Alzheimer's disease, a debilitating degenerative disorder, poses a formidable challenge in terms of treatment, with a projected surge in the number of afflicted individuals annually. The imperative quest for novel anti-Alzheimer's compounds derived from natural sources is underscored by the urgency to address this escalating health crisis. Austricin, identified in langsat kombucha, emerges as a promising candidate due to its demonstrated affinity for the muscarinic acetylcholine receptor M1 and anti-inflammatory properties. In this study, we conduct an extensive validation of austricin's potential through assessments of blood–brain barrier permeability, absorption, distribution, metabolism, and excretion. Additionally, we explore its binding capabilities with the pivotal protein steril-sulfatase, identified as a primary target in Alzheimer's pathology. Comparative analyses are performed with established compounds, donepezil and galantamine. Analysis reveals that austricin successfully traverses the blood–brain barrier (LogBBB -0.19498) with a solubility of 3.54e+00 mg/ml, high gastrointestinal absorption, and Lipinski's Rule of Five compliance. Importantly, it exhibits a bioavailability score of 0.55 and a synthetic accessibility of 4.60, establishing its potential as a viable drug candidate. The compound shows no substrate inhibition for major cytochrome P450 enzymes (CYP1A2, CYP2C19, CYP2C9, CYP2D6, and CYP3A4). Furthermore, molecular docking analyses reveal austricin's superior ΔG-binding affinity (-7.9 kcal/mol) compared to donepezil (7.4 kcal/mol) and galantamine (7.2 kcal/mol) for steril-sulfatase. While these findings suggest austricin's promise as an anti-Alzheimer's compound, further investigations on key Alzheimer's-associated proteins and in vitro testing are indispensable for conclusive validation and development. This study provides a foundation for the potential therapeutic application of austricin, paving the way for subsequent experimental endeavors and clinical investigations in the pursuit of effective Alzheimer's treatments.

Malaria is one of the infectious illnesses causing a public health burden worldwide. Plasmodium vivax (P. vivax) is the most prevalent malaria parasite in Asia and Asia Pacific. P. vivax is resistant to sulfadoxine–pyrimethamine (SP) and mefloquine. This resistance makes it extremely difficult to control and eradicate due to its ability to survive in the liver and reactivate if the person infected has a weakened immune system. Thus, this study aims to inhibit P. vivax via targeting Duffy-binding protein (DBP) with active compounds from Hops (Humulus lupulus). The inhibition of DBP is essential to reduce malaria invasion of human red blood cells. We performed a quality assessment and prediction of the active site of DBP to determine the effectiveness and prediction of ligands in inhibiting DBP. Furthermore, the mechanism and structural stability of active compounds against DBP were evaluated using a combination of molecular docking and molecular dynamics simulation and a density-functional theory (DFT) study. The results showed that rutin had the highest binding of 8.852 kcal/mol. However, after the molecular dynamics simulation was run for 50 ns, the ligand 6-prenylnaringenin via MM-PBSA calculation showed the most positive value of 106.760 kJ/mol. In addition, 6-prenylnaringenin is the most stable ligand via the analysis of root-mean-square deviation backbone (RMSDBb), root-mean-square deviation c-alpha (RMSDCa), root-mean-square fluctuation (RMSF), solvent-accessible surface area (SASA), radius of gyration (Rg), and the hydrogen bond formation. We conclude that 6-prenylnaringenin has a tight and stable bond with the targeted DBP protein. Finally, we propose the use of 6-prenylnaringenin as a potential antimalarial compound via in silico studies.

Introduction: This research work is designed to identify biomolecules from Earthworm Coelomic Fluid (ECF) of Eudrilus Eugeniae (EE) that can inhibit cancer cellproliferation. This study aims to construct a homology model of the 18 kDa protein from the ECF of EE (18-ECFP) with molecular dynamics simulation (MDS) to enable its molecular docking with pro-apoptotic caspase receptors with a determination of binding energy scores. This study also evaluates the anti-cancer potential of 18-ECFP on SCC-9 cells in vitro by wet lab techniques.

