CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

Ranking Single Fluorescent Protein-Based Calcium Biosensor Performance by Molecular Dynamics Simulations

Genetically encoded fluorescent biosensors (GEFBs) have become indispensable tools for visualizing biological processes in vivo. A typical GEFB is composed of a sensory domain (SD) that undergoes a conformational change upon ligand binding or enzymatic reaction; the SD is genetically fused with a fluorescent protein (FP). The changes in the SD allosterically modulate the chromophore environment whose spectral properties are changed. Single fluorescent (FP)-based biosensors, a subclass of GEFBs, offer a simple experimental setup; they are easy to produce in living cells, structurally stable, and simple to use due to their single-wavelength operation. However, they pose a significant challenge for structure optimization, especially concerning the length and residue content of linkers between the FP and SD, which affect how well the chromophore responds to conformational change in the SD. In this work, we use all-atom molecular dynamics simulations to analyze the dynamic properties of a series of calmodulin-based calcium biosensors, all with different FP-SD interaction interfaces and varying degrees of calcium binding-dependent fluorescence change. Our results indicate that biosensor performance can be predicted based on distribution of water molecules around the chromophore and shifts in hydrogen bond occupancies between the ligand-bound and ligand-free sensor structures.

Structure-Based Discovery of MolPort-137: A Novel Autotaxin Inhibitor That Improves Paclitaxel Efficacy

The autotaxin-lysophosphatidic acid receptor (ATX-LPAR) signaling axis is pivotal in various clinical conditions, including cancer and autoimmune disorders. This axis promotes tumorigenicity by interacting with the tumor microenvironment, facilitating metastasis, and conceding antitumor immunity, thereby fostering resistance to conventional cancer therapies. Recent studies highlight the promise of ATX/LPAR inhibitors in combination with conventional chemotherapeutic drugs to overcome some forms of this resistance, representing a novel therapeutic strategy. In the current study, we employed structure-based virtual screening, integrating pharmacophore modeling and molecular docking, to identify MolPort-137 as a novel ATX inhibitor with an IC50 value of 1.6 ± 0.2 μM in an autotaxin enzyme inhibition assay. Molecular dynamics simulations and binding free energy calculations elucidated the binding mode of MolPort-137 and its critical amino acid interactions. Remarkably, MolPort-137 exhibited no cytotoxicity as a single agent but enhanced the effectiveness of paclitaxel in 4T1 murine breast carcinoma cells and resensitized taxol-resistant cells to paclitaxel treatment, which highlights its potential in combination therapy.

Adaptive sampling-based structural prediction reveals opening of a GABAA receptor through the αβ interface

γ-Aminobutyric acid type A (GABAA) receptors are ligand-gated ion channels in the central nervous system with largely inhibitory function. Despite being a target for drugs including general anesthetics and benzodiazepines, experimental structures have yet to capture an open state of classical synaptic α1β2γ2 GABAA receptors. Here, we use a goal-oriented adaptive sampling strategy in molecular dynamics simulations followed by Markov state modeling to capture an energetically stable putative open state of the receptor. The model conducts chloride ions with comparable conductance as in electrophysiology measurements. Relative to experimental structures, our open model is relatively expanded at both the cytoplasmic (-2') and central (9') gates, coordinated with distinctive rearrangements at the transmembrane αβ subunit interface. Consistent with previous experiments, targeted substitutions disrupting interactions at this interface slowed the open-to-desensitized transition rate. This work demonstrates the capacity of advanced simulation techniques to investigate a computationally and experimentally plausible functionally critical of a complex membrane protein yet to be resolved by experimental methods.

Molecular Insight into the Catalytic Mechanism of the Sesquiterpene Cyclase BcABA3

BcABA3 is an unusual sesquiterpene synthase that lacks the conserved DDxxD and DTE/NSE motifs. Despite this, it can catalyze the conversion of farnesyl diphosphate to 2Z,4E-α-ionylideneethane. We used structure prediction, multiscale simulations, and site-directed mutagenesis experiments to investigate BcABA3 and its catalytic mechanism. BcABA3 has structural similarity to typical class I terpenoid cyclases in its active site. Based on simulation results, we identified two discontinuous glutamate residues, E124 and E88, which compensate for the absence of the aspartate-rich DDxxD motif. Quantum chemical calculations show that BcABA3 adopts a direct rotation mechanism for allyl cation isomerization rather than via the nerolidyl diphosphate. Then, it can achieve a successive proton transfer reaction, which is difficult to achieve by intramolecular rearrangement via the protruding outward carbonyl oxygen of A206. This reaction is then directed forward by two relatively stable intermediates containing a cation-conjugated double-bond structure. E124 is also proposed as the proton receptor in the final deprotonation to couple this step with 2Z,4E-α-ionylideneethane release. These findings provide valuable insight into the catalytic mechanisms of BcABA3 and can aid in its engineering, which will facilitate studies of abscisic acid biosynthesis.

Molecular basis of Spns1-mediated lysophospholipid transport from the lysosome

Spns1 mediates the rate-limiting efflux of lysophospholipids from the lysosome to the cytosol. Deficiency of Spns1 is associated with embryonic senescence, as well as liver and skeletal muscle atrophy in animal models. However, the mechanisms by which Spns1 transports lysophospholipid and proton sensing remain unclear. Here, we present a cryogenic electron microscopy structure of human Spns1 in lysophosphatidylcholine (LPC)-bound lumen-facing conformation. Notably, LPC snugly binds within the luminal-open cavity, where the molecular dynamics simulations reveal that LPC presents a propensity to enter between transmembrane-helices (TM) 5 and 8. Structural comparisons and cell-based transport assays uncover several pivotal residues at TM 5/8 that orchestrate the transport cycle, which are unique to Spns1. Furthermore, we identify a five-residue network that is crucial for proton-sensing by Spns1. Transference of these network residues to Spns2, a sphingosine-1-phosphate uniporter, causes the chimeric Spns2 to be low pH dependent. Our results reveal molecular insights into lysosomal LPC transport and the proton-sensing mechanism by Spns1.

Exploring novel inhibitors for Babesia bigemina lactate dehydrogenase: a computational structural biology perspective

Babesia bigemina is an apicomplexan parasite responsible for causing "Texas fever" in bovines. Current treatments for bovine babesiosis are hindered by several limitations, including toxicity, insufficient efficacy in eliminating the parasite, and the potential for resistance development. A promising approach to overcome these challenges is the identification of compounds that specifically target essential metabolic pathways unique to the parasite. One such target is lactate dehydrogenase (LDH), a critical enzyme involved in the regulation of anaerobic glycolysis. Notably, Babesia bigemina LDH (BbigLDH) exhibits a five-amino acid insertion in the active site, a feature that differentiates it from the host's LDH. This structural divergence makes apicomplexan LDH an attractive and potentially selective drug target for therapeutic intervention. In this study, a structure-based drug discovery approach was implemented to find novel inhibitor candidates. Potential candidates were identified using a virtual screening workflow. The compounds with favorable docking scores were filtered using the QM-polarized ligand docking and induced fit docking methods. As a result, 20 novel compounds were identified that bind to the active site of BbigLDH but show low affinity to the host LDHs. Molecular dynamics simulations of the complexes (8.8 µs in total) were performed, and binding free energies were calculated. As a result, protein structures containing compounds C9, C16 and C18 maintained their stability throughout 1 µs simulations with low binding free energies and conserved interactions with known catalytic residues. Therefore, these three compounds deserve further investigation to better understand their mode of action and therapeutic potential for babesiosis. The results of this study elucidate the structural features of the BbigLDH enzyme and provide novel LDH binders that may pave the way for further research into the development of parasite-specific LDH inhibitors.

Additive CHARMM Force Field for Pterins and Folates

Folates comprise a crucial class of biologically active compounds related to folic acid, playing a vital role in numerous enzymatic reactions. One-carbon metabolism, facilitated by the folate cofactor, supports numerous physiological processes, including biosynthesis, amino acid homeostasis, epigenetic maintenance, and redox defense. Folates share a common pterin heterocyclic ring structure capable of undergoing redox reactions and existing in various protonation states. This study aimed to derive molecular mechanics (MM) parameters compatible with the CHARMM36 all-atom additive force field for pterins and biologically important folates, including pterin, biopterin, and folic acid. Three redox forms were considered: oxidized, dihydrofolate, and tetrahydrofolate states. Across all protonation states, a total of 18 folates were parameterized. Partial charges were derived using the CHARMM force field parametrization protocol, based on targeting reference quantum mechanics monohydrate interactions, electrostatic potential, and dipole moment. Bonded terms were parameterized using one-dimensional adiabatic potential energy surface scans, and two-dimensional scans to parametrize in-ring torsions associated with the puckering states of dihydropterin and tetrahydropterin. The quality of the model was demonstrated through simulations of three protein complexes using optimized and initial parameters. These simulations underscored the significantly enhanced performance of the folate model developed in this study compared to the initial model without optimization in reproducing structural properties of folate-protein complexes. Overall, the presented MM model will be valuable for modeling folates in various redox states and serve as a starting point for parameterizing other folate derivatives.

