screening of NPASS library to uncover potential Dipeptidyl peptidase-IV enzyme inhibitors using structure-based virtual screening and molecular dynamics.","authors":"Surendra Kumar Gautam, Kailash Jangid, Bharti Devi, Nikita Kumari","doi":"10.1007/s40203-026-00629-0","DOIUrl":"https://doi.org/10.1007/s40203-026-00629-0","url":null,"abstract":"<p><p>Diabetes mellitus is a chronic metabolic disorder characterised by hyperglycaemia due to insulin resistance and insufficient insulin production. Currently, multiple drugs exist for managing diabetes mellitus. However, the demand for herbal medicines is still required as the present treatments have a few challenges like toxicity, drug resistance and side effects. Therefore, in order to identify potent natural drug candidates, the NPASS database was selected for structure-based virtual screening. Lipinski's rule of five and PAINs removing filters were applied for pre-processing, prior to actual screening. Subsequently, filtered molecules were subjected to three modes of molecular docking, viz. HTVS, SP and XP, where the topmost 10%, 20% and 30% molecules were selected, respectively, followed by binding free energy calculations. Based on dock score evaluation and protein-ligand interaction analysis, the top five candidates were processed for ADME predictions along with the reference drug, sitagliptin. Out of which, two hits, NPC14706 and NPC319625, and Sitagliptin, showing respective ∆GMMGBSA values of - 49.53, - 50.93, and - 27.97 kcal/mol, respectively, with acceptable pharmacokinetic properties (ADME), were subjected to investigate MD simulation studies of about 100 ns. The MD results revealed that compound NPC14706 showed an average RMSD value of ~ 2.5 nm that remained stable throughout the trajectory, while compound NPC319625 exhibited an average RMSD value of ~ 2.9 nm with some fluctuations in between the trajectory. Therefore, the present study indicated that the lead compound NPC41706 could be further assessed for its potential inhibitory activity against the human DPP-IV enzyme through appropriate in-vitro, ADME and Phytomedicine studies for the management of diabetes mellitus.</p><p><strong>Graphical abstract: </strong></p>","PeriodicalId":94038,"journal":{"name":"In silico pharmacology","volume":"14 2","pages":"129"},"PeriodicalIF":0.0,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13125555/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147825097","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Linamarin and its analogues as targeted therapeutic agents in cervical cancer: insights from atomistic molecular docking, dynamics and MMPBSA calculations.","authors":"Halima Kawia, James Mgaya, Lucas Paul","doi":"10.1007/s40203-026-00619-2","DOIUrl":"https://doi.org/10.1007/s40203-026-00619-2","url":null,"abstract":"<p><p>The HPV16 E6 oncoprotein is a critical target for therapeutic intervention in cervical cancerIn this study, we investigated the interactions of linamarin and its analogues ZINC146037704, ZINC141150528 and ZINC146038957 with HPV16 E6 protein using molecular docking, dynamics, MMPBSA and ADMET predictions. Docking and MD confirmed ZINC146037704 analogue as the most favourable binding candidate with the lowest binding free energy (-74.93 ± 13.05 kJ/mol), stable RMSD (≈0.35 nm) and Rg (2.1988 nm) values, and the highest number of hydrogen bonds (14), indicating strong and persistent ligand-protein interactions. Per-residue decomposition highlighted key contributions from sub-interface I, II, LxxL motif consistent with critical residues in E6-p53 interface stabilization. Ligand interactions were primarily mediated by hydrogen bonds, π-stacking, and van der Waals forces, with glycosylated moieties enhancing polar contacts and binding stability compared to the control drug, topotecan. ADMET evaluation indicated generally favourable pharmacokinetic and safety profiles, with ZINC146037704 and ZINC3984017 showing balanced properties for further development. Overall, these results identify ZINC146037704 as a promising lead molecule for targeting HPV16 E6 and provide a foundation for future experimental validation of linamarin-derived inhibitors in cervical cancer therapy.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s40203-026-00619-2.