Methods: Following SDS-PAGE and MALDI-TOF/MS-MS sequencing, the 18kDa protein was subjected to Nano-LCMS-based AA sequencing. Due to the unavailability of a 3D structure in Protein Data Bank (PDB), it had to be modelled via energy-based methods using Prime module—Schrödinger. The MDS of the protein was analyzed followed by Protein–Protein Docking (PPD) using Schrödinger 2020 software. The op 5 poses exhibiting a high PIPER score were subjected to energy calculations. The 18-ECFP was also evaluated by RT-PCR, Western blot and Q-PCR techniques on SCC-9 cells in vitro to further establish its anti-cancer potential.

Results: The homology model of the 18-ECFP was constructed with Schrödinger software with stable molecular dynamics. PPD demonstrated binding affinity of 18-ECFP with the pro-apoptotic genes Caspase-3 and Caspase-8. The MM-GBSA revealed satisfactory binding energy scores. Gene expression studies revealed an upregulation of the apoptotic genes Caspase-3 and Caspase-8 induced by the 18-ECFP, validating the in silico findings.

Conclusions: This is the first report of a homology model with MDS of an anti-cancer protein from an earthworm source docked to human caspase receptors with a determination of binding energy values supported by validation through multiple in vitro gene expression techniques. The current study has provided valuable insights pertaining to the molecular structure of the novel anti-cancer protein of ECF. The findings may contribute to the development of naturally available drugs to combat cancer.

Background: Neural Wiskott–Aldrich Syndrome Protein (N-WASP) is a key regulator of the actin cytoskeleton and is implicated in various cellular processes, including cell motility and invasion. In cancer biology, the role of N-WASP in cell motility and metastasis is of particular interest, yet its specific functions in breast cancer remain to be fully understood.

Method: To investigate the impact of N-WASP on breast cancer cell behaviour, we employed siRNA to knock down N-WASP expression in the MDA-MB-231 breast cancer cell line. After the knockdown, proteomic changes in the cells were analysed using mass spectrometry. Notable alterations in the genes present in both total and phosphorylated proteins were further analysed.

Results: The proteomic data analysis ranked 50 genes that exhibited the most up-regulation and down-regulation in total and phosphorylated proteins. These 200 genes were further examined using the REACTOME database to identify affected signalling pathways. Knockdown of N-WASP led to significant changes in the RHOD, RHOF, and RHOG GTPase cycles (P=0.015, P=0.01, and P=0.027), pathways closely associated with cell motility and actin cytoskeleton organisation. These cycles are crucial in modulating cellular dynamics, impacting a range of processes from immune response to neuronal development, wound healing, and, particularly, cancer metastasis. Furthermore, the findings highlighted the role of non-integrin membrane–ECM interactions in cell motility and cytoskeleton dynamics (p=0.021). The altered protein expression patterns suggest a link between N-WASP, non-integrin membrane–ECM interactions, and the cytoskeletal changes essential for cell migration and invasion—key factors in cancer metastasis.

Conclusion: Our findings reinforce the critical role of N-WASP in regulating the cytoskeleton and influencing cell motility, invasion, and metastasis in breast cancer. This study not only provides deeper insights into the molecular mechanism of breast cancer progression but also highlights N-WASP as a potential therapeutic target for intervention strategies in breast cancer treatment.

In humans, cytochrome P450 (CYP450) enzymes play a pivotal role in catalyzing over 90% of the enzymatic reactions associated with xenobiotic metabolism. Accurately predicting whether interested chemicals act as substrates or inhibitors of different CYP450 isoforms can assist in preselecting hit compounds and optimizing lead compounds for further drug discovery and chemical toxicology study. This work embarks on a comprehensive overview of recently developed in silico prediction tools of CYP450 isoform specificity. We summarize information on these models by two major categories of computational approaches: structure-based and ligand-based. We also analyze various aspects of these models, including their datasets, algorithms, and performance metrics. Subsequently, we employ 100 of the most frequently prescribed drugs to evaluate ten prediction tools which were developed via different classical machine learning methods (e.g., support vector machine, random forest, learning-based approaches, etc.) or deep learning approaches (e.g., graph attention neural network and ESM-1b Transformer). We point out that deep learning-based models like admetLab and ESP can quickly and accurately predict results. However, the coverage and performance of the investigated models are constrained by the limited quantity and quality of their datasets. We discuss both the advantages and limitations of the evaluated models, providing guidance for selecting appropriate computational tools to carry out predictions, and highlighting trends in the field of computational CYP450 isoform specificity prediction.