A propofol binding site in the voltage sensor domain mediates inhibition of HCN1 channel activity

Hyperpolarization-activated and cyclic nucleotide-gated (HCN) ion channels are members of the cyclic nucleotide-binding family and are crucial for regulating cellular automaticity in many excitable cells. HCN channel activation contributes to pain perception, and propofol, a widely used anesthetic, acts as an analgesic by inhibiting the voltage-dependent activity of HCN channels. However, the molecular determinants of propofol action on HCN channels remain unknown. Here, we use a propofol-analog photoaffinity labeling reagent to identify propofol binding sites in the human HCN1 isoform. Mass spectrometry analyses combined with molecular dynamics simulations show that a binding pocket is formed by extracellularly facing residues in the S3 and S4 transmembrane segments in the resting voltage-sensor conformation. Mutations of residues within the putative binding pocket mitigate or eliminate voltage-dependent modulation of HCN1 currents by propofol. Together, these findings reveal a conformation-specific propofol binding site that underlies voltage-dependent inhibition of HCN currents and provides a framework for identifying highly specific modulators of HCN channel gating.

Enhanced motivated behavior mediated by pharmacological targeting of the FGF14/Nav1.6 complex in nucleus accumbens neurons

Protein/protein interactions (PPI) play crucial roles in neuronal functions. Yet, their potential as drug targets for brain disorders remains underexplored. The fibroblast growth factor 14 (FGF14)/voltage-gated Na+ channel 1.6 (Nav1.6) complex regulates excitability of medium spiny neurons (MSN) of the nucleus accumbens (NAc), a central hub of reward circuitry that controls motivated behaviors. Here, we identified compound 1028 (IUPAC: ethyl 3-(2-(3-(hydroxymethyl)-1H-indol-1-yl)acetamido)benzoate), a brain-permeable small molecule that targets FGF14R117, a critical residue located within a druggable pocket at the FGF14/Nav1.6 PPI interface. We found that 1028 modulates FGF14/Nav1.6 complex assembly and depolarizes the voltage-dependence of Nav1.6 channel inactivation with nanomolar potency by modulating the intramolecular interaction between the III-IV linker and C-terminal domain of the Nav1.6 channel. Consistent with the compound's effects on Nav1.6 channel inactivation, 1028 enhances MSN excitability ex vivo and accumbal neuron firing rate in vivo in murine models. Systemic administration of 1028 maintains behavioral motivation preferentially during motivationally deficient conditions in murine models. These behavioral effects were abrogated by in vivo gene silencing of Fgf14 in the NAc and were accompanied by a selective reduction in accumbal dopamine levels during reward consumption in murine models. These findings underscore the potential to selectively regulate complex behaviors associated with neuropsychiatric disorders through targeting of PPIs in neurons.

Unveiling the potential of RADA16-I peptide-coated silver nanoparticles for biomedical uses: a computational study

Nanomaterials, specifically silver nanoparticles (AgNPs), have demonstrated great potential in biomedical applications due to their unique properties, such as antimicrobial activity and conductivity. One promising strategy to improve their biocompatibility and functional specificity is through the functionalization of AgNPs with peptides. By attaching peptides to the surface of AgNPs, their interaction with biological systems can be enhanced and tailored for specific applications. This computational study uses classical molecular dynamics and enhancement sampling techniques to investigate the interaction between AgNPs and RADA16-I peptides, as well as their derivative CLKRADA16-I. It utilizes classical molecular dynamics and enhanced sampling methods to gain insights into the structural information and details of their interaction. Furthermore, this study addresses the need for a better understanding of the interaction between composite materials made of nanoparticles and peptides. Our results demonstrate that the incorporation of the CLK motif significantly augments both structural stability and the binding affinity of peptides to silver nanoparticles. Through computational simulations, we observed that peptides modified with the CLK motif (CLKRADA16-I) exhibit a higher binding affinity toward a silver surface model, with the adsorption energy increasing by up to 4.2 kcal mol-1 relative to unmodified peptides. This calculated interaction energy boosts adsorption and surface coverage, facilitating a packed and more effective peptide coating on the silver nanoparticles. These findings pave the way for the advancement of AgNPs as versatile agents in nanomedicine, particularly necessitating precise molecular recognition and robust bioactive scaffolding. Our study enhances the understanding of nanoparticle-peptide conjugates and their implications for designing next-generation nanomaterials.

Atomistic Simulations and Analysis of Peripheral Membrane Proteins with Model Lipid Bilayers

All-atom molecular dynamics (AAMD) is a computational technique that predicts the movement of particles based on the intermolecular forces acting on the system. It enables the study of biological systems at atomic detail, complements observations from experiments, and can help the selection of experimental targets. Here, we describe the applications of MD simulations to study the interaction between peripheral membrane proteins and lipid bilayers. Specifically, we provide step-by-step instructions to set up MD simulations to study the binding and interaction of ALPS, the amphipathic helix of the lipid transport protein Osh4, and Thanatin, an antimicrobial peptide with model membranes. We describe examples of systems built with fully atomistic lipid tails and those truncated with the highly-mobile-membrane-mimetic method to enhance conformational sampling. We also comment on the importance of lipid diversity, molecular resolution, and best practices for constructing, running, and analyzing protein-lipid simulation systems. In this second edition, we include a brief discussion on alternative approaches and software to construct protein-membrane coordinate systems, as well as analysis tools and practices that have become relevant to examining protein-lipid interactions since the first edition of this chapter.

Novel bis-benzimidazole-triazole hybrids: anticancer study, in silico approaches, and mechanistic investigation

AIM

Benzimidazole-triazole conjugates are very active hotspot for design and synthesis of promising anticancer agents. The target analogs showed potent and selective cytotoxicity over different cancer cell lines for breast and lung ones.

MATERIALS & METHODS

A new series of bis-1,4-disubstituted-1,2,3-triazoles moieties conjugated with a 2-mercapto-benzimidazole 4a-h and 7a-g was synthesized via the click cycloaddition (CuAAC) reaction. The synthesized triazoles were characterized using several spectroscopic tools. In addition, they were tested against variable cell lines representing different cancer types; HepG-2, MCF-7, HCT-116, and A-549. Computational experiments were introduced for understanding their structure-activity relationships.

RESULTS & CONCLUSION

The data revealed the outperformance of 7a-g analogs over 4a-h one with very effective IC50 values; 4-13 µg/mL compared to the reference drugs. Moreover, detailed mechanistic analyses showed potent Aurora-A Kinase expression for the most active analogs 7a and 7d exhibiting IC50; 3.5 and 5.3 over the control cells 8 ng/mL respectively. Additionally, based on their Aurora-A Kinase inhibitory activity, compound 7a was promising in apoptosis induction and cell cycle arrest. Molecular docking studies with Aurora-A Kinase revealed binding behaviors similar to the co-crystallized ligand sunitinib. Finally, this scaffold exhibits cytotoxic activity via apoptosis, enzyme downregulation, and suppression of cell division.

Repurposing Phytochemicals against Breast Cancer (MCF-7) using Classical Structure-Based Drug Design

BACKGROUND

The significant public health effect of breast cancer is demonstrated by its high global prevalence and the potential for severe health consequences. The suppression of the proliferative effects facilitated by the estrogen receptor alpha (ERα) in the MCF-7 cell line is significant for breast cancer therapy.

OBJECTIVE

The current work involves in-silico techniques for identifying potential inhibitors of ERα.

METHODS

The method combines QSAR models based on machine learning with molecular docking to identify potential binders for the ERα. Further, molecular dynamics simulation studied the stability of the complexes, and ADMET analysis validated the compound's properties.

RESULTS

Two compounds (162412 and 443440) showed significant binding affinities with ERα, with binding energies comparable to the established binder RL4. The ADMET qualities showed advantageous characteristics resembling pharmaceutical drugs. The stable binding of these ligands in the active region of ERα during dynamic conditions was confirmed by molecular dynamics simulations. RMSD plots and conformational stability supported the ligands' persistent occupancy in the protein's binding site. After simulation, two hydrogen bonds were found within the protein-ligand complexes of 162412 and 443440, with binding free energy values of -27.32 kcal/mol and -25.00 kcal/mol.

CONCLUSION

The study suggests that compounds 162412 and 443440 could be useful for developing innovative anti-ERα medicines. However, more research is needed to prove the compounds' breast cancer treatment efficacy. This will help develop new treatments for ERα-associated breast cancer.