</p>","PeriodicalId":94038,"journal":{"name":"In silico pharmacology","volume":"14 2","pages":"132"},"PeriodicalIF":0.0,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13125437/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147825085","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rosmarinic acid as a potential GSK3β inhibitor for autism spectrum disorder: insights from an integrative in silico study.","authors":"Priya Joon, Saumya Bansal, Jesil Mathew Aranjani, Anil Kumar, Deepak Deepak","doi":"10.1007/s40203-026-00627-2","DOIUrl":"https://doi.org/10.1007/s40203-026-00627-2","url":null,"abstract":"<p><p>Autism Spectrum Disorder (ASD) is characterized by dysregulated signaling pathways, notably involving Glycogen Synthase Kinase 3 Beta (GSK3β). The present study investigates Rosmarinic acid (RA), a natural polyphenol, as a potential GSK3β inhibitor for ASD using an integrative in silico framework. Multiple sequence alignment across six species revealed high conservation of GSK3β's ATP-binding pocket, underscoring its therapeutic relevance and translatability across model organisms. Molecular docking showed RA binds robustly to GSK3β's ATP-binding pocket (estimated affinity: 58.11 nM in SeeSAR scoring), compared to previously validated inhibitors such as Tideglusib (4077.20 nM in SeeSAR scoring) and Laduviglusib (93.26 nM in SeeSAR scoring). Independent Glide docking reproduced the binding orientation (GlideScore: - 7.548 kcal/mol), and MM-GBSA refinement indicated favorable binding free energy (ΔG_bind = - 42.37 kcal/mol). A 100 ns molecular dynamics simulation demonstrated stable ligand retention and sustained catalytic pocket interactions with the engagement of catalytic amino acid residues including Lys85 and Asp200. Off-target docking against CDK2, CDK5, and GSK3α suggested preferential binding toward GSK3β. Structure-activity exploration of RA analogs identified aromatic balance and moderated polarity as determinants of predicted affinity. Together, these findings provide convergent computational evidence that RA may directly interact with GSK3β, supporting further biochemical and cellular validation studies to assess its potential as a modulator of GSK3β-associated pathways relevant to ASD pathophysiology.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s40203-026-00627-2.</p>","PeriodicalId":94038,"journal":{"name":"In silico pharmacology","volume":"14 2","pages":"124"},"PeriodicalIF":0.0,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13125612/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147825031","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-epitope vaccine design against Nipah virus: An immunoinformatics approach targeting South and Southeast Asia populations.","authors":"Moh Royhan Afnani, Viol Dhea Kharisma, Aswin Rafif Khairullah, Abdugani Abdurasulov, Roza Abdyldayeva, Maksim Rebezov, Arli Aditya Parikesit, Vikash Jakhmola, Rollando Rollando, Arif Nur Muhammad Ansori","doi":"10.1007/s40203-026-00607-6","DOIUrl":"https://doi.org/10.1007/s40203-026-00607-6","url":null,"abstract":"<p><p>Nipah virus (NiV) remains a critical zoonotic threat in South and Southeast Asia due to its high fatality rate and the absence of a licensed human vaccine. In this study, an immunoinformatics-driven strategy was employed to design a population-specific multi-epitope vaccine targeting the fusion (F) and glycoprotein (G) of NiV. A total of four B-cell epitopes, ten cytotoxic T lymphocyte (CTL) epitopes, and eight helper T lymphocyte (HTL) epitopes were selected based on strong HLA binding affinity, high antigenicity, and favorable safety profiles. All selected epitopes were predicted to be non-allergenic and non-toxic, with VaxiJen antigenicity. Population coverage analysis revealed extensive coverage across endemic regions, exceeding 97.98% in South Asia and 99.41% in Southeast Asia. The final multi-epitope construct demonstrated favorable physicochemical properties, including structural stability and hydrophilic characteristics. Structural modeling and validation confirmed a reliable tertiary structure, with 92.2% of residues located in favored regions of the Ramachandran plot and an ERRAT score of 90.5. Molecular docking analysis showed strong binding affinities between the vaccine construct and Toll-like receptors, particularly TLR3 (-17.0 ΔG kcal/mol, 8 hydrogen bonds, 7 salt bridges), followed by TLR4 (-15.8 ΔG kcal/mol, 14 hydrogen bonds, 3 salt bridges) and TLR2 (-15.1 ΔG kcal/mol, 10 hydrogen bonds, 3 salt bridges), suggesting a potential for innate immune receptor engagement that warrants further experimental validation. Structure-based flexibility analyses suggested limited conformational fluctuations at the predicted vaccine-receptor interaction interfaces. Immune simulation predicted robust humoral and cellular immune responses, characterized by elevated IgG titers, cytokine production, and the generation of memory B and T cells. Codon optimization and in silico cloning into the pET-28a(+) vector indicated high expression feasibility in <i>Escherichia coli</i> K12. Overall, this study presents a rational computational framework for developing a safe, immunogenic, and region-specific NiV vaccine candidate, warranting further experimental validation.