3 Biotech最新文献

{"title":"Identification of differentially expressed miRNAs between male sterile and fertile floral buds in watermelon (<i>Citrullus lanatus</i> L.) via high-throughput sequencing.","authors":"Gaoyuan Zhang, Bingqiang Wei, Qian Ding","doi":"10.1007/s13205-024-04084-6","DOIUrl":"10.1007/s13205-024-04084-6","url":null,"abstract":"<p><p>This experiment used floral buds from watermelon genic male sterile dual-purpose lines as materials to explore the differentially expressed miRNAs (DEMs) between male fertile and sterile floral buds of watermelon. Paraffin sectioning technology was employed for a cytological analysis, and small RNA sequencing was used to explore miRNAs related to anther or pollen development. Cytological analysis indicated that the abnormal development of tapetal cells may cause microspore abortion. Small RNA sequencing identified a total of 314 miRNAs (29 known and 285 novel, which belonged to 12 and 61 miRNA families, respectively) in floral buds. Differential expression revealed 36 (5 known and 31 novel) DEMs between male fertile and sterile buds, 7 and 29 of which were up-regulated and down-regulated, respectively. Target genes analysis showed that the 36 DEMs were predicted to target 577 genes, and these targets might participate in various biological processes, such as response to metal ions, floral organ development, stamen development, anther development, pollen maturation, and programmed cell death. Moreover, pathway analysis indicated that these genes were mainly enriched in purine metabolism, starch and sucrose metabolism, RNA transport, and other pathways. In addition, the 55 miRNA-target modules, including 3 known and 16 novel miRNAs with 30 target genes, might be related to anther or pollen development in watermelon. Our findings provide important miRNA-target modules related to watermelon anther or pollen development and can lay the foundation for biological functional analysis.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s13205-024-04084-6.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11424599/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142339004","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Stimulating action of sodium nitroprusside and vinasse on salicin and direct regeneration in <i>Salix Safsaf</i> Forssk.","authors":"Rania Saber Yousef, Osama Konsowa Ahmed, Zeinab K Taha","doi":"10.1007/s13205-024-04068-6","DOIUrl":"10.1007/s13205-024-04068-6","url":null,"abstract":"<p><p>The present study aimed to enhance salicin and direct regeneration in willow (<i>Salix safsaf</i> Forssk) using the sodium nitroprusside (SNP) regulation of nitric oxide (NO) and vinasse for its nutrition effect in culture medium. Internodes of <i>Salix safsaf</i> were cultured on Murashige and Skoog (MS) medium supplemented with benzyl adenine (BA) (0.25 mg L^-1) and different concentrations of SNP (0, 5, 10, 15, and 20 mg L^-1) or vinasse (0, 5, 10, and 20%) to examine shoot regeneration, antioxidant defense enzyme activity, total phenolic compounds, flavonoids, and salicine contents. The reported data revealed that application of SNP at 15 mg L^-1 and vinasse at 10% induced a significant effect in vitro <i>Salix safsaf</i> shoot regeneration. To confirm that, nitric oxide is required for auxin-mediated activation of cell division in a dose-dependent manner. A concentration of 15 mg L^-1 SNP promotes regeneration and salicin accumulation (3162.16 mg/100 g) during signaling action. On the other hand, the cross talk effect of nitric oxide and vinasse combination in <i>Salix safsaf</i> significantly induced a synergistic effect on direct propagation more than vinasse alone. SNP significantly stimulates salicylate accumulation in a dose-dependent manner, but the data on the association of vinasse and SNP on salicylate up-regulation showed a significant reduction in salicin accumulation when SNP was combined with 10% vinasse, which directly affected the signaling action of SNP as secondary product stimulators. Vinasse's phenolic compounds affect directly on the reduction activity of SNP to suppress its signaling action, or indirectly by inhibiting the sequence cascade of the SNP signaling transduction process to decrease the accumulation of salicin contents. Data confirmed that vinasse and SNP stimulated the antioxidant enzymes activity throw quenching the stimulated reactive oxygen species that produced via SNP. Results show that modified media with SNP administration at 15 mg L^-1 and the combination of vinasse at 10% and SNP at 15 mg L^-1 are recommended for modifying tissue culture media for induced direct regeneration and salicin accumulation in tissue culture applications, which will be very useful for commercial salicin overproduction as a biological active ingredient in willows.