Omics-centric evidences of fipronil biodegradation by Rhodococcus sp. FIP_B3

The widespread use of the pesticide fipronil in domestic and agriculture sectors has resulted in its accumulation across the environment. Its use to assure food security has inadvertently affected soil microbiome composition, fertility and, ultimately, human health. Degradation of residual fipronil present in the environment using specific microbial species is a promising strategy for its removal. The present study delves into the omics approach for fipronil biodegradation using the native bacterium Rhodococcus sp. FIP_B3. It has been observed that within 40 days, nearly 84% of the insecticide gets degraded. The biodegradation follows a pseudo-first-order kinetics (k = 0.0197/d with a half-life of ∼11 days). Whole genome analysis revealed Cytochrome P450 monooxygenase, peroxidase-related enzyme, haloalkane dehalogenase, 2-nitropropane dioxygenase, and aconitate hydratase are involved in the degradation process. Fipronil-sulfone, 5-amino-1-(2-chloro-4-(trifluoromethyl)phenyl)-4- ((trifluoromethyl)sulfonyl)-1H-pyrazole-3-carbonitrile, (E)-5-chloro-2-oxo-3- (trifluoromethyl)pent-4-enoic acid, 4,4,4-trifluoro-2-oxobutanoic acid, and 3,3,3- trifluoropropanoic acid were identified as the major metabolites that support the bacterial degradation of fipronil. In-silico molecular docking and molecular dynamic simulation-based analyses of degradation pathway intermediates with their respective enzymes have indicated stable interactions with significant binding energies (-5.9 to -9.7 kcal/mol). These results have provided the mechanistic cause of the elevated potential of Rhodococcus sp. FIP_B3 for fipronil degradation and will be advantageous in framing appropriate strategies for the bioremediation of fipronil-contaminated environment.

Role of sequence length and functionalization in interactions of bioconjugated peptides with mitomembranes

Cell-penetrating peptides are efficient tools for intracellular delivery of a variety of cargoes. In this study, we explored the effect of chain length, side chain chemistry, and the locations of conjugated molecules on the interaction between iron-chelating peptides and a mitochondrial-mimicking membrane. We report that a longer chain length enhanced peptide/membrane interactions, and conjugation at the N-terminus lowered the free-energy barrier for peptide translocation across the membrane. Peptides containing Phe side chains and those containing modified Phe (cyclohexane) side chains showed comparable peptide/membrane energetics and translocation energy barriers. Using steered molecular dynamics (SMD) simulations, we further probed the mechanistic details of translocation of each N-terminated peptide across the membrane and compared their metastable states. At a higher steering velocity, the peptide adopted a compact structure due to frequent π-π interactions among conjugated molecules, but at lower steering velocities, each N-terminated peptide adopted an extended structure. This structure allowed cationic residues to maximize their interactions with phosphate headgroups in the mitomembrane. The hydrophobic residues also formed interactions with the lipid acyl tails, facilitating the passage of peptides across the membrane with decreased free energy barriers. Our results highlight the significance of peptide chain length and conjugation in facilitating peptide transport across the membrane.

Network Pharmacology, Molecular Docking, and Molecular Dynamics Study to Explore the Effect of Resveratrol on Type 2 Diabetes

This network pharmacology study represents a significant step in understanding the potential of Resveratrol as an antidiabetic agent and its molecular targets. Targets for Type 2 diabetes were obtained from the MalaCards and DisGeNET databases, while targets for Resveratrol were sourced from the STP and CTD databases. Subsequently, we performed matching to identify common disease-compound targets. The identified genes were analyzed using the ShinGO-0.76.3 database for functional enrichment analysis and KEGG pathway mapping. A protein-protein interaction network was then constructed using Cytoscape software, and hub genes were identified. These hub genes were subjected to molecular docking and dynamic simulations using AutoDock Vina and Gromacs software. According to functional enrichment and KEGG pathway analysis, Resveratrol influences insulin receptors, endoplasmic reticulum functions, and oxidoreductase activity and is involved in the estrogen and HIF-1 pathways. Ten hub genes were identified, including ESR1, PTGS2, SRC, NOS3, MMP9, IGF1R, CYP19A1, MTOR, MMP2, and PIK3CA. The proteins associated with these genes exhibited high interaction with Resveratrol in the molecular docking analysis, and molecular dynamics showed a stable interaction of Resveratrol with ESR1, MMP9, PIK3CA, and PTGS2. In conclusion, our work enhances the understanding of the antidiabetic activity of Resveratrol, which future studies should experimentally corroborate.

Screening and in vitro Biological Evaluation of Novel Multiple Tyrosine Kinases Inhibitors as Promising Anticancer Agents

BACKGROUND

Tyrosine kinases have emerged as key stimulatory drivers in several cancer-related pathways. This is particularly evident in non-small cell lung cancer with regulating cell growth and apoptosis and so on. Tyrosine kinase inhibitors (TKI) are one breakthrough option that could improve the life quality of cancer patients.

OBJECTIVE

This study aims to find more effective tyrosine kinase inhibitors.

METHODS

In this study, natural products from TargetMol that may be the potential TKI for lung cancer were screened through structure-based virtual screening and experimental validation. Moreover, the binding between the hit compounds and tyrosine kinase was explored.

RESULTS

From the study findings, Gramicidin and Tannic acid have strong interactions with the four tyrosine kinases (ALK, TRK, MET, and ABL), and this could significantly inhibit the viability of A549 cells in a concentrationdependent manner.

CONCLUSION

These findings indicated that Gramicidin and Tannic acid might be potential multiple TKI and are promising anticancer agents that call for further study.

Structural Insight on the Selectivity of Calyx[4]Arene-Based Inhibitors of Mg2+-Dependent Atp-Hydrolases

Located in plasma membranes, ATP hydrolases are involved in several dynamic transport processes, helping to control the movement of ions across cell membranes. ATP hydrolase acts as a transport protein, converting energy from ATP hydrolysis into transport molecules against their concentration gradients. In addition to energy metabolism and active transport, ATP hydrolase is essential for maintaining cellular homeostasis and cell function. This study focused on the domain architecture model of P-type ATPases, which participate in the reaction cycles of ATP hydrolysis carried out by membrane transport systems - Na+, K+-ATPase and Ca2+, Mg2+-ATPase. Targeted modulation of Na+, K+-ATPase and Ca2+, Mg2+-ATPase by unnatural drugs is of greatest interest due to the lack of known effectors. This new discovery presents a convenient model based on our recent experimental studies of the membrane structures and myocytes of the uterine smooth muscle, the myometrium. This current study strongly supports the fact that nanosized calix[4]arenes functionalised on the upper rings of the macrocycle with biologically active phosphonic acid fragments can serve as selective and potent inhibitors of cation-transporting electroenzymes. This is how we discovered that calix[4]arene of methylenebisphosphonic acid C-97 and calix[4]arene of bis-aminophosphonic acid C-107 selectively and effectively (I0.5 <100 nM) inhibit the activity of Mg2+, ATP-dependent electrogenic Na+ K+ plasma membrane pump. As drug discovery in the field of Mg2+-ATPase inhibitors is uncharted territory, basic research holds the key to explaining and predicting the mechanism of interaction and action of different classes of compounds. In light of the presented results, new calix[4]arene compounds can be used as potent inhibitors of Mg2+, ATP-dependent electrogenic ion pumps.

Evaluating Cryo-TEM Reconstruction Accuracy of Self-Assembled Polymer Nanostructures

Cryogenic transmission electron microscopy (cryo-TEM) combined with single particle analysis (SPA) is an emerging imaging approach for soft materials. However, the accuracy of SPA-reconstructed nanostructures, particularly those formed by synthetic polymers, remains uncertain due to potential packing heterogeneity of the nanostructures. In this study, the combination of molecular dynamics (MD) simulations and image simulations is utilized to validate the accuracy of cryo-TEM 3D reconstructions of self-assembled polypeptoid fibril nanostructures. Using CryoSPARC software, image simulations, 2D classifications, ab initio reconstructions, and homogenous refinements are performed. By comparing the results with atomic models, the recovery of molecular details is assessed, heterogeneous structures are identified, and the influence of extraction location on the reconstructions is evaluated. These findings confirm the fidelity of single particle analysis in accurately resolving complex structural characteristics and heterogeneous structures, exhibiting its potential as a valuable tool for detailed structural analysis of synthetic polymers and soft materials.

Assessment of lapachol's anti-inflammatory effectiveness in mitigating sepsis-induced acute lung injury

Sepsis-induced Acute Lung Injury (ALI) and Acute Respiratory Distress Syndrome (ARDS) pose life-threatening risks due to an excessive activation of proinflammatory cytokines via the JAK pathway. Currently, no confirmed drug treatment exists for ALI. In this study, we explored JAK1 as a potential therapeutic target to address this issue. This study evaluates lapachol, a bioactive secondary metabolite, for its potential in treating sepsis-induced Acute Lung Injury (ALI). Lapachol was selected based on in-silico analyses such as binding energy, RMSD, RMSF, H-bond graphs, and lig plots supported the hypothesis that Lapachol binds to JAK1 in a manner similar to Tofacitinib JAK1/3 inhibitor (Positive control). Lapachol, derived from the heartwood of Tecomella undulata, was used in this investigation. Swiss albino mice were categorized into control, LPS treated, positive control (Tofacitinib), and experimental groups (Lapachol at 20 and 40 mg/kg doses). Throughout the experiment, mice behaviour was monitored, and euthanasia was performed at 12 and 24-h intervals. Various analyses, including body weight, W/D ratio, lung weight/body weight ratio, flow cytometry of BAL fluid (at 12 and 24 h), histology, myeloperoxidase assays were performed. Results indicated that both Tofacitinib and Lapachol significantly reduced ALI markers, including lung weight/body weight ratio, cell counts, and granulocytes in bronchoalveolar lavage fluid. Moreover, histopathology and MPO analysis suggested that Lapachol, particularly at 40 mg/kg, exhibited anti-inflammatory effects comparable to Tofacitinib. Conclusively, the findings suggest that Lapachol possesses the potential to inhibit JAK1 kinase domains and mitigate ALI associated with sepsis similar to Tofacitinib.