</p>","PeriodicalId":94038,"journal":{"name":"In silico pharmacology","volume":"14 2","pages":"133"},"PeriodicalIF":0.0,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13125468/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147825039","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Personalized mRNA vaccine for breast cancer: in silico neoantigen discovery and immunogenic validation in a Pakistani patient cohort.","authors":"Kayode Raheem, Mariyam Nawaz, Khalid J Alzahrani, Ijaz Ali, Muhammad Muddassar","doi":"10.1007/s40203-026-00631-6","DOIUrl":"https://doi.org/10.1007/s40203-026-00631-6","url":null,"abstract":"<p><p>Breast cancer is a common cancer type that occurs among women in Pakistan, and the rising incidence and mortality rate underline the need to develop effective, patient-tailored immunotherapies. In this study, we implemented an end-to-end immunoinformatics workflow using publicly available whole-exome sequencing (WES) data deposited under NCBI BioProject PRJNA941166, a cohort-derived resource from the Khyber Pakhtunkhwa region; as a proof of concept, we analyzed all sequencing runs associated with the available case to demonstrate a personalized vaccine design workflow. Somatic variant analysis indicated a high mutational burden, including 6005 missense mutations in genes such as MUC3A and TTN. From > 43,000 candidate mutant peptides, we prioritized seven non-allergenic neoantigens with strong predicted HLA binding (ΔG ≤ - 13.0 kcal/mol). These epitopes were assembled into a 285-amino acid multi-epitope antigen incorporating a GM-CSF adjuvant and helper epitopes. AlphaFold2 modeling and in silico quality assessment supported construct stability (ProSA Z-score - 7.14; ERRAT 96.59%). Across 500 ns molecular dynamics simulations, the vaccine construct remained conformationally stable and showed favorable predicted interactions with innate immune receptors, with strong binding free energies for TLR9 (ΔG = - 148.8 kcal/mol) and TLR2 (ΔG = - 16.7 kcal/mol). Immune simulations using C-IMMSIM suggested a Th1-skewed response characterized by induction of cytotoxic T lymphocytes, memory T-cell formation, and elevated IFN-γ. Although limited to computational predictions and a single publicly available case, the predicted receptor engagement and immunogenicity provide a rationale for preclinical evaluation of this personalized mRNA vaccine design workflow in high-risk populations.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s40203-026-00631-6.</p>","PeriodicalId":94038,"journal":{"name":"In silico pharmacology","volume":"14 2","pages":"127"},"PeriodicalIF":0.0,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13125589/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147825047","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In silico discovery of fructosamine-3-kinase inhibitors targeting the Nrf2-mediated antioxidant response in cancer cells: a molecular dynamics approach.","authors":"Mohammad A Ansari, Nikhat Parween","doi":"10.1007/s40203-026-00635-2","DOIUrl":"https://doi.org/10.1007/s40203-026-00635-2","url":null,"abstract":"<p><p>Fructosamine-3-kinase is an enzyme responsible for deglycating the transcription factor nuclear factor erythroid 2-related factor 2 (Nrf2) which regulates the expression of numerous genes involved in the cellular defence against oxidative stress. To identify inhibitors against FN3K, which may disrupt antioxidant-homeostasis in cancer cells, noncovalent docking was performed for a set of 83 ATP-mimicking kinase inhibitors, followed by flexible side-chain docking to re-confirm the trend in binding energies. Covalent docking was also performed for a set of 36 known covalent kinase inhibitors with the active site Cys150 residue. The recently reported crystal structure of Human FN3K [PDB:8UE1] was employed for docking. The pharmacokinetic and toxicological properties of the top noncovalent and covalent inhibitors were subsequently studied. Kinase inhibitors with appropriate ADMET properties that are suitable for human administration and have favourable binding energies were subjected to molecular dynamics simulations to study the stability of their protein-ligand complexes. On the basis of 110 ns MD simulations, it was concluded that trilaciclib, tucatinib and olmutinib can be considered candidate inhibitors for HsFN3K inhibition. Trilaciclib and tucatinib also showed favourable thermodynamic binding free energies of - 23.37 ± 3.03 and - 18.36 ± 1.83 kcal/mol respectively, as calculated via MM/PBSA method. Olmutinib displayed very stable binding as a complex with FN3K with no dramatic shifts in protein structure or having any impact on its folding. The solvation and hydration effects seen on the ATP-binding site in response to ligand-binding were also extensively studied which corresponds to efficient ligand entry. These drugs are expected to have favourable in-vitro and in-vivo activity inhibiting HsFN3K on the basis of our results.