Introduction: Human onchocerciasis affects an estimated 21 million people, with 99% of cases reported in 31 sub-Saharan countries (WHO, 2020a). The Expanded Special Program for Elimination of Neglected Tropical Diseases (ESPEN) has as objective to eliminate onchocerciasis with other Neglected Tropical Diseases (NTDs) by 2030. But one problem faced by the control programs is the absence of an antigen based diagnostic test to determine an active infection with Onchocerca volvulus. Onchocerciasis diagnosis is hampered by the lack of early, sensitive and objective laboratory tests.

Methods: We mined for O. volvulus proteins in patient urine and assessed the suitability of one of the proteins as antigenic diagnostic marker for human onchocerciasis. We describe a facile method for the diagnosis of the filarial Onchocerca volvulus based on specific detection of the antigen which has been shown to be components of extracellular secretory proteins in human urine. Dot blot filtration assays allow for the filtration and concentration of proteins from human urine.

Results: Standard antibody techniques using an antibody raised against this antigen allowed for the detection of as little as fmol of the protein in urine. Most importantly, using urine samples from endemic areas, we were able to distinguish filariasis patients from control individuals not affected with any form of filariasis. Using urine samples from other endemic parasitic diseases, our test showed an overall sensitivity of 80% and specificity of 90%. These findings provide the proof of principle for developing a cheap highly sensitive and specific tests for filarial diseases

Conclusion: Development of a more efficient diagnostic test for human onchocerciasis will serve control programs to map for the disease and follow up treatment, especially as onchocerciasis and other NTDs are programed for elimination by 2030 by WHO.

Microbacteria offer protection against the penetration of foreign DNA with not only RMS, but also the DISARM and BREX systems [1, 2]. RMS consists of 2 or 3 genes, while DISARM and BREX systems contain 5-6 genes. We report on the discovery of the mesophilic Microbacterium sp. Gd 4-13 taken from permafrost soils dating back 34,400 years. The study of this bacterium has garnered interest due to the presence of a endonuclease restriction (ERse) and DNA-methyltransferase genes (MTse). The endonuclease restriction is currently the only one that recognizes the site at the 5´-GCCGG↓C with the 3´overhanging end.

An analysis of the flanking region of the RMS of MspGI was carried out to detect the cassette composition of RMS MspGI genes similar to DISARM or BREX. Thus, three short ORFs are located upstream of the MTse gene in the region of ~3.5 kb and their function is unknown. Downstream of the ERse gene is the HNH ENse gene, followed by hp and recombinase (Fig. 2) [5].
Thus, an analysis of the flanking region RMS MspGI showed the presence of the helicase and HNH endonuclease genes. The presence of MTse and ERse, as well as the fact that these genes are part of the DISARM gene cassette, could suggest that although RMS MspGI does not belong to the DISARM or BREX systems, the flanking genes may be involved in protecting the cell from the penetration of foreign DNA in vivo in the complex with RMS MspGI genes.

Introduction:

Dermo-cosmetics are cosmetics combined with bioactive ingredients to impart therapeutic benefits on the skin and have made significant advances in recent decades. Synthetic peptides stand out among these bioactive molecules, exhibiting improved capabilities due to their synthetic nature. Wound healing and cosmetic peptides share similarities in tissue repair and regeneration. Cosmetic peptides enhance fibroblasts, boosting collagen formation, improving skin firmness, and aiding wrinkle removal. E-cadherin, a key molecule, plays a role in both wound healing and cellular processes. Genetic validation of cosmetic peptides' effects is often lacking despite clinical trials examining their impact on skin physiology. This study examines acetyl hexapeptide-1 genetic impact for wound healing and anti-aging properties.

Methods:

Acetyl hexapeptide-1 was synthesized in-house, and human hepatocytes (HepG2) were exposed for cytotoxicity assessment. Furthermore, gene expression was evaluated, through qPCR analysis, for the apoptosis-related gene BAX and the wound healing-associated gene CDH-1.