Interactions of Li+ ions with NCS1: A potential mechanism of Li+ neuroprotective action against psychotic disorders

Li+ based drugs have been used for the treatment of psychiatric disorders due to their mood stabilizing role for decades. Recently, several studies reported the protective effect of Li+ against severe neuropathologies such as Parkinson's, Alzheimer's, and Huntington's disease. Surprisingly, despite a broad range of Li+ effects on neurological conditions, little is known about its molecular mechanism. In this study, we propose that neuronal calcium sensor 1 (NCS1), can be an effective molecular target for Li+ action. Here we show that the EF-hands in ApoNCS1 have submillimolar affinity for Li+ with Kd = 223 ± 19 μM. Li+ binding to ApoNCS1 quenches Trp emission intensity, suggesting distinct Trp sidechains environment in Li+NCS1 compared to ApoNCS1 and Ca2+NCS1. Li+ association also stabilizes the protein α-helical structure, in a similar way to Ca2+. Li+ association does not promote NCS1 dimerization. Association of Li+ increases NCS1 affinity for the D2R receptor binding peptide, in a similar way to Ca2+, however, the affinity of NCS1 for chlorpromazine is reduced with respect to Ca2+NCS1, possibly due to a decrease in solvent exposed hydrophobic area on the NCS1 surface in the presence of Li+. MD simulation data suggests that Li+ ions are coordinated by four oxygens from Asp and Glu sidechains and one carbonyl oxygen, in a similar way as reported previously for Li+ binding to DREAM. Overall, the data shows that Li+ binds to EF-hands of NCS1 and Li+NCS1 interactions may be involved in the potential neuroprotective role of Li+ against psychotic disorders.

Membrane-targeted push-pull azobenzenes for the optical modulation of membrane potential

We introduce a family of membrane-targeted azobenzenes (MTs) with a push-pull character as a new tool for cell stimulation. These molecules are water soluble and spontaneously partition in the cell membrane. Upon light irradiation, they isomerize from trans to cis, changing the local charge distribution and thus stimulating the cell response. Specifically, MTs photoisomerization induces clear and reproducible depolarization. The most promising species, MTP2, was extensively studied. Time-resolved spectroscopy techniques provide insights into the excited state evolution and a complete understanding of its isomerization reaction. Molecular Dynamics simulations reveal the spontaneous and stable partitioning of the compound into the cellular membrane, without significant alterations to the bilayer thickness. MTP2 was tested in different cell types, including HEK293T cells, primary neurons, and cardiomyocytes, and a steady depolarization is always recorded. The observed membrane potential modulation in in-vitro models is attributed to the variation in membrane surface charge, resulting from the light-driven modulation of the MT dipole moment within the cell membrane. Additionally, a developed mathematical model successfully captures the temporal evolution of the membrane potential upon photostimulation. Despite being insufficient for triggering action potentials, the rapid light-induced depolarization holds potential applications, particularly in cardiac electrophysiology. Low-intensity optical stimulation with these modulators could influence cardiac electrical activity, demonstrating potential efficacy in destabilizing and terminating cardiac arrhythmias. We anticipate the MTs approach to find applications in neuroscience, biomedicine, and biophotonics, providing a tool for modulating cell physiology without genetic interventions.

The Role of Protonation in the PfMATE Transporter Protein Structural Transitions

Multi-antimicrobial extrusion (MATE) transporter membrane proteins provide drug and toxin resistivity by expelling compounds from cells. MATE proteins can be pictured as V-shaped. To regulate its functioning, the protein structure can switch between outward-facing (OF) and inward-facing (IF). Pyrococcus furiosus MATE (PfMATE) is the only member of the multidrug/oligosaccharidyl-lipid/polysaccharide (MOP) superfamily that has available both the IF and OF crystal structures. With the availability of both the IF and OF structures, we are able to perform computational investigations to determine how protonation of specific amino acids causes a cascade of changes in the protein conformation that allow PfMATE to change its state from OF to IF in order to regulate its antiporter function. Using a variety of computational and theoretical techniques, we investigated four different systems of IF and OF PfMATE along with the native archaeal lipid bilayer, without or with protonation at the experimentally determined locations within the protein. We performed molecular dynamics (MD) simulations to investigate the flexibility of the four different PfMATE structures and also performed targeted molecular dynamics (TMD) simulations, during which we observed occluded conformations. Our analysis of hydrogen bond changes, potential of mean force, dynamic network analysis, and transfer entropy analysis provides information on how protonation can induce cascading structural changes responsible for the transition between the IF and OF configurations.

Identification and study of new NF-κB-inducing kinase ligands derived from the imidazolone scaffold

Chronic kidney disease (CKD) is a growing health concern, projected to be a major cause of death by 2040, due to an increasing risk of acute kidney injury (AKI). Systems biology-derived data suggest that the unmet need for an orally available drug to treat AKI and improve CKD outcomes may be addressed by targeting kidney inflammation and, specifically, nuclear factor κB-inducing kinase (NIK), a key signaling molecule that activates the noncanonical nuclear factor κB (NF-κB) pathway. We have prepared and identified a small family of imidazolone derivatives that bind NIK and inhibit the noncanonical NF-κB activation pathway. The introduction of heterocyclic substituents in position 2 of the imidazolone core provides compounds with affinity against human NIK. Three candidates, with best affinity profile, were tested in phenotypic experiments of noncanonical NF-κB activation, confirming that the derivative bearing the 4-pyridyl ring can inhibit the processing of NFκB p100 to NFkB2 p52, which is NIK-dependent in cultured kidney tubular cells. Finally, exhaustive docking calculations combined with molecular dynamics studies led us to propose a theoretical binding mode and rationalize affinity measures, in which the aminopyridine motif is a key anchoring point to the hinge region thanks to several hydrogen bonds and the interaction of heterocyclic rings in position 2 with Ser476 and Lys482. Our result will pave the way for the development of potential drug candidates targeting NIK in the context of CKD.

Membrane fusion by dengue virus: The first step

Flaviviruses include important human pathogens such as Dengue, Zika, West Nile, Yellow fever, Japanese encephalitis, and Tick-borne encephalitis viruses as well as some emerging viruses that affect millions of people worldwide. They fuse their membrane with the late endosomal one in a pH-dependent way and therefore the merging of the membranes is one of the main goals for obtaining new antivirals. The envelope E protein, a membrane fusion protein, is accountable for fusion and encompasses different domains involved in the fusion mechanism, including the fusion peptide segment. In this work we have used molecular dynamics to study the interaction of the distal end of domain II of the DENV envelope E protein with a membrane like the late endosomal membrane in order to observe the initiation of membrane fusion carried out by a number of trimers of the DENV envelope E protein interacting with a complex biomembrane and demonstrate its feasibility. Our results demonstrate the likelihood of membrane disorganization and pore formation by trimer complex organization, the amino acids responsible for such condition and the secondary structure arrangements needed for such fundamental process. At the same time, we define new targets of the envelope E protein sequence which could permit designing potent antiviral bioactive molecules.

Insights into podophyllotoxin lactone features: New cyclolignans as potential dual tubulin-topoisomerase II inhibitors

Chemomodulation of natural cyclolignans as podophyllotoxin has been a successful approach to obtain semisynthetic bioactive derivates. One example of this approach is the FDA-approved drug etoposide for solid and hematological tumors. It differs from the antimitotic activity of the natural product in its mechanism of action, this drug being a topoisomerase II inhibitor instead of a tubulin antimitotic. Within the molecular requirements for the activity of these compounds, the trans-γ-lactone moiety presented in the parent compound has always been a feature to be explored to chemomodulate its bioactivity. In this study, we have obtained different compounds that comply with the molecular characteristics for antitubulin and antitopoisomerase II activity combined in a single molecule. Furthermore, we explored the influence of the trans-lactone moiety on the final activity, finding that the cis-lactone was also interesting in terms of bioactivity. The best values of cytotoxicity and cell cycle inhibition were obtained for a compound lacking the lactone ring, thus mimicking the podophyllic aldehyde functionalization, a selective antimitotic podophyllotoxin derivate. The analogs with cis-lactone also presented interesting cytotoxic activity. The present study illustrates the potential of the chemomodulation of natural products such as natural cyclolignan podophyllotoxin derivates for the discovery of new antitumor agents.

Use of Steered Molecular Dynamics to Explore the Conformational Changes of SNARE Proteins

Steered Molecular Dynamics (SMD) simulation is a powerful computational simulation technique that enables the controlled manipulation of molecular systems by applying external forces. This method is frequently utilized to investigate the slow processes of biomolecular systems that occur within sub-second to second time scales, achieved through SMD simulations that only span nanoseconds. SMD simulation can be utilized to study the detailed mechanism of protein conformational changes, protein unfolding, and ligand dissociation, etc. Here, we introduce the application of SMD in the study of intra-molecular interactions and regulatory mechanisms in SNAREs by analyzing their conformational change pathways.