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11413276/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142278670","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biological roles of THRAP3, STMN1 and GNA13 in human blood cancer cells.","authors":"Suliman A Alsagaby","doi":"10.1007/s13205-024-04093-5","DOIUrl":"10.1007/s13205-024-04093-5","url":null,"abstract":"<p><p>Blood cancers, such as diffuse large B-cell lymphoma (DLBCL), Burkitt's lymphoma (BL) and acute myeloid leukemia (AML), are aggressive neoplasms that are characterized by undesired clinical courses with dismal survival rates. The objective of the current work is to study the expression THRAP3, STMN1 and GNA13 in DLBCL, BL and AML, and to investigate if these proteins are implicated in the prognosis and progression of the blood cancers. Isolation of normal blood cells was performed using lymphoprep coupled with gradient centrifugation and magnetic beads. Flow-cytometric analysis showed high quality of the isolated cells. Western blotting identified THRAP3, STMN1 and GNA13 to be overexpressed in the blood cancer cells but hardly detected in normal blood cells from healthy donors. Consistently, investigations performed using genotype-tissue expression (GTEx) and gene expression profiling interactive analysis (GEPIA) showed that the three proteins had higher mRNA expression in various cancers compared with matched normal tissues (<i>p</i> ≤ 0.01). Furthermore, the up-regulated transcript expression of these proteins was a feature of short overall survival (OS; <i>p</i> ≤ 0.02) in patients with the blood cancers. Interestingly, functional profiling using gProfiler and protein-protein interaction network analysis using STRING with cytoscape reported THRAP3 to be associated with cancer-dependent proliferation and survival pathways (corrected <i>p</i> ≤ 0.05) and to interact with proteins (<i>p</i> = 1 × 10^-16) implicated in tumourigenesis and chemotherapy resistance. Taken together, these findings indicated a possible implication of THRAP3, STMN1 and GNA13 in the progression and prognosis of the blood cancers. Additional work using clinical samples of the blood cancers is required to further investigate and validate the results reported here.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s13205-024-04093-5.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11424602/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142338999","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Upcycling of tea processing waste into kombucha-derived bioactive cellulosic composite for prospective wound dressing action.","authors":"Baishali Dey, Sivaraman Jayaraman, Paramasivan Balasubramanian","doi":"10.1007/s13205-024-04095-3","DOIUrl":"10.1007/s13205-024-04095-3","url":null,"abstract":"<p><p>The aim of the study was to utilize kombucha-derived bacterial cellulosic sheet [<i>KBC</i>], formed as a by-product of fermented, sugared black tea (in the presence of a symbiotic culture of bacteria and yeast), for potential wound dressing applications. <i>KBC</i> was functionalized using aqueous and ethanolic extracts of different phytochemical agents using two ex-situ methods- casting and impregnation. It was observed that casted <i>KBC</i> functionalized with ethanolic extract of Turmeric (1.2% w/w) yielded a maximum zone of inhibition (24.37 ± 0.42 mm) against <i>Pseudomonas aeruginosa</i>. The hemocompatibility test confirmed the composite's biocompatible nature as the percentage hemocompatibility was found to be less than 5%. The MTT assay established its viability and anti-cancerous properties with Turmeric extract loaded KBC showing higher efficiency compared to Tulsi extract. FTIR analysis and SEM imaging confirmed the functionalization of cellulose sheets and the change in morphology. The contact angle analysis showed improved hydrophilic properties of the sheets for absorbing wound exudates, and the water absorption study revealed maximum absorptivity of up to 321.20 ± 6.23%. Thus, it can be concluded from the study that tea processing waste can be reused to produce a value-added product that can act as an efficient, cost-effective biomaterial for wound dressing applications.