Mohammad Oliur Rahman

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.

Francisella tularensis Schu S4 is the most virulent strain responsible for tularemia, a highly infectious zoonotic disease. Despite its potential as a pathogen of concern, no effective vaccine has been developed for this pathogen. In this study, two multi-epitope subunit vaccine candidates were designed targeting the virulence factors DacD and DsbA to reduce disease severity caused by F. tularensis Schu S4. Using a comprehensive immunoinformatics approach, the most efficient B- and T-cell epitopes were identified from conserved sequences and linked with adjuvants and linkers to generate two vaccine constructs. These constructs were modeled, refined, and validated through molecular docking against Toll-Like Receptors (TLRs) and MHC alleles, followed by 200 ns molecular dynamics simulations. Their immunogenic potential and expression efficiency were further evaluated through immune simulations and computational cloning into the pET30a( +) vector. Both the constructed vaccine candidates, TulaVac1 and TulaVac2, showed high antigenicity, immunogenicity, stability, and solubility. The epitope conservancy was nearly 100%, with global population coverage rates of 73.19% and 99.74% for MHC class I and II epitopes, respectively. Docking analyses revealed six CTL epitopes with binding energies of ≤ -9.0 kcal/mol, while vaccine-TLR and MHC docking suggested superior performance of TulaVac1. MM/GBSA analysis yielded favorable binding energies ranging from - 87.22 to - 161.30 kcal/mol, MD simulations confirmed the stable interaction for 200 ns, and immune simulations showed robust immune responses with satisfactory codon adaptation. These findings position TulaVac1 and TulaVac2 as promising candidates for effective prophylaxis against tularemia.

Byttnerioideae Burnett is an economically and medicinally important subfamily belonging to Malvaceae. A molecular phylogenetic and dating approach was undertaken to elucidate the evolutionary relationships and divergence history of the Byttnerioideae species available in Bangladesh based on the matK gene. A multifaceted, algorithm-driven strategy was applied with Maximum-Likelihood (ML), Maximum-Parsimony (MP), and Bayesian Inference (BI) algorithms that resulted in a consistent tree topology for the four tribes, namely as Byttnerieae, Hermannieae, Theobromateae and Lasiopetaleae. All the tribes exhibited monophyletic origin with strong bootstrap and posterior probability support. Byttnerieae, Hermannieae and Theobromateae were found to be more closely related to each other than to Lasiopetaleae. Molecular dating analysis revealed Lasiopetaleae as the oldest tribe, diverging approximately 39.51 million years ago (MYA) in the Bartonian age of the Cenozoic era, while Byttnerieae was identified as the most recent tribe, diverging around 33.24 MYA in the Rupelian age of the same era. These findings would update the phylogenetic relationship of Byttnerioideae and provide valuable insights for the development of the historical biogeography of Byttnerioideae in future endeavors. J. Asiat. Soc. Bangladesh, Sci. 51(2): 151-163, December 2025

Lycium shawii Roem. & Schult., a stress‐resilient medicinal plant native to the deserts of Saudi Arabia, possesses notable bioactive compounds used in traditional medicine for treating inflammation, oxidative stress, and other ailments. However, its chloroplast (Cp) genome has not previously been sequenced or described, limiting accurate molecular identification and phylogenetic resolution. In this study, we present the first complete Cp genome of L. shawii . The plastome spans 155,936 bp and is organized into a large single‐copy (LSC) region (86,608 bp), a small single‐copy (SSC) region (18,430 bp), and two inverted repeats regions (IRA and IRB), each spanning 25,449 bp. A total of 128 genes were annotated, comprising 84 protein‐coding genes, 36 tRNAs, and eight rRNAs. Comparative genomic analyses revealed conservation of genome structure without major rearrangements across Solanaceae. Forty simple sequence repeats (SSRs) and 50 oligonucleotide repeats were identified, with mononucleotides (38) as the dominant SSR type, and forward repeats as the most common among longer repeats. RNA‐editing sites were unevenly distributed, with the highest proportion in the LSC region (48%), followed by the SSC (29%) and IRs (23%). Nucleotide diversity analysis highlighted atpI , rbcL , and accD within the LSC region as hypervariable loci suitable for DNA barcoding. Plastome‐wide phylogenetic reconstruction confirmed the placement of L. shawii within the tribe Lycieae of the subfamily Solanoideae. Molecular dating analysis suggested its emergence around 1.40 MYA, during the Calabrian stage of the Cenozoic era. This study provides the first Cp genome resource for L. shawii , offering new perspectives for evolutionary and comparative genomics within Solanaceae.

