Journal of Basic and Emerging Sciences

Domain-Specific interactions of HPV16 E2 with TopBP1: Insights from Molecular Docking and Dynamics

2025-12-31T05:17:35+00:00

Cervical cancer, a major contributor to worldwide cancer-related deaths, is primarily driven by persistent infections with oncogenic human papillomavirus (HPV) types, most notably HPV16. The viral E2 protein is a master regulator, playing pivotal roles in replication, transcription, and episomal maintenance, largely through interactions with host cellular proteins. A key interaction partner is Topoisomerase IIβ-binding protein 1 (TopBP1), a scaffold protein essential for DNA damage response and genome stability. However, the mechanistic details of E2's engagement with TopBP1's individual BRCT domains remain poorly characterized. This study employed an integrated in silico approach to elucidate the molecular basis of HPV16 E2's transactivation domain (TAD) interaction with all eight BRCT domains of TopBP1. High-confidence structural models were predicted, refined, and rigorously validated. Comprehensive protein-protein docking revealed domain-specific binding profiles, identifying E2-D4 and E2-D7 as the most promising complexes based on binding energy and interfacial interactions. Molecular dynamics simulations and MM-GBSA binding free energy calculations for these complexes demonstrated that E2-D4 forms a stable, hydrophobic-driven complex ideal for structural anchoring, while E2-D7 exhibits dynamic, electrostatically stabilized interactions suited for flexible recruitment. These findings provide unprecedented atomistic insight into the HPV16 E2-TopBP1 interactome, revealing novel domain-specific vulnerabilities that could be targeted to disrupt viral persistence and prevent oncogenic progression.

Phytochemical Profiling and FT-IR Spectroscopic Analysis of Selected Anti-Leishmanial Plants

2025-12-31T05:27:43+00:00

Bioactive chemicals found in medicinal plants have long been used to treat and prevent a wide range of human illnesses. As they are essential in the fight against infectious disorders like leishmaniasis. Eucalyptus globulus, Lawsonia inermis, and Syzygium jambolana were selected to determine the phytochemical components in their leaves that may have anti-leishmanial qualities. The leaves of selected plants were dried and grounded into fine powder and extracted using a solvent system of methanol, chloroform and water, (80ml:10 ml:10 ml). After filteration, the filterate was concentrated using a rotary evaporator. The extracts were subjected to phytochemical analysis, organoleptic evaluation and Fourier-transform infrared (FTIR) spectroscopy. The results showed the occurrence of flavonoids, saponins, terpenoids, phenolics and tannins but no proteins was found in leaves of aforementioned plants. FTIR analysis of Eucalyptus globulus leaves revealed the presence of alkenes and hydroxyl functional groups that indicating phenols, carboxylic acids or alcohols. Similarly Lawsonia inermis's FTIR analysis revealed several functional groups by identification of characteristic vibrational bands. Numerous functional groups, such as phenolic compounds, carboxylic acids and alkyl groups were detected in Lawsonia inermis FTIR analysis. FTIR spectrum showed 11 distinct peaks indicating the presence of important functional groups such as carboxylic acids, phenolics, alkyl groups, and aromatic rings in leaves of Syzygium jambolana. These peaks indicated a high concentration of bioactive substances with strong anti-leishmanial effects, such as alkaloids, flavonoids, and phenolic compounds. Due to high medicinal potential, these plant were considered as potent sources of bioactive constituents to be used against leishmaniasis.

Exploring the different inhibitors of Apis dorsata amylase inhibitors from different plant sources using docking approach

2025-12-31T05:33:15+00:00

The putative protein sequence of amylase from honey bee Apis dorsata was retrieved through NCBI database (GenBank ID XP_006614569.1) consisting of 493 amino acids. To identify the conserved residues, and domains in Apis α-amylase, the protein sequence was aligned with six other amylase sequences from Apis cerana (95%), Apis mellifera (94%), Drosophila ananassae (65%), Drosophila punjabiensis (61%), Drosophila melanogaster (59%) and Tenebrio molitor (59%). The presence of three active site residues (Asp²⁰⁷, Glu²⁴⁴ and Asp³⁰⁹) in catalytic domain along with domain B, and CBM-domain C showed that A. dorsata amylase is active and belong to family GH13. Plant inhibitors like luteolin, rosmarinic acid, saponin II and azadiriadone were docked on active site of amylase using Autodock Vina program with binding energy -9.2 to -6.3 Kcal/mol. Azadiradone, luteolin and rosmarinic acid interacted with catalytic residues as well as substrate binding site, thus blocking both sites. While saponin II showed little interactions with catalytic site residues but it was strongly associated with Lys³⁵² present in a loop right above the active site, which is conserved in all α-amylases of Apis species. Amylase of Apis dorsata is a calcium dependent enzyme like all Apis amylases due to the presence of four functional active residues (Asn¹¹⁸, Arg¹⁶⁸, Asp¹⁷⁷ and His²¹¹). This inhibitor’s effect shall be useful in developing potential insecticides and pesticides.