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s40203-026-00635-2.</p>","PeriodicalId":94038,"journal":{"name":"In silico pharmacology","volume":"14 2","pages":"131"},"PeriodicalIF":0.0,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13125660/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147825017","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Immunoinformatics-guided design and molecular evaluation of a TLR4-adjuvanted multiepitope vaccine against multidrug-resistant Enteroinvasive <i>Escherichia coli</i> and <i>Shigella</i> spp.","authors":"Pinkan Sadhukhan, Nibedita Mahata","doi":"10.1007/s40203-026-00618-3","DOIUrl":"https://doi.org/10.1007/s40203-026-00618-3","url":null,"abstract":"<p><p>Enteroinvasive <i>Escherichia coli</i> is a gram-negative pathogen closely related to <i>Shigella</i>, and it is one of the leading causes of bacillary dysentery acquired in South Asia and worldwide. The emergence of multidrug-resistant serotypes has severely limited treatment options, with an urgent requirement for vaccines. This study applied immunoinformatics to design a multiepitope vaccine candidate targeting the O96:H19 strain. Here, four invasion plasmid antigens (IpaA, IpaB, IpaC, and IpaD) were taken as targets. Designed vaccine construct integrates three 9-mer PAP (possessing both MHC & B cell inducing properties) linked by proteasomal and lysosomally cleavable spacers. 7-mer TLR4 agonist (RS-04) fused with both its terminals. Computational analysis of the 69-mer vaccine construct predicted strong antigenicity, non-allergenicity and optimum solubility. In Ramachandran's plot, 100% of the residues were located in the most favourable regions. Molecular docking revealed a high affinity of the construct towards the human TLR4 model. Additionally, a 100 ns all-atom molecular dynamics simulation further confirmed the TLR4-vaccine complex formation through 14 H-bonds, 131 non-bonded contacts, and five salt bridges. Post-simulation (100 ns) molecular interaction maps identified specific interactions of TLR4 agonists with the TLR4 model. Immunosimulation for 365 days was associated with rising titers of IgG and IgM antibodies, as well as pro-inflammatory cytokine responses. To express the construct in <i>E.coli</i> expression system, the vaccine sequence was reverse-translated. The codon-optimized sequence was recombined into a modified pET vector using an <i>in-silico</i> method. Hence, laboratory validation was required to assess the real-time efficacy of the EIEC and <i>Shigella</i> cross-protective multiepitope vaccine.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s40203-026-00618-3.</p>","PeriodicalId":94038,"journal":{"name":"In silico pharmacology","volume":"14 2","pages":"130"},"PeriodicalIF":0.0,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13125459/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147825058","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular docking and dynamics simulations of aptamers for sandwich-type detection of <i>Trichomonas vaginalis</i>.","authors":"Jon Patrick T Garcia, Brian Harvey Avanceña Villanueva, Christine Joyce F Rejano, Mike Anthony D Ganzon, Jay Marie V Lumantas, Christian Adam L Espiritu, Ymir M Garcia","doi":"10.1007/s40203-026-00614-7","DOIUrl":"https://doi.org/10.1007/s40203-026-00614-7","url":null,"abstract":"<p><p>Aptamer-based biosensing has gained recognition in the scientific community for its analytical, diagnostic, and economic advantages, underscoring the need to innovate beyond conventional infectious disease detection methods such as PCR and immunoassays. Trichomoniasis, one of the most prevalent nonviral sexually transmitted infections worldwide, remains a global health concern due to the absence of more specific and sensitive diagnostic tools. To address this issue, the study employed advanced computational approaches to evaluate the potential use of aptamers, previously obtained through SELEX, for detecting the AP65 