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11436509/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142339021","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cytotoxic activity of callus extract from Vachellia farnesiana (L) Wight & Arn.","authors":"José Alejandro Domínguez-Colín, Leticia Buendía-González, Carmen Hernández-Jaimes, Francisco Cruz-Sosa, Juan Orozco-Villafuerte","doi":"10.1007/s13205-024-04085-5","DOIUrl":"https://doi.org/10.1007/s13205-024-04085-5","url":null,"abstract":"<p>The in vitro cultures of <i>Vachellia farnesiana</i> (L) Wight &amp; Arn. have demonstrated cytotoxic activity through callus extract on the HeLa cell line. Explants excised from in vitro-grown seedlings from seeds of two different locations were inoculated on Murashige and Skoog (MS) culture media containing various concentrations of N-6 benzyladenine (BA) or kinetin with 2,4-dichlorophenoxyacetic acid (2,4-D). Optimal efficiency in friable callus induction (100%) was achieved in leaf explants cultured on MS media containing 2.32 µM BA + 13.57 µM 2,4-D. Plant tissues (callus and leaf) were extracted and subjected to quantitative phytochemical analysis, revealing the highest total alkaloid and phenolic content in leaf extracts from Queretaro adult specimens (339.5 ± 20.9 mg atropine equivalents (AE) per g dry extract (DE) and 158.4 ± 12.5 mg gallic acid equivalents (GAE) per g DE, respectively). In contrast, callus cultures exhibited significantly higher total triterpene content (356–381 mg ursolic acid equivalents (UAE) per g DE) compared to leaf extracts (208–243 mg UAE/g DE). Both leaf and callus extracts displayed cytotoxic activity against the HeLa cell line, with a significantly lower half-maximal inhibitory concentration (IC₅₀) for leaf extracts (28–32 µg/mL) compared to callus cultures (43–66 µg/mL), suggesting that alkaloids were primarily responsible for the cytotoxic activity. Furthermore, this study provides valuable insights into the controlled production of bioactive compounds with cytotoxic activity, with callus serving as a rich source.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142260277","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Betanin-encapsulated starch nanoparticles: synthesis and cytotoxic effect on colon cancer","authors":"Suhail Ahmad Bhat, Sathyapriya Chandramohan, Guguloth Sai Krishna, Chandansri Hiranmaya, Sankar Pajaniradje, Anjali Suresh Nair, Debabrata Mohanty, Rukkumani Rajagopalan","doi":"10.1007/s13205-024-04078-4","DOIUrl":"https://doi.org/10.1007/s13205-024-04078-4","url":null,"abstract":"<p>Colorectal cancer (CRC) is a common and life-threatening neoplastic disease that continues to pose a formidable challenge to global health. The present work was performed to evaluate the anticancer properties of betanin and betanin (BT) loaded starch nanoparticles (S-BT). The BT and S-BT were characterized by DLS, SEM, UV spectroscopy, XPS and FTIR. The cytotoxic effect was assessed by MTT and LDH assay. The apoptotic potential of BT and S-BT was assessed by DCFDA, Rh123, AO/EB and DAPI staining methods. Cell cycle arrest was depicted using flow cytometry. The antimetastatic potential of BT and S-BT was evaluated by wound healing assay. The S-BT showed a spherical morphology with a size of 175 nm. The betanin contained SNPs were found to have strong encapsulation efficiency and favorable release profiles. Both BT and S-BT exhibited cytotoxicity in SW480 cells but S-BT displayed increased cytotoxicity when compared to BT alone. Loss of mitochondrial membrane potential, nuclear fragmentation, chromatin condensation and generation of ROS, all indicative of apoptotic mode of cell death, were revealed by fluorescence imaging. The cells were arrested in the G₂M phase. Moreover, both BT and S-BT were able to inhibit the migratory potential of SW480 cells. Overall, our results indicated that both BT and S-BT were able to induce anticancer effects; and, S-BT was found to have increased therapeutic efficacy when compared to BT alone.