Organocatalysed synthesis of N-(4-oxo-2-phenyl-1,2-dihydroquinazolin-3(4H)-yl)isonicotinamide: computational, electrochemical, drug-likeness and antimicrobial studies

We have developed novel and sustainable homogeneous catalysts employing Glutamic acid (Glu) as a biodegradable and eco-friendly organocatalyst for the synthesis of N-(4-oxo-2-phenyl-1,2-dihydroquinazolin-3(4H)-yl)isonicotinamide derivatives (5a-l) via multicomponent reactions (MCRs) of isatoic anhydride, isoniazid and heteroaromatic/aromatic aldehyde in ethanol on oil bath stirring at 60 °C. Selected final product homogeneity was examined by various spectroscopic techniques such as 13C-, 1H- NMR, FT-IR and LC-MS. For the first time, herein investigated electrochemical behavior of selected derivatives (5c, 5h-l) using cyclic voltammetry method. The results of this investigation indicated compounds 5i, 5h and 5l exhibited highest levels of oxidation and reduction potential. Further, pharmacokinetic properties were assessed via SwissADME online tool, derivatives tested complied with Lipinski's rule of five for drug-likeness. Furthermore, molecular docking studies demonstrated for significant binding between the protein and ligand, and affinity values ranged from - 8.91 to - 8.45 kcal/mol, and MM/PBSA estimated high negative values suggested significant interactions between ligand and protein. Moreover, antibacterial evaluation of compounds 5i in water, and 5k in DMSO on Salmonella typhimurium showed pronounced effect with inhibition zone of 15 ± 0.6 mm and 20 ± 0.4 mm, respectively as compared to the standard tetracycline inhibition zone of 15 ± 0.5 mm.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-024-04188-z.

Elucidating the potential of bioactive of Trichoderma sp.. in combating pathogenesis by Fusarium sp.. by targeting pectin lyases: a bioinformatics approach

Pectin lyase is an industrially important enzyme, predominately used in fruit juice clarification and retting of fibers. It also promotes pathogenesis via the degradation of the pectin. The phytopathogen, Fusarium infects various crops and causes several diseases. Trichoderma sp. is a promising biocontrol agent that is vital in maintaining plant health and disease prevention. In the current study, a computational approach utilizing structure prediction, molecular docking, molecular dynamics, and MM-PBSA analysis was used to analyze the potential role of bioactive compounds secreted by Trichoderma sp. in inhibiting the pectin lyase enzyme from Fusarium proliferatum, F. fujikuroi, F. graminearum, F. oxysporum and F. verticillioides. Molecular docking with secondary metabolites revealed that Viridiofungin A secreted by Trichoderma harzianum and Virone secreted by T. virens are bioactive compounds with immense potential to inhibit PNLs of Fusarium species. Further, the rigidity of the structure and stability of the docked complex were confirmed via Molecular dynamic simulations assessed through multiple parameters from the simulation trajectory data. Dual culture assay of T. harzianum and T. virens with F. proliferatum, F. fujikuroi, F. graminearum, F. oxysporum, and F. verticillioides showed variable mycelial inhibition. The research provides insight into the potential of the bioactive compounds secreted by Trichoderma species as an effective agent for the inhibition of pectin lyases produced by phytopathogens, especially Fusarium species. The proposed research can be used to develop bioformulations that function as biopesticides, offering a sustainable replacement for chemical products.

An immunoinformatics and extensive molecular dynamics study to develop a polyvalent multi-epitope vaccine against cryptococcosis

Cryptococcosis is a lethal mycosis instigated by the pathogenic species Cryptococcus neoformans and Cryptococcus gattii, primarily affects the lungs, manifesting as pneumonia, and the brain, where it presents as meningitis. Mortality rate could reach 100% if infections remain untreated in cryptococcal meningitis. Treatment options for cryptococcosis are limited and and there are no licensed vaccines clinically available to treat or prevent cryptococcosis. Our study utilizes an integrated bioinformatics approaches to develop a polyvalent multiepitope subunit vaccine focusing on the key virulent proteins Heat shock transcription factor and Chaperone DnaK of both C. neoformans and C. gatti. Then in silico analysis was done to predict highly antigenic epitopes by assessing antigenicity, transmembrane topology screening, allergenecity, toxicity, and molecular docking approaches. Following this analysis, we designed two vaccine constructs integrating a compatible adjuvant and suitable linkers. These constructs exhibited notable characteristics including high antigenicity, non-toxicity, solubility, stability, and compatibility with Toll-like receptors (TLRs). The interaction between both vaccine constructs and TLR2, TLR3, and TLR9 was assessed through molecular docking analysis. Molecular dynamics simulations and MM-PBSA calculations suggest the substantial stabilizing property and binding affinity of Vaccine Construct V1 against TLR9. Both the vaccines revealed to have a higher number of interchain hydrogen bond with TLR9. These findings serve as a crucial stepping stone towards a comprehensive solution for combating cryptococcus infections induced by both C. neoformans and C. gattii. Further validation through in vivo studies is crucial to confirm the effectiveness and potential of the vaccine to curb the spread of cryptococcosis. Subsequent validation through in vivo studies is paramount to confirm the effectiveness and potential of the vaccine in reducing the spread of cryptococcosis.

Synthesis of Novel Benzothiazole-Profen Hybrid Amides as Potential NSAID Candidates

Herein, we report the synthesis of a series of new compounds by combining 2-aminobenzothiazole with various profens. The compounds were characterized using techniques such as 1H- and 13C-NMR, FT-IR spectrometry, and high-resolution mass spectrometry (HRMS), with detailed HRMS analysis conducted for each molecule. Their biological activities were tested in vitro, revealing significant anti-inflammatory and antioxidant effects, comparable to those of standard reference compounds. Lipophilicity was experimentally determined through partition coefficient (RM) measurements. To understand their binding affinity, molecular docking studies were perfsormed to analyze interactions with human serum albumin (HSA). The stability of these predicted complexes was further evaluated through molecular dynamics simulations. The results highlight the compounds' promising biological activity and strong affinity for HSA. The new hybrid molecule between 2-ABT and ketoprofen 3b demonstrates significant promise based on the experimental data and is further supported by in silico calculations. Compound 3b exhibits the best hydrogen peroxide scavenging activity among the tested compounds, with an IC50 of 60.24 μg/mL. Furthermore, 3b also displays superior anti-inflammatory activity, with an IC50 of 54.64 μg/mL, making it more effective than the standard ibuprofen (76.05 μg/mL).

A modular and extensible CHARMM-compatible model for all-atom simulation of polypeptoids

Peptoids (N-substituted glycines) are a class of sequence-defined synthetic peptidomimetic polymers with applications including drug delivery, catalysis, and biomimicry. Classical molecular simulations have been used to predict and understand the conformational dynamics of single chains and their self-assembly into morphologies including sheets, tubes, spheres, and fibrils. The CGenFF-NTOID model based on the CHARMM General Force Field has demonstrated success in accurate all-atom molecular modeling of peptoid structure and thermodynamics. Extension of this force field to new peptoid side chains has historically required reparameterization of side chain bonded interactions against ab initio data. This fitting protocol improves the accuracy of the force field but is also burdensome and precludes modular extensibility of the model to arbitrary peptoid sequences. In this work, we develop and demonstrate a Modular Side Chain CGenFF-NTOID (MoSiC-CGenFF-NTOID) as an extension of CGenFF-NTOID employing a modular decomposition of the peptoid backbone and side chain parameterizations, wherein arbitrary side chains within the large family of substituted methyl groups (i.e., -CH3, -CH2R, -CHRR', and -CRR'R″) are directly ported from CGenFF. We validate this approach against ab initio calculations and experimental data to develop a MoSiC-CGenFF-NTOID model for all 20 natural amino acid side chains along with 13 commonly used synthetic side chains and present an extensible paradigm to efficiently determine whether a novel side chain can be directly incorporated into the model or whether refitting of the CGenFF parameters is warranted. We make the model freely available to the community along with a tool to perform automated initial structure generation.

Development and characterization of fluorescent cholesteryl probes with enhanced solvatochromic and pH-sensitive properties for live-cell imaging

We present novel fluorescent cholesteryl probes (CNDs) with a modular design based on the solvatochromic 1,8-phthalimide scaffold. We have explored how different modules-linkers and head groups-affect the ability of these probes to integrate into lipid membranes and how they distribute intracellularly in mouse astrocytes and fibroblasts targeting lysosomes and lipid droplets. Each compound was assessed for its solvatochromic behavior in organic solvents and model membranes. Molecular dynamics simulations and lipid partitioning using giant unilamellar vesicles showed how these analogs behave in model membranes compared to cholesterol. Live-cell imaging demonstrated distinct staining patterns and cellular uptake behaviors, further validating the utility of these probes in biological systems. We compared the empirical results with those of BODIPY-cholesterol, a well-regarded fluorescent cholesterol analog. The internalization efficiency of fluorescent CND probes varies in different cell types and is affected mainly by the head groups. Our results demonstrate that the modular design significantly simplifies the creation of fluorescent cholesteryl probes bearing distinct spectral, biophysical, and cellular targeting features. It is a valuable toolkit for imaging in live cells, measuring cellular membrane dynamics, and studying cholesterol-related processes.