protein expressed on <i>Trichomonas vaginalis</i> cells. Molecular docking and molecular dynamics simulations were conducted to predict and analyze the presence and behavior of biomolecular interactions relevant to the design. Three capture probes and three reporter probes were initially screened through rigid docking of binary complexes. These were then further assessed to identify aptamer pairs that could form the most stable ternary complex through flexible docking. Of the four ternary complexes formed, three were subjected to molecular dynamics simulations to investigate their structural integrity over time. Additionally, the selected probes were assessed for cross-reactivity with other AP65 variants. Results showed that the AP65-A1-A6₃ complex had the most stable conformations, suggesting that the pairing of A1 as capture probe and A6₃ as reporter probe was the best option in the design of sandwich-type assays for detecting AP65. It was also found that the selected probes had significant affinity to other AP65 variants, which may potentially contribute to more efficient aptamer-protein interactions. This study demonstrated that the capture and reporter probes synthesized are promising candidates for trichomoniasis detection. It also provided essential preliminary findings to support the effective optimization of in vitro sandwich-type models for future point-of-care device development.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s40203-026-00614-7.</p>","PeriodicalId":94038,"journal":{"name":"In silico pharmacology","volume":"14 2","pages":"126"},"PeriodicalIF":0.0,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13125432/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147825082","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Network pharmacology prediction and molecular docking-based strategy to explore the potential mechanism of phytoconstituents identified from <i>Oxalis triangularis</i> by GC-MS and LC-MS analysis against colorectal cancer.","authors":"Safal Sharma, Nihar Ranjan Bhuyan, Jyochhana Priya Mohanty, Ravi Kumar Rajan, Farak Ali, Abdul Baquee Ahmed","doi":"10.1007/s40203-026-00632-5","DOIUrl":"https://doi.org/10.1007/s40203-026-00632-5","url":null,"abstract":"<p><p>Colorectal cancer (CRCs) is one of the prominent malignancies which ranks 2nd among all cancers worldwide in terms of mortality. Given the significant impact of CRC worldwide, the identification of effective drug for the treatment remains a considerable challenge. <i>Oxalis</i> genus especially <i>Oxalis triangularis</i> A. St.-Hil (OT) belonging to family Oxalidaceae, exerts numerous pharmacological effects, including anti-inflammatory, anti-oxidant and anti-bacterial effects. However, the mechanism underlying the effect of OT against CRC treatment remains unexplored. In this study, target identification was carried out using network pharmacology (NP). The top targets from NP were taken further for CDOCKER molecular docking with 131 phytoconstituents identified from OT by LC-MS and GC-MS analysis. The NP study revealed 3 important targets namely signal transducer and activator of transcription 3 (STAT3), hypoxia-inducible factor 1 subunit alpha (HIF1A) and estrogen receptor 1 (ESR1). These three targets were utilized for docking studies for the lead identification. Top 5 phyto-constituents (lead) identified during docking had a docking score ranges from \"- 62.2026 to - 50.167 kcal/mol\" for STAT3, \"- 79.9526 to - 58.4467 kcal/mol\" for HIF1A, and \"- 73.5511 to - 59.8775 kcal/mol\" for ESR1 suggesting strong binding affinity of phyto-constituents with the target protein. Common amino acid interactions between STAT3 and HIF1A with top 5 phytoconstituents are GLU 638 and ILE 659, and common amino acid interaction between ESR1 and phytoconstituents are LYS 529 and LEU 525. Further, molecular dynamics simulations position the 6PSJ ligand as a high-affinity lead, 6NJS as a candidate for polypharmacological targeting, and 3HQU as a reference for refining smaller scaffolds. The present study revealed that OT exerts anti-cancer effects, by targeting multiple pathways, laying a theoretical background for its use as a therapeutic candidate for CRC.</p><p><strong>Graphical abstract: </strong></p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s40203-026-00632-5.</p>","PeriodicalId":94038,"journal":{"name":"In silico pharmacology","volume":"14 2","pages":"125"},"PeriodicalIF":0.0,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13125545/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147825111","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}