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142260134","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Computational screening of chemical constituents derived from berry fruits as allosteric caspace-3/-7 inhibitors","authors":"Waseem Ahmad Ansari, Mohsin Ali Khan, S. M. Mahfooz Hasan, Zainab Siddiqui, Saheem Ahmad, Mohd Shahnawaz Khan, Mohammad Faheem Khan","doi":"10.1007/s13205-024-04067-7","DOIUrl":"https://doi.org/10.1007/s13205-024-04067-7","url":null,"abstract":"<p>With the aim of finding the plant-derived allosteric inhibitors of caspase-3/-7, we conducted computational investigations of bioactive compounds present in various berry fruits. In a molecular docking study, perulactone demonstrated excellent binding affinity scores of −12.1 kcal/mol and −9.1 kcal/mol for caspase 7 and 3, respectively, whereas FDA-approved allosteric inhibitors (DICA and FICA) were found to show lower docking scores (−5.6 and −6.1 kcal/mol) against caspase 7 while (−5.0 and −5.1 kcal/mol) for caspase 3, respectively. MD simulations were used to validate the binding stability of perulactone in the active sites of caspase-7/-3, and the results showed outstanding stability with lower ligand RMSDs of 1.270–3.088 Å and 2.426–9.850 Å against the targeted receptor. Furthermore, we performed MMGBSA free binding energy, where the perulactone values of Δ<i>G</i>_Bind were determined to be −63.98 kcal/mol and −66.32 kcal/mol for both receptors (3IBF and 1NME), which are significantly better than the −45.16 kcal/mol and −39.51 kcal/mol for DICA as well as −26.37 kcal/mol and −15.50 kcal/mol for FICA, respectively. The drug resemblance of perulactone was effectively evaluated by ADMET. Thus, our findings indicated that perulactone could be an orally administered therapeutic candidate for regulating apoptosis in a variety of disorders. However, there may be an urgent need to study using in vitro and in vivo experiments.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142260276","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prediction of molecular targets for antidepressant potential of hydroalcoholic extract of Tamarindus indica using network pharmacology approach and evaluating its efficacy in Chronic Unpredictable Mild Stress model in mice","authors":"Vishnusai Beere, Khushboo Choudhary, Priya Bisht, Amita Rai, Nitesh Kumar","doi":"10.1007/s13205-024-04081-9","DOIUrl":"https://doi.org/10.1007/s13205-024-04081-9","url":null,"abstract":"<p>The prevalence of psychological disorders has surged since the 1990s, posing a significant global health burden with depressed individuals averaging six lost hours per week and contributing to over 20% of all missed workdays. Current antidepressants, while effective for some, have limited efficacy, dietary restrictions, and adverse effects, including liver damage and hypertension. Natural remedies offer promising therapeutic potential with minimal side effects. <i>Tamarindus indica</i> (TI) is a plant that grows in the shape of a tree. Network pharmacology of TI revealed the key targets MAPK, D1-6, 5HT, DAT, MAO, COMT, PKA, PKC, AKT, and VMAT, which are linked to prominent key pathways such as dopaminergic and serotonergic. The cell viability assays on SH-Sy5y cells indicated a favourable safety profile with an IC50 of 573.99 µg/ml and further, the in vivo efficacy was observed through Chronic Unpredictable Mild Stress (CUMS) model in mice. The hydroalcoholic extract of TI demonstrated antidepressant effects, significantly reducing immobility time in the Tail Suspension Test (TST) and Forced Swim Test (FST). Additionally, locomotor activity, assessed via the Open Field Test (OFT), was significantly increased in the treatment group compared to CUMS mice. Biochemical analyses revealed elevated Brain Derived Neurotropic Factor (BDNF), decreased cortisol levels, and reduced catechol-<i>O</i>-methyltransferase (COMT) concentration in TI-treated (50 mg/kg) groups. These findings underscore the potential of TI as a natural antidepressant, offering a promising avenue for further therapeutic development in depression management. The current study did not evaluate the level of neurotransmitters in the brain, which will be evaluated in future studies.