Comparative analysis of backbone atom cross-correlation matrices and folding dynamics of amyloid fibril and its complexes with novel biosurfactants isolated from Bacillus strain: a binding free energy calculation (mM-PBSA) and MD simulation approach

In the relentless pursuit of unraveling the intricate pathophysiology of Alzheimer's disease (AD), amyloid β (Aβ) proteins emerge as focal points due to their pivotal role in disease progression. The pathological hallmark of AD involves the aberrant aggregation of Aβ peptides into amyloid fibrils, precipitating a cascade of neurodegenerative events culminating in cognitive decline and neuronal loss. This study adopts a computational framework to investigate the potential therapeutic efficacy of novel biosurfactants (BS) in mitigating Aβ fibril formation. Initial analyses encompassing sequence alignment, structural elucidation, and functional characterization reveal distinctive attributes of the Aβ peptide and the identified BS candidates. Quantum chemical calculations, using the ORCA Program (v4.0) employed Density Functional Theory (DFT), specifically the Becke 3-parameter Lee-Yang-Parr (B3LYP) method, to investigate the electronic structure and energetics of novel isolates. Molecular docking through AutoDock Vina (version 1.1.2) employing advanced algorithms elucidates the binding affinities and interaction energies between Aβ fibrils and BS molecules. The observed binding energy of -7.0 kcal/mol for BG2A and -6.6 kcal/mol for BG2B, underscoring the robustness and stability of the formed complexes. The binding mechanism of docked complexes was predicted through molecular dynamics (MD) simulations using GROMACS 2021.3 and Charmm36 force field, capture complex dynamics over 100 nanoseconds. Analysis via RMSD, RMSF, Rg, PCA, and SASA offers insights into Aβ-BS complex stability and dynamics. These promising results highlight the potential of BG2A and BG2B as therapeutic candidates against AD. However, rigorous preclinical and clinical validation is crucial to ascertain their safety, efficacy, and translational relevance.

An in-silico study of FIKK9.5 protein of Plasmodium falciparum for identification of therapeutics

The FIKK protein family, encompassing 21 serine-threonine protein kinases, is a distinctive cluster exclusive to the Apicomplexa phylum. Predominantly located in Plasmodium falciparum which is a malarial parasite, with a solitary gene identified in a distinct apicomplexan species, this family derives its nomenclature from - phenylalanine, isoleucine, lysine, lysine (FIKK), a conserved amino acid motif. Integral to the parasite's life cycle and consequential to malaria pathogenesis, the absence of orthologous proteins in eukaryotic organisms designates it as a promising antimalarial drug target. Among the FIKKs, FIKK9.5 plays a pivotal role in the parasite's development within red blood cells (RBCs). This investigation acquired the three-dimensional structure of FIKK9.5 and its ligands through extensive database searches and literature review. Computational screening of natural phytochemicals derived from plants traditionally used in antimalarial remedies was conducted by employing the Glide docking suite. AutoDock Vina was utilized to discern the inhibitor exhibiting optimal binding affinity. Subsequently, Molecular Dynamics (MD) simulations employing GROMACS validated Rufigallol as the most potent inhibitory compound against FIKK9.5. The robustness of the protein-ligand complex was scrutinized through a 200 nanosecond molecular dynamics (MD) trajectory. Trajectory analysis and determination of binding free energies were accomplished using MM-GBSA and MM-PBSA approaches. The ligand-binding exhibited sustained stability throughout the simulation, manifesting an approximate binding free energy of -25.5986 kcal/mol. This comprehensive computational study lays the groundwork for potential experimental validation in the laboratory, paving the way for the development of novel therapeutics targeting FIKK9.5 in the pursuit of innovative antimalarial.

Antioxidant Bio-Compounds from Chestnut Waste: A Value-Adding and Food Sustainability Strategy

In an era of escalating environmental challenges, converting organic residues into high-value bioactive compounds provides a sustainable way to reduce waste and enhance resource efficiency. This study explores the potential of the circular bioeconomy through the valorization of agricultural byproducts, with a focus on the antioxidant properties of specific chestnut burr cultivars. Currently, over one-third of food production is wasted, contributing to both humanitarian and environmental crises. Through circular bioeconomy, we can transform biological waste into valuable products for use in fields like food innovation and sustainability. The antioxidant effects of three chestnut cultivars, Bastarda Rossa, Cecio, and Marroni, were assessed through in vitro assays, highlighting their potential to combat oxidative stress-an important factor for health-related applications. The characterization of the three cultivars showed the major presence of ellagic acid and gallic acid in the extract, renowned for their antioxidant activity. In vitro assays evaluated the phenolic and flavonoid content, as well as the antioxidant activity of the three extracts, confirming the cultivar Cecio as the richest in these bioactive compounds and the most performative in antioxidant assays. In vitro antioxidant and oxidative stress recovery assays on SaOS-2, fibroblast, and chondrocyte cell lines displayed a strong antioxidant activity. Furthermore, the cytotoxicity assay demonstrated the safety of all three extracts in the tested human cell lines. In silico docking simulations further validated the biological relevance of these compounds by predicting strong hydrophobic and polar interactions with oxidative stress-related protein targets. Overall, this study demonstrates the antioxidant properties of chestnut byproducts. The findings contribute to the development of functional foods, nutraceuticals, and other applications, underscoring the role of chestnut cultivars in advancing circular bioeconomy practices.

Structure-based identification of HNF4α agonists: Rosmarinic acid as a promising candidate for NAFLD treatment

The prevention and treatment of metabolic disorders, such as non-alcoholic fatty liver disease (NAFLD), have emerged as critical global health challenges. Current lipid-lowering pharmacotherapies are associated with side effects, including hepatotoxicity, rhabdomyolysis, and decreased erythrocyte counts, underscoring the urgent need for safer therapeutic alternatives. Hepatocyte nuclear factor 4α (HNF4α) has been identified as a pivotal regulator of lipid metabolism, making it an attractive target for drug development. In this study, we investigated the structural characteristics and binding interactions of four HNF4α agonists: Alverine, Benfluorex, N-trans caffeoyltyramine (NCT), and N-trans feruloyltyramine (NFT). Our results indicate that the conjugated structure formed by the amide bond and the aromatic ring in NCT and NFT enhances electron density, potentially contributing to their increased specificity for HNF4α relative to Alverine and Benfluorex. Additionally, electrostatic interactions between the aromatic moieties of the compounds and HNF4α residues were found to play a crucial role in ligand binding. Leveraging these insights, we performed a high-throughput virtual screening of 2131 natural compounds, using the binding modes of NCT and NFT as reference templates. Rosmarinic acid emerged as a promising HNF4α agonist, exhibiting a high consensus score and favorable binding affinity. Subsequent biological assays demonstrated that rosmarinic acid significantly inhibited HepG2 cell proliferation which related to the enhancement of autophagy. After the knockdown of P2 isoform of HNF4α, HepG2 was more sensitive to the administration of NCT and rosmarinic acid. Furthermore, the proliferation of DLD-1 cell, which only expresses the P2 isoform of HNF4α, was not significantly inhibited by the administration of NCT and rosmarinic acid. Collectively, these findings suggest that rosmarinic acid is a promising HNF4α agonist which is more effective to activate the P1 isoform of HNF4α and holds potential as an effective treatment for NAFLD, providing a foundation for the development of novel lipid-lowering drugs with enhanced efficacy and reduced side effect.

Data Availability

Data will be made available on request.

In silico vaccine design for Yersinia enterocolitica: A comprehensive approach to enhanced immunogenicity, efficacy and protection

Yersinia enterocolitica, a foodborne pathogen, has emerged as a significant public health concern due to its increased prevalence and multidrug resistance. This study employed reverse vaccinology to identify novel vaccine candidates against Y. enterocolitica through comprehensive in silico analyses. The core genome's conserved protein translocase subunit SecY was selected as the target, and potential B-cell, MHC class I, and MHC class II epitopes were mapped. 3B-cell epitopes, 3 MHCI and 11 MHCII epitopes were acquired. A multi-epitope vaccine construct was designed by incorporating the identified epitopes, TLR4 Agonist was used as adjuvants to enhance the immunogenic response. EAAAK, CPGPG and AYY linkers were used to form a vaccine construct, followed by extensive computational evaluations. The vaccine exhibited desirable physicochemical properties, stable secondary and tertiary structures as evaluated by PDBSum and trRosetta. Moreover, favorable interactions with the human Toll-like receptor 4 (TLR4) was observed by ClusPro. Population coverage analysis estimated the vaccine's applicability across 99.74 % in diverse populations. In addition, molecular dynamics simulations and normal mode analysis confirmed the vaccine's structural stability and dynamics in a simulated biological environment. Furthermore, codon optimization and in silico cloning facilitated the evaluation of the vaccine's expression potential in E. coli and pET-28a was used a recombinant plasmid. This study provides a promising foundation for the development of an efficacious vaccine against Y. enterocolitica infections.