Hypercholesterolemia, a major risk factor for cardiovascular diseases, arises from elevated blood cholesterol levels and remains a global health concern. The limitations of current therapies underscore the need for alternative drugs from natural sources. Mikania cordata (Asteraceae) is an ethnomedicinally important species that harbors numerous bioactive phytoconstituents. In this study, 91 phytocompounds of this medicinal species were virtually screened targeting the HMG-CoA (3-hydroxy-3-methylglutaryl-coenzyme A) reductase protein. Molecular docking, ADMET (absorption, distribution, metabolism, excretion, and toxicity), and MM/GBSA (molecular mechanics/generalized born surface area) analyses identified epifriedelanol as the best lead candidate among the phytocompounds with strong binding affinity (−8.6 kcal/mol), drug-likeness, and free binding energy (−39.5 kcal/mol), outperforming the standard drug atorvastatin (−7.7 kcal/mol and −21.4 kcal/mol). Analogs of epifriedelanol (EA) were further explored, generating 451 compounds. High-throughput screening of these analogs identified 244 compounds with a docking score higher than atorvastatin (−7.7 kcal/mol). The ADMET evaluation highlighted two analogs, EA2 and EA3, with docking scores of −9.3 kcal/mol and supportive MM/GBSA free energies (−31.9 and −43.7 kcal/mol). Molecular dynamics simulation (500 ns) confirmed the structural stability of epifriedelanol, EA2, and EA3, while essential dynamics and Gibbs free energy landscape analyses indicated a binding behavior comparable to that of atorvastatin. Target class analysis predicted interactions with nuclear receptors. These findings suggest that epifriedelanol and its analogs are promising natural leads against hypercholesterolemia, warranting further in vitro and in vivo validation.

Alzheimer’s disease (AD), a progressive neurodegenerative disorder, poses a significant global health burden due to its intricate pathology and the absence of curative treatments. Current therapies primarily offer symptomatic relief, often with limited efficacy and complications, thereby underscoring the urgent need for innovative, safer, and more effective interventions. Stigmasterol, a plant-derived phytosterol, has demonstrated neuroprotective properties, including anti-inflammatory and antioxidant effects, which positions this sterol as a compelling candidate for further investigation in AD treatment. In this investigation, high-throughput virtual screening of 972 stigmasterol analogs (SAs) was conducted to identify potential acetylcholinesterase (AChE) inhibitors, followed by ADMET filtering, molecular dynamics (MD) simulations, MM/GBSA free binding energy estimations, and DFT calculations. Three lead compounds, including SA4 (-10.9 kcal/mol), SA12 (-10.6 kcal/mol), and SA15 (-10.5 kcal/mol), demonstrated superior binding affinities compared to stigmasterol (-9.6 kcal/mol) and the control drug donepezil (-8.6 kcal/mol). Docking interaction analysis revealed strong binding by hydrogen bonds and hydrophobic interactions, whereas pharmacokinetic, pharmacodynamic, and toxicity assessments confirmed the favorable characteristics of these compounds. MD simulations (200 ns) demonstrated the structural compactness of the compounds, which was further supported by principal component analysis and Gibbs free energy landscape experiments. MM/GBSA identified SA4 as the most potent analog (-82.21 kcal/mol), followed by SA15 (-80.40 kcal/mol) and SA12 (-69.72 kcal/mol). A DFT-based molecular reactivity analysis revealed decreased reactivity and increased kinetic stability of the lead candidates in their transition from free to bound states. These findings provide insights into the therapeutic potential of stigmasterol analogs as AChE inhibitors, thus offering the groundwork for in vivo and in vitro validation for advancing AD treatment.

In this investigation, whole genome sequencing and assembly of medicinally important species Aizoon canariense L. were performed to unveil its nuclear genome. The assembled nuclear genome length was 661.14 Mb, with an N50 value of 25,334 bp. The genome was largely homozygous, with a low level of heterozygosity ranging from 0.077 to 0.078%. BUSCO assessment exhibited 91.8% completeness based on the Viridiplantae database. Orthologous gene-based analysis revealed that the highest number of genes were associated with replication, recombination, and repair category. Gene Ontology (GO)-based annotation identified 5,814 genes involved in biological processes (BP), 25,137 genes linked to cellular components (CC), and 16,644 genes associated with molecular functions (MF). Pathway enrichment analysis identified the protein modification pathway representing the highest number of genes (807), whereas the pigment biosynthesis pathway exhibiting the lowest number of genes (75). A total of 20,448 repeat elements across 57 distinct types were identified in the assembled genome, with LTR/Gypsy being the most abundant, comprising 7,532 copies and spanning approximately 27,750 bp. These findings lay a strong foundation for future research on the molecular mechanisms of stress resilience in arid ecosystems targeting A. canariense. Bangladesh J. Plant Taxon. 32(1): 1-16, 2025 (June)

