Sheikh Sunzid Ahmed

Calamus erectus Roxb. is a medicinally important and vulnerable shrub native to Bangladesh. Despite its ecological and ethnobotanical importance, no complete chloroplast genome has been reported for this species. In this study, we characterized the complete plastome of C. erectus. The assembled plastome was 157,887 bp in length and exhibited a typical quadripartite circular structure, comprising a large single-copy (85,756 bp), a small single-copy (17,593 bp), and a pair of inverted repeats (27,269 bp each). The plastome encoded 131 genes, consisting of 86 protein-coding genes, 37 transfer RNA genes, and eight ribosomal RNA genes. Seventy simple sequence repeats were identified, mostly mononucleotides (49). A codon usage analysis exhibited a strong preference for codons ending in the adenine or uracil base, reflecting an overall A/T bias in the genome. Plastome-based phylogenetic analyses placed C. erectus within the monophyletic tribe Calameae and indicated a close relationship with C. exilis. A molecular dating analysis indicated that C. erectus diverged approximately 7.6 million years ago during the Tortonian age, while the subfamily Calamoideae originated about 46.2 million years ago in the early Miocene. These findings provide the first complete cp genome resource for C. erectus, offering a foundation for further phylogenomic and conservation studies within Arecaceae.

Prasoxylon excelsum (Spreng.) Mabb., a medicinal tree of the family Meliaceae, is traditionally used to treat diarrhoea, dysentery, and food poisoning. Despite its ethnobotanical significance, no genomic resources have been available to date. This study presents the first de novo assembly and characterization of both the chloroplast (Cp) and nuclear genomes of P. excelsum. The complete Cp genome spans 160,299 bp and exhibits a typical quadripartite structure, comprising a large single-copy (LSC) region of 87,832 bp, a small single-copy (SSC) region of 18,360 bp, and a pair of inverted repeats (IRs) of 27,054 bp each. The plastome encodes 81 protein-coding genes, 37 transfer RNAs, and eight ribosomal RNAs. A total of 98 simple sequence repeats (SSRs) were identified, predominantly mononucleotide motifs (68). Nucleotide diversity analysis revealed atpB and ycf1 as the most variable regions, suggesting their potential as DNA barcodes. Phylogenetic reconstruction using the maximum-likelihood method confirmed the placement of P. excelsum within the subfamily Melioideae. Molecular dating analysis indicated that P. excelsum diverged during the late Burdigalian age of the Miocene epoch, approximately 16.21 million years ago. The nuclear genome assembly totaled 676.45 Mb with an N50 of 3,686 bp, showing 87.8% BUSCO completeness. Gene prediction identified 44,465 genes, with KEGG analysis indicating enrichment in metabolic pathways. These findings provide a valuable foundation for evolutionary, phylogenomic, and functional studies in Prasoxylon and related Meliaceae species, aiding future research in conservation genomics, phytochemistry, and molecular breeding. Bangladesh J. Plant Taxon. 32(2): 139-160, 2025 (December)

Addition to the angiosperm flora provides essential insights into the biodiversity of a region, contributing to ecological understanding and conservation planning. Gafargaon subdistrict under Mymensingh district in Bangladesh represents a diverse population of angiosperms with a multifaceted ecosystem that demands re-evaluation of the existing angiosperm diversity of Gafargaon to update the status of angiosperm taxa and facilitate their conservation efforts. With this endeavor, a total of 100 angiosperm taxa belonging to 90 genera and 46 families were uncovered as additional occurrence in Gafargaon. The species in the area showcased a variety of life forms, including 63 herbs, 14 shrubs, 14 trees, and 9 climbers. Among the recorded taxa, Chamaecostus cuspidatus (Nees & Mart.) C.D. Specht & D.W. Stev. was selected for antidiabetic drug design endeavor based on citation frequency and ethnomedicinal evidence. A total of 41 phytochemicals of C. cuspidatus were screened virtually, targeting the Dipeptidyl peptidase 4 protein through structure-based drug design approach, which unveiled two lead compounds, such as Tigogenin (-9.0 kcal/mol) and Diosgenin (-8.5 kcal/mol). The lead candidates demonstrated favorable pharmacokinetic and pharmacodynamic properties with no major side effects. Molecular dynamics simulation revealed notable stability and structural compactness of the lead compounds. Principal component analysis and Gibbs free energy landscape further supported the results of molecular dynamics simulation. Molecular mechanics-based MM/GBSA approach unraveled higher free binding energies of Diosgenin (-47.36 kcal/mol) and Tigogenin (-46.70 kcal/mol) over Alogliptin (-46.32 kcal/mol). The outcome of the present investigation would enrich angiosperm flora of Gafargaon and shed light on the role of C. cuspidatus to develop novel antidiabetic therapeutics to combat diabetes.