Modeling Ligand Binding Site Water Networks with Site Identification by Ligand Competitive Saturation: Impact on Ligand Binding Orientations and Relative Binding Affinities

Appropriate treatment of water contributions to protein-ligand interactions is a very challenging problem in the context of adequately determining the number of waters to investigate and undertaking conformational sampling of the ligands, the waters, and the surrounding protein. In the present study, an extension of the Site Identification by Ligand Competitive Saturation-Monte Carlo (SILCS-MC) docking approach is presented that enables the determination of the location of water molecules in the binding pocket and their impact on the predicted ligand binding orientation and affinities. The approach, termed SILCS-WATER, involves MC sampling of the ligand along with explicit water molecules in a binding site followed by selection of a subset of waters within specified energetic and distance cutoffs that contribute to ligand binding and orientation. To allow for convergence of both the water and ligand orientations, SILCS-WATER is based on just the overlap of the ligand and water with the SILCS FragMaps and the interaction energy between the waters and ligand. Results show that the SILCS-WATER methodology can capture important waters and improve ligand binding orientations. For 6 of 10 multiple ligand-protein systems, the method improved relative binding affinity prediction against experimental results, with substantial improvements in five systems, when compared to standard SILCS-MC. Improved reproduction of crystallographic ligand binding orientations is shown to be an indicator of when SILCS-WATER will yield improved binding affinity correlations. The method also identifies waters interacting with ligands that occupy unfavorable locations with respect to the protein whose displacement through the appropriate ligand modifications should improve ligand binding affinity. Results are consistent with the binding affinity being modeled as a ligand-water complex interacting with the protein. The presented approach offers new possibilities in revealing water networks and their contributions to the binding orientation and affinity of a ligand for a protein and is anticipated to be of utility for computer-aided drug design.

In silico identification of Nipah virus protein inhibitors from secondary metabolites of medicinal plants using a high-throughput virtual screening approach

The Nipah virus (NiV), a highly pathogenic zoonotic virus of the Paramyxoviridae family, poses significant threats with its alarming mortality rates and pandemic potential. Despite historical cases, effective therapeutics remain elusive, prompting urgent exploration of potential antivirals. In this study, a structure-based virtual screening approach was employed to evaluate 690 metabolites sourced from ten medicinal plants (Allium sativum, Andrographis paniculata, Cocos nucifera, Euphorbia hirta, Euphorbia neriifolia, Moringa oreifera, Ocimum basilicum, Piper nigrum, Vitex negundo, and Zingiber officinale) for their antiviral activity against Nipah virus proteins. Through targeted and blind docking experiments, forty-three (43) compounds were found to exhibit high binding affinities (≤ -8 Kcal mol-1) and validated site-specificity. Subsequent analysis of the ADMET properties of these compounds, along with off-target docking to swine receptors, six (6) compounds with profiles akin to approved drugs and minimal off-target binding were identified. Stability screening via 100 ns and 300 ns molecular dynamics simulations identified two (2) of the six compounds that demonstrated sustained dynamic stability over an extended duration, coupled with favorable binding energies from MM-(GB/PB)SA calculations and biologically significant binding modes and residue interactions. Betulinic acid and CID 118716357 exhibited significant potential as inhibitors of Nipah virus fusion (F) glycoprotein trimer by targeting the oligomerization sites used to form the functional hexamer-of-trimer assembly. Coupled with their dynamic stability and favorable ADMET profiles in both human and swine conditions, these findings make them good candidates for subsequent in vitro testing and further biological screening in the quest for potent antiviral drugs targeting Nipah virus proteins.

Mannich Base Derived from Lawsone Inhibits PKM2 and Induces Neoplastic Cell Death

Background/Objectives: Pyruvate kinase M2, a central regulator of cancer cell metabolism, has garnered significant attention as a promising target for disrupting the metabolic adaptability of tumor cells. This study explores the potential of the Mannich base derived from lawsone (MB-6a) to interfere with PKM2 enzymatic activity both in vitro and in silico. Methods: The antiproliferative potential of MB-6a was tested using MTT assay in various cell lines, including SCC-9, Hep-G2, HT-29, B16-F10, and normal human gingival fibroblast (HGF). The inhibition of PKM2 mediated by MB-6a was assessed using an LDH-coupled assay and by measuring ATP production. Docking studies and molecular dynamics calculations were performed using Autodock 4 and GROMACS, respectively, on the tetrameric PKM2 crystallographic structure. Results: The Mannich base 6a demonstrated selective cytotoxicity against all cancer cell lines tested without affecting cell migration, with the highest selectivity index (SI) of 4.63 in SCC-9, followed by B16-F10 (SI = 3.9), Hep-G2 (SI = 3.4), and HT-29 (SI = 2.03). The compound effectively inhibited PKM2 glycolytic activity, leading to a reduction of ATP production both in the enzymatic reaction and in cells treated with this naphthoquinone derivative. MB-6a showed favorable binding to PKM2 in the ATP-bound monomers through docking studies (PDB ID: 4FXF; binding affinity scores ranging from -6.94 to -9.79 kcal/mol) and MD simulations, revealing binding affinities stabilized by key interactions including hydrogen bonds, halogen bonds, and hydrophobic contacts. Conclusions: The findings suggest that MB-6a exerts its antiproliferative activity by disrupting cell glucose metabolism, consequently reducing ATP production and triggering energetic collapse in cancer cells. This study highlights the potential of MB-6a as a lead compound targeting PKM2 and warrants further investigation into its mechanism of action and potential clinical applications.

Identification of novel inhibitors of cancer target telomerase using a dual structure-based pharmacophore approach to virtually screen libraries, molecular docking and validation by molecular dynamics simulations

In about 85% of cancer malignancies, replicative immortality caused by increased telomerase activity makes it an attractive target for developing anticancer therapeutics. However, the lack of approved small-molecule inhibitors rooted in the structural ambiguity of telomerase has impeded drug development for decades. In this study, we have exploited the FVYL pocket in the thumb domain, which plays a key role in the enzyme's processivity. Due to the unavailability of a co-crystalized structure of BIBR1532 with the catalytic hTERT thumb domain, we utilized the molecular dynamics method to identify the precise binding site of the inhibitor. Two pharmacophore models were generated and validated for the putative (Site-I) and newly identified (Site-II) binding pockets which were screened virtually through the ChemDiv anticancer library, Otava drug-like green collection to identify novel lead compounds, and Binding database to screen out thumb domain-specific telomerase inhibitors. The top hits obtained were filtered using drug-likeliness parameters followed by redocking using a three-level screening strategy into their binding site. The structural investigation, molecular docking studies, and confirmatory molecular dynamics revealed that the exact binding site of BIBR1532 is away from the reported FVYL pocket with characteristic interactions conserved. Subsequently, the lead compounds with the highest docking scores and significant interactions in the newly discovered extended FVYL pocket were validated using 100 ns MD simulations. Additionally, cross-validated binding free energy calculations were performed using MM-PB(GB)SA methods followed by PCA and FEL characterization. The identified top lead compounds can be validated in vitro and taken forward for anticancer drug development.

Bioinformatic approach to identifying causative missense polymorphisms in animal genomes

BACKGROUND

Trends in the development of genetic markers for the purposes of genomic and marker-assisted selection primarily focus on identifying causative polymorphisms. Using these polymorphisms as markers enables a more accurate association between genotype and phenotype. Bioinformatic analysis allows calculating the impact of missense polymorphisms on the structural and functional characteristics of proteins, which makes it promising for identifying causative polymorphisms. In this study, a bioinformatic approach is applied to evaluate and differentiate polymorphisms based on their causality in genes that affect the production traits of pigs and cows, which are two important livestock species.

RESULTS

The influence of both known causative and candidate missense polymorphisms in the MC4R, NR6A1, PRKAG3, RYR1, and SYNGR2 genes of pigs, as well as the ABCG2, DGAT1, GHR, and MSTN genes of cows, was assessed. The study included an evaluation of the effect of polymorphisms on protein functions, considering the evolutionary and physicochemical characteristics of amino acids at polymorphic sites. Additionally, it examined the impact of polymorphisms on the stability of tertiary protein structures, including changes in folding, binding of protein monomers, and interaction with ligands.

CONCLUSIONS

The comprehensive bioinformatic analysis used in this study enables the differentiation of polymorphisms into neutral, where both amino acids in the polymorphic site do not significantly affect the structure and function of the protein, and causative, where one of the amino acids significantly impacts the protein's properties. This approach can be employed in future research to screen extensive sets of polymorphisms in animal genomes, identifying the most promising polymorphisms for further investigation in association studies.