Results:

In the assessment conducted in cell cultures, the peptide demonstrated a notable absence of cytotoxic effects. Upon comprehensive gene expression analysis, noteworthy observations included a significant increase in E-cadherin expression, from the first 24 h, and a slight reduction in apoptotic BAX gene expression.

Conclusions:

The findings of this study provide promising insights into the molecular properties of synthetic acetyl hexapeptide-1, suggesting its potential in cosmeceuticals and dermo-cosmetics. While already proven effective in wrinkle reduction through fibroblast activation and collagen enhancement, these cosmetic peptides present vast potential and diverse applications beyond skincare. Further investigations are needed to fully comprehend their benefits and broaden their scope by exploring their molecular mechanisms across various applications.

The aim of this research is to study the light phase of photosynthesis based on X-ray diffraction data from photosystems I and II (PS-I and PS-II), and the molecular structures of solar energy conversion and electron flow control systems.

Structural analysis of PS-II showed that the manganese cluster Mn₄O₅Ca(Н₂О)₄ is an electron generator, where solar energy breaks the chemical bonds of water, which is accompanied by H₂O₂ formation. Electrochemical oxidation of Н₂О₂ by Mn⁴⁺ ion leads to the formation of oxygen and two protons Н₂О₂-2е^-→О₂^↑+2Н⁺+23,5 kcal, while Mn4+ is reduced to Mn²⁺. Mn⁴⁺ regeneration occurs by donating 2 electrons to PS-I to NADPH·H.

Uncontrolled generation of electrons in chloroplasts leads to the appearance of free radicals that destroy cellular structures. In this regard, chloroplasts have protective mechanisms to remove excess electrons. X-ray diffraction studies of PS-I and PS-II showed that the active centers P680 and P700 have formed photoelectrolysis systems in which chlorophyll molecules act as electrodes (cathode and anode). Electronic circuits P680 and P700 close iron-sulfur trigger clusters that control the flow of electrons. Triggers switch electron flows to reduce NADPH·H or send excess electrons to electrolyzers to oxidize water at the anode: 2H₂O → O₂↑+ 4H⁺ + 4e^– and reduce protons at the cathode: 2H⁺ + 2e^- → ↑H₂.

Conclusions. Based on the results of X-ray diffraction studies of H₂O-plastoquinone oxidoreductase (PS-ΙΙ), the mechanism of electron generation of Mn₄O₅Ca(Н₂О)₄ is considered. Photoelectrolysis systems in the P680 PS-II and P700 PS-I structures have been identified and the principle of their operation is described. A natural molecular electronic device that controls and monitors the processes occurring in the ETC of the light phase of photosynthesis is considered.

The mitochondrial carrier family (MCF) consists of nuclear-encoded proteins which catalyze the transport of a wide variety of compounds across the mitochondrial inner membrane. These proteins present common structural features, which consist of three repeats of two transmembrane helices enclosing a translocation pore with a single substrate binding site. Access to the pore from the matrix side is controlled by a network of salt bridges formed by conserved charged residues of the signature motifs PX[D/E]XX[R/K] (M-gate) on the transmembrane helices H1, H3, and H5. On the cytosolic side, a less-conserved network is formed by the residues of the motifs [F/Y][D/E]XX[R/K] (C-gate) on H2, H4, and H6. In this work, to test the role of the charged residues of the C-gate in transport, we analyzed the charged residues of the cytoplasmic motifs of the yeast NAD⁺ mitochondrial transporter (Ndt1p). Single cysteine mutations of the negatively and positively charged residues were introduced by site-directed mutagenesis and only three of them (H4:E258, H4:K261, and H6:E359) completely inactivated the carrier. The double cysteine salt-bridge pair mutant H4-H6:K261C/E359C exhibited a higher transport rate than the corresponding single mutants as well as when the charged residues were swapped in these positions (H4-H6:K261E/E359K). The double mutant H2-H4:K164C/E258C and the swapped H2-H4:K164E/E258K exhibited transport rates at similar levels to the single K164C. The sextuple mutant with all the charged residues inverted was inactive. These preliminary results suggest that not all the charged C-gate residues are essential for transport and that some of them may have additional roles in transport besides forming salt-bridges.