This study deciphers the first complete chloroplast (Cp) genome of Fraxinus griffithii C.B. Clarke (Oleaceae), a medicinally important tree species native to Bangladesh, providing new insights into its genome structure and phylogenetic relationships. The circular Cp genome comprises a total length of 155,683 bp with a large single-copy region (86,466 bp), small single-copy region (17831 bp), and two inverted repeat regions (51,386 bp). The plastome encodes 130 genes, including 86 protein-coding genes, 36 transfer RNAs and eight ribosomal RNAs. Comparative genomic analysis revealed genome divergence, similar genomic architecture, and lack of large rearrangements within the Oleaceae family. The plastome harbored 46 simple sequence repeats (SSRs) and 49 longer repeats. Among the identified SSRs, mononucleotides (39) were the most frequent, while palindromic repeats predominated among the longer repeats. Nucleotide diversity analysis revealed rpl32 and ndhF genes of the SSC region as the most hypervariable DNA barcodes. Plastome-wide phylogeny supported the systematic position of F. griffithii within the subtribe Fraxininae of the tribe Oleeae. Molecular dating analysis suggests that F. griffithii originated approximately 15.07 million years ago, during the Langhian stage of the Middle Miocene epoch in the Neogene period of the Cenozoic era. The findings of this study provide the first Cp genome data for F. griffithii (GenBank Accession: PP669282.1), contributing to valuable insights into the evolutionary genomics of the family Oleaceae. Bangladesh J. Plant Taxon. 32(1): 27–44, 2025 (June)

The present study explored morphometric relationships of 24 species belonging to 14 genera of Anacardiaceae (R. Br.) Lindl. for the very first time in Bangladesh, using a numerical systematic approach. A total of 33 vegetative and reproductive characters were analyzed through cluster analysis (CA) and principal component analysis (PCA). The UPGMA dendrogram revealed two major clades, comprising 18 and six species, respectively. In the first clade, Mangifera indica and M. longipes (tribe Anacardieae) exhibited the highest similarity, while in the second clade, the highest affinity was found between Spondias dulcis and S. pinnata (tribe Spondiadeae). PCA explained 85.70% cumulative variance across the first six principal components, with scatter and projection plots aligning with the cluster analysis results. These findings provide the insights into the taxonomic relationships of Anacardiaceae in Bangladesh, aiding conservation strategies, particularly for threatened and medicinally important species, and serving as a foundation for future molecular phylogenetic endeavor. Bangladesh J. Bot. 54(2): 199-209, 2025 (June)

Non-small cell lung cancer (NSCLC) accounts for 85-90% of global lung cancer cases and causes over 1.7 million deaths annually worldwide. Despite therapeutic advancements, existing treatments remain expensive and are often associated with significant side effects, underscoring the need for alternative drug candidates. Natural compounds offer promising prospects as safer and more affordable therapeutic options for NSCLC. Toxicodendron succedaneum, a medicinally important plant species from the family Anacardiaceae, contains a diverse phytoconstituents with potential anticancer activity. Investigating these bioactive compounds may uncover therapeutic potential to facilitate NSCLC drug discovery. In this study, a comprehensive structure-based drug design approach was employed to identify drug candidates targeting the extracellular signal-regulated kinase 2 (ERK2) receptor. Using molecular docking, molecular dynamics (MD) simulation, ADMET analysis, MM/GBSA calculations, and DFT assessments, two lead compounds: rhusflavone ( - 10.9 kcal/mol) and hinokiflavone ( - 9.9 kcal/mol), were identified, both revealing favorable drug-likeness and toxicity profiles. MD simulation spanning 500 ns timescale confirmed the structural stability of the identified leads, further corroborated by principal component analysis (PCA) and Gibbs free energy landscape (FEL) evaluations. Rhusflavone emerged as the most promising candidate, with a free binding energy of - 57.15 ± 5.28 kcal/mol. DFT analysis revealed enhanced molecular reactivity of the lead compounds upon transitioning from the free to the bound states. These results could contribute to the development of novel lung anticancer drugs, warranting further in vitro and in vivo validation.