Assessing Computational Methods to Calculate the Binding Energies of Dimers of Five-Membered Heterocyclic Molecules

Computational electronic structure methods, including ab initio and density functional theory (DFT), have been assessed in calculating the binding energies of 14 five-membered heterocyclic dimers. The configurations were generated using classical molecular dynamics before optimization at the MP2/aug-cc-pVTZ. Benchmark binding energies are calculated at the CCSD(T)/CBS level of theory. Among the ab initio methods, the DLPNO-CCSD(T)/CBS method has the best performance, reproducing CCSD(T)/CBS with a mean absolute deviation (MAD) of 0.17 kcal/mol. In addition, a schematic CCSD(T)/CBS approach perfectly reproduces the canonical CCSD(T)/CBS with a mean absolute error of 0.08 kcal/mol. Regarding DFT functionals, it has been found that counterpoise corrections have negligible effects on the accuracy of the functionals. Furthermore, including the D3 empirical dispersion considerably enhances the accuracy of the DFT functionals. As a result, outstanding performance is noted for the double hybrid functional B2K-PLYP, with a mean absolute error of 0.25 kcal/mol. In addition to the B2K-PLYP double hybrid functional, M05-D3, B97D, M05-2X-D3, M05-2X, M06-HF, M08-HX, M11, TPSSh-D3, and RSX-0DH-D3(BJ) have MAD values lower than 0.5 kcal/mol. These functionals are recommended for further investigations of five-membered heterocyclic clusters.

Rational design and synthesis of novel phenyltriazole derivatives targeting MRSA cell wall biosynthesis

Antimicrobial resistance in methicillin-resistant Staphylococcus aureus (MRSA) is a major global health challenge. This study reports the design and synthesis of novel phenyltriazole derivatives as potential anti-MRSA agents. The new scaffold replaces the thiazole core with a 1,2,3-triazole ring, enhancing antimicrobial efficacy and physicochemical properties. A series of derivatives were synthesized and evaluated, with four compounds (20, 23, 29 and 30) showing significant activity against MRSA (MIC ≤ 4 μg mL-1). Compound 29 emerged as the most promising candidate, showing rapid bactericidal activity and superior performance over vancomycin in time-kill assays. It exhibited selective toxicity against bacterial cells, minimal cytotoxicity in human cell lines and low hemolytic activity. Mechanistic studies showed that compound 29 targets the bacterial cell wall by binding to penicillin-binding protein 2a (PBP2a), disrupting cell wall integrity. Additionally, it showed strong anti-biofilm activity and reduced MRSA biofilms by up to 40%. Preliminary pharmacokinetic profiles suggested a favorable profile, including a prolonged plasma half-life and good oral bioavailability. These results suggest that compound 29 is a promising lead for further development in the fight against MRSA.

The C-terminal activating domain promotes pannexin 1 channel opening

Pannexin 1 (Panx1) constitutes a large pore channel responsible for the release of adenosine triphosphate (ATP) from apoptotic cells. Strong evidence indicates that caspase-mediated cleavage of the C-terminus promotes the opening of the Panx1 channel by unplugging the pore. However, this simple pore-plugging mechanism alone cannot account for the observation that a Panx1 construct ending before the caspase cleavage site remains closed. Here, we show that a helical region located immediately before the caspase cleavage site, referred to as the "C-terminal activating domain (CAD)", plays a pivotal role in facilitating Panx1 activation. Electrophysiology and mutagenesis studies uncovered that two conserved leucine residues within the CAD play a pivotal role. Cryoelectron microscopy (Cryo-EM) analysis of the construct ending before reaching the CAD demonstrated that the N terminus extends into an intracellular pocket. In contrast, the construct including the CAD revealed that this domain occupies the intracellular pocket, causing the N terminus to flip upward within the pore. Analysis of electrostatic free energy landscape in the closed conformation indicated that the intracellular side of the ion permeation pore may be occupied by anions like ATP, creating an electrostatic barrier for anions attempting to permeate the pore. When the N terminus flips up, it diminishes the positively charged surface, thereby reducing the drive to accumulate anions inside the pore. This dynamic change in the electrostatic landscape likely contributes to the selection of permeant ions. Collectively, these experiments put forth a mechanism in which C-terminal cleavage liberates the CAD, causing the repositioning of the N terminus to promote Panx1 channel opening.

Assessment of inhibitory potentiality of natural compounds against worrisome rice blast fungus

Rice blast, a severe fungal disease, is a substantial threat to global food security, particularly in rice-oriented areas. The Magnaporthe oryzae fungus is increasingly resistant and fast developing in nature. However, chemical fungicides are not only detrimental to the environment but eventually also lose their efficiency. To Tackle this issue, we used an in silico based strategy to identify plant metabolites as bio-fungicides to combat rice blast. Therefore, we screened a total of 56 antifungal natural compounds for the ability to inhibit fungal development through the targeted inhibition of essential proteins in the rice blast pathogen. Molecular docking analysis identified curcumin, myricetin, sterigmatocystin, and versicolorin B as promising candidates with superior binding affinities compared to conventional fungicides like strobilurin, azoxystrobin, and tricyclazole. Notably, myricetin showed the docking score for the SD protein of -233.20, whereas versicolorin B demonstrated the highest binding affinity for the SD protein of -234.23. Among the control fungicides, azoxystrobin displayed the lowest docking score of -177.53. The docked complexes were found to be stable based on molecular dynamics simulations results; the binding free energies of SD-Versicolorin B (-156.018 ± 24.881 kJ/mol) and SD-Myricetin (-137.526 ± 19.977 kJ/mol) complexes were also found to be favorable. Taking everything considered, these naturally occurring substances showed strong fungicidal effects against rice blast causative agent while remaining non-toxic, providing encouraging substitutes for traditional fungicides. In conclusion, these non-toxic natural compounds exhibited strong fungicidal action against rice blast, suggesting promising alternatives to conventional fungicides.

An influence of electronic structure theory method, thermodynamic and implicit solvation corrections on the organic carbonates conformational and binding energies

An impact of an electronic structure or force field method, gas-phase thermodynamic correction, and continuum solvation model on organic carbonate clusters (S)n conformational and binding energies is explored. None of the tested force field (GFN-FF, GAFF, MMFF94) and standard semiempirical methods (PM3, AM1, RM1, PM6, PM6-D3, PM6-D3H4, PM7) can reproduce reference RI-SCS-MP2 conformational energies. Tight-binding GFNn-xTB methods provide more realistic conformational energies which are accurate enough to discard the least stable conformers. The effect of thermodynamic correction is moderate and can be ignored if the gas phase conformational stability ranking is a goal. The influence of continuum solvation is stronger, especially if reinforced with the Gibbs free energy thermodynamic correction, and results in the reduced spread of conformational energies. The cluster formation binding energies strongly depend on a particular approach to vibrational thermochemistry with the difference between traditional harmonic and modified scaled rigid - harmonic oscillator approximations reaching 10 kcal mol-1.

Elucidation of the hydration pattern of trifluoroacetic acid in dilute solutions: FTIR and computational study

The atmospheric partitioning of trifluoroacetic acid (TFA) in aerosol is a complex function of the size of suspended water droplets and their pH value. The unraveling of the affinity of TFA towards basic but not acidic conditions may be accomplished by providing an insight into the hydration pattern of undissociated TFA. Owing to rather scarce details on very dilute aqueous solutions of trifluoroacetic acid (TFA), we examined CF3COOD and CF3COONa solutions in D2O in the concentration range 0.001-0.1 mol dm-3 using transmission FTIR spectroscopy and computational methods. Besides detecting the signals originated from undissociated species in both CF3COOD (1787 cm-1 and 1766 cm-1 at c0 = 0.1 mol dm-3) and CF3COONa (1807 cm-1 at c0 = 0.1 mol dm-3) D2O solutions, through computational techniques we identified different TFA hydrates that contribute to the complexity of the spectral appearance. The combination of experimental and computational data suggested the concentration dependence of the predominant hydrogen bonding pattern of TFA. The results obtained in this work should help in understanding the partitioning of TFA into micron-size water droplets in the atmosphere in molecular and structural terms, i.e. the eventual stability of a hydrated complex for a particular TFA conformer.

Investigating the impact of SOD1 mutations on amyotrophic lateral sclerosis progression and potential drug repurposing through in silico analysis

Superoxide dismutase 1 (SOD1) is a vital enzyme responsible for attenuating oxidative stress through its ability to facilitate the dismutation of the superoxide radical into oxygen and hydrogen peroxide. The progressive loss of motor neurons characterize amyotrophic lateral sclerosis (ALS), a crippling neurodegenerative disease that is caused by mutations in the SOD1 gene. In this study, in silico mutational analysis was performed to study the various mutations, the pathogenicity and stability ΔΔG (binding free energy) of the variant of SOD1. x in the protein variant analysis showed a considerable destabilizing effect with a ΔΔG value of -4.2 kcal/mol, signifying a notable impact on protein stability. Molecular dynamics simulations were conducted on both wild-type and C146R mutant SOD1. RMSD profiles indicated that both maintained consistent structural conformation over time. Additionally, virtual screening of 3067 FDA-approved drugs against the mutant SOD1 identified two potential binders, Tucatinib (51039094) and Regorafenib (11167602), which interacted with Leu106, similar to the control drug, Ebselen. Further simulations assessed the dynamic properties of SOD1 in monomeric and dimeric forms while bound to these compounds. 11167602 maintained stable interaction with the monomeric SOD1 mutant, whereas 51039094 and Ebselen dissociated from the monomeric protein's binding site. However, all three compounds were stably bound to the dimeric SOD1. MM/GBSA analysis revealed similar negative binding free energies for 11167602 and 51039094, identifying them as strong binders due to their interaction with Cys111. Experimental validation, including in vitro, cell-based, and in vivo assays are essential to confirm these candidates before advancing to clinical trials.