Studies on the Suitability of the Hiran Minar for Fish Culture and Interrelated Activities

2025-12-31T05:46:34+00:00

Hiran Minar is a monument of Mughal Empire. It is located in distt. Sheikhupura and is 45 km to the north west of Lahore. Emperor Jhangir, in the memory of his the dearest deer (Mansraj), erected this monument and is named Hiran Minar (Hiran means deer). Later on, Shah Jahan Mughal Emperor (son of Shah Jahangir) built a square water reservoir adjacent to this monument. This reservoir with octagonal pavilion served as drinking water source for royal animals. Presently Government controls these installations along with all the ongoing activities. Punjab Fisheries Department stock in this reservoir and utilizes it for fish production. Archaeology Department is taking care of the brick building portion. Punjab Fisheries Department invite professional anglers and hold the fishing competitions in that reservoir. The children swim in this reservoir while women from the nearby villages wash clothes. People from the nearby villages bring their livestock to this reservoir. They drink water and take baths. Most of the people go there when they are free. Some of them enjoy picnic and boating. From the last few years, the villagers were complaining about this reservoir. They reported about the denial of their animals towards this reservoir. If by hook or crook they visit this reservoir they feel uncomfortable. They suffered from loose motions and refused to eat fodder. Fisheries Department has its complaints.They reported that fish appeared lethargic, it did not grow properly, majority of fishes died. Fishes displayed aberrations and spots on their bodies. Irrespective of the season of the year oxygen depleted frequently. Therefore, studies were conducted to explore the probable reasons that induced such uncommon outcomes in the reservoir water.Data collected showed unusual changes in the composition of water.Quality of water became unsuitable for fish culture and livestock visits. Even it was inappropriate for bathing, swimming and washing activities of the human beings.

Kinetic Study of Crystal Violet Dye Adsorption from Wastewater Using Populus nigra Leaf Powder

2025-12-31T05:51:04+00:00

This study investigates the potential of Populus nigra (black poplar) leaf powder as a low-cost, eco-friendly adsorbent for the removal of Crystal Violet dye from wastewater. Batch adsorption experiments were conducted to assess the effects of pH, contact time, adsorbent dosage, initial dye concentration, and temperature. Optimal removal conditions were observed at pH 10 and 15 °C, achieving an adsorption efficiency of 84%. The adsorption followed the Langmuir isotherm model (R² = 0.9696), indicating monolayer adsorption, and the kinetics fit the pseudo-second-order model (R² = 1), suggesting chemisorption as the rate-limiting step. These results highlight Populus nigra leaves as a sustainable biosorbent capable of reducing dye pollution in industrial effluents, offering a promising alternative to conventional treatment methods

Association of Diabetes Mellitus with COVID-19 Severity and Prognosis

2025-12-31T06:12:29+00:00

The global COVID-19 pandemic has posed a major health crisis, particularly affecting individuals with pre-existing chronic conditions such as diabetes mellitus. This retrospective cohort study aimed to explore the association between diabetes mellitus (both Type 1 and Type 2) and COVID-19 in the public of Pakistan. 1,514 diabetic patients were surveyed between October 2024 and April 2025 from various hospitals in Lahore, 635 were found to be co-infected with COVID-19. The study analyzed the prevalence of comorbidities such as cardiovascular, kidney, liver, pulmonary diseases, and neuropathy, along with factors such as BMI, smoking, and blood pressure. Results showed that COVID-19 prevalence was higher in males (57.6%) and primarily affected the 41–60 age group. Type 2 diabetes was predominant among co-infected patients (89.4%). Mortality was significantly higher in diabetic patients with COVID-19 (36.7%) compared to those without (5.2%). Chi-square analysis confirmed significant associations between COVID-19 in diabetics and risk factors such as pulmonary problems, smoking, liver disease, kidney disease, and cardiovascular conditions. These findings emphasize the critical need for focused healthcare strategies for diabetic patients during respiratory pandemics.