Chagas disease is a tropical ailment indigenous to South America and caused by the protozoan parasite Trypanosoma cruzi, which has serious health consequences globally. Insect vectors transmit the parasite and, due to the lack of vaccine availability and limited treatment options, we implemented an integrated core proteomics analysis to design a reverse vaccine candidate based on immune epitopes for disease control. Firstly, T. cruzi core proteomics was used to identify immunodominant epitopes. Therefore, we designed the vaccine sequence to be non-allergic, antigenic, immunogenic, and to have better solubility. After predicting the tertiary structure, docking and molecular dynamics simulation (MDS) were performed with TLR4, MHC-I, and MHC-II receptors to discover the binding affinities. The final vaccine design demonstrated significant hydrogen bond interactions upon docking with TLR4, MHC-I, and MHC-II receptors. This indicated the efficacy of the vaccine candidate. A server-based immune simulation approach was generated to predict the efficacy. Significant structural compactness and binding stability were found based on MDS. Finally, by optimizing codons on Escherichia coli K12, a high GC content and CAI value were obtained, which were then incorporated into the cloning vector pET2+ (a). Thus, the developed vaccine sequence may be a viable therapy option for Chagas disease.

Cancer is one of the leading causes of death due to its very high rate of morbidity and mortality, and there is a constant demand of effective drugs for cancer therapy. Vascular endothelial growth factor receptor-2 (VEGFR-2) plays a significant role as central modulator of angiogenesis and is targeted frequently for developing anti-angiogenic agents to fight cancer. Helicteres isora L. (Malvaceae) is reported to possess diverse medicinal properties including anti-cancer potentials. In the current investigation, 38 bioactive phytochemicals of H. isora were screened virtually to evaluate their anti-angiogenic potentials targeting VEGFR-2. The study unveiled three potential candidates such as, Diosgenin (-9.8 Kcal//mol), Trifolin (-8.4 Kcal/mol) and Yohimbine (-8.1 Kcal/mol) that showed favorable pharmacokinetic, pharmacodynamic and toxicity properties with no significant side effects. Molecular dynamics simulation employing 100 ns revealed noteworthy structural stability and compactness for all the top three candidates. The MM/GBSA binding free energy estimation corroborated the docking interactions where Yohimbine (-30.47 Kcal/mol) scored better than Diosgenin (-27.54 Kcal/mol) and Trifolin (-29.58 Kcal/mol). Target class prediction revealed enzymes in most of the cases and some FDA approved drugs were found as structurally similar analogs for Trifolin and Yohimbine. These findings could lead to the development of novel and effective anti-angiogenic agents. Graphical Abstract Communicated by Ramaswamy H. Sarma

The SARS-CoV-2 has severely impacted the lives of people worldwide. Global concern is on the rise due to a large number of unexpected mutations in the viral genome, resulting in new variants. Nature-based bioactive phytochemicals hold great promise as inhibitors against pathogenic viruses. The current study was aimed at evaluating some bioactive antiviral phytochemicals against SARS-CoV-2 variants of concern. A total of 46 phytochemicals were screened against the pathogenic spike protein of Alpha, Beta, Delta, Gamma, and Omicron variants. In addition to molecular docking, screening for favorable pharmacokinetic and pharmacodynamic properties such as absorption, distribution, metabolism, excretion, and toxicity was undertaken. For each of the aforementioned five SARS-CoV-2 variants of concern, a 100 ns molecular dynamics simulation was run to assess the stability of the complexes between their respective spike protein receptor-binding domain and the best-selected compound. From our current investigation, the natural compound liquiritigenin turned out to be the most promising potential lead compound against almost all the variants. These findings could pave the way for the development of effective medications against SARS-CoV-2 variants. However, in vivo trials in future studies are necessary for further validation of our results. Communicated by Ramaswamy H. Sarma

Francisella tularensis Schu S4 is the causal agent of a sporadic zoonotic disease known as Tularemia, which has shown epidemic outbreaks recently in certain parts of the world. This pathogen is a potential agent of biowarfare or bioterrorism and is classified as a category A pathogen by the National Institute of Allergy and Infectious Diseases. In this virulent strain, 453 genes have been identified as essential genes, indispensable for growth and survival of the pathogen. The functions of 44 proteins encoded by those essential genes were found to be hypothetical and thus defined as essential hypothetical proteins (EHPs). The current study used a wide range of in silico tools and servers to annotate the physicochemical, structural, and functional properties of these EHPs. Of all the EHPs, 24 were functionally annotated with a high degree of confidence and validated by Receiver Operating Characteristic curve analysis. Non-homology assessment revealed 20 pathogen-specific EHPs, which were further analyzed for protein-protein interactions and predicted for secondary and tertiary structure. All the 3D structures were checked on multiple quality assessment servers, and the best models were visualized. The outcome of the study could aid in enhancing current understanding of bacterial pathogenesis with novel drug and vaccine investigations.