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142182824","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The structural insights of L-asparaginase from Pseudomonas aeruginosa CSPS4 at elevated temperatures highlight its thermophilic nature","authors":"Vinay Kumar, Pragya Anand, Ankita Srivastava, Yusuf Akhter, Digvijay Verma","doi":"10.1007/s13205-024-04072-w","DOIUrl":"https://doi.org/10.1007/s13205-024-04072-w","url":null,"abstract":"<p>In the present investigation, a novel thermophilic L-asparaginase (Asn_PA) from <i>Pseudomonas aeruginosa</i> CSPS4 was investigated to explore its structural insights at elevated temperatures. Sequence analysis of Asn_PA depicted three conserved motifs (VVILATGGTIAG, DGIVITHGTDTLEETAYFL, and, LRKQGVQIIRSSHVNAGGF), of them, two motifs exhibit catalytically-important residues i.e., T⁴⁵ and T¹²⁵. A homology modelling-based structure model for Asn_PA was generated with 4PGA as the top-matched template. The predicted structure was validated and energy was minimized. Molecular docking was carried out cantered at the active site for asparagine and glutamine as its substrate ligands. The enzyme–substrate interaction analysis showed binding affinities of – 4.8 and – 4.1 kcal/mol for asparagine and glutamine respectively. Molecular dynamics (MD) simulation studies showed a better stability of Asn_PA at temperatures of 60 °C, over 40, 50 and, 80 °C, making this enzyme a novel L-asparaginase from other mesophilic <i>P. aeruginosa</i> strain. The trajectory analysis showed that RMSD, Rg, and, SASA values correlate well with each other in the different tested temperatures during the MD analysis. Thus, the present findings encourage extensive characterization of the Asn_PA using laboratory experiments to understand the structural behavior of the active site loop in an open or closed state with and without the substrate molecules.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142182841","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Virtual screening and molecular dynamics simulations of phytochemicals targeting cofactor-independent phosphoglycerate mutase in antimicrobial-resistant Mycoplasma genitalium","authors":"Krishnendu Barik, Pranabesh Mandal, Praffulla Kumar Arya, Durg Vijay Singh, Anil Kumar","doi":"10.1007/s13205-024-04082-8","DOIUrl":"https://doi.org/10.1007/s13205-024-04082-8","url":null,"abstract":"<p><i>Mycoplasma genitalium (M. genitalium)</i> poses a significant challenge in clinical treatment due to its increasing antimicrobial resistance. This study investigates alternative therapeutic approaches by targeting the cofactor-independent phosphoglycerate mutase (iPGM) enzyme with phytochemicals derived from ethnobotanical plants. In silico screening identified several promising inhibitors, with 2-carboxy-D-arabinitol demonstrating the highest binding affinity (− 9.77 kcal/mol), followed by gluconic acid (− 9.03 kcal/mol) and citric acid (− 8.68 kcal/mol). Further analysis through molecular dynamics (MD) simulations revealed insights into the binding mechanisms and stability of these phytochemicals within the iPGM active site. The MD simulations indicated initial fluctuations followed by stability, with intermittent spikes in RMSD values. The lowest RMSF values confirmed the stability of the ligand–protein complexes. Key residues, including Ser-61, Arg-188, Glu-62, Asp-397, and Arg-260, were found to play crucial roles in the binding and retention of inhibitors within the active pocket. These findings suggest that the identified phytochemicals could serve as novel antimicrobial agents against <i>M. genitalium</i> by effectively inhibiting iPGM activity.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142182823","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}