Biology subjects

Moradi, M.

Publications and source records attributed to Moradi, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Free-Energy and Molecular Dynamics Analysis of Ser195 and Thr195 Rotameric States in Thrombin

Ser195 is highly conserved as the catalytic nucleophile in trypsin like serine proteases, yet the molecular basis for the strong preference for serine over the chemically similar threonine residue remains unclear. Here, we used well tempered metadynamics and microsecond long molecular dynamics (MD) simulations to characterize the conformational energetics of S195 and T195 in thrombin. Well tempered metadynamics revealed distinct rotameric free energy landscapes in both the apo and the ligand bound systems. In the apo state, S195 preferentially occupied a lower angle rotameric state, while T195 exhibited two low energy states with similar free energies. Unbiased simulations further showed greater conformational heterogeneity and increased higher angle sampling for T195. Evaluation of the His57 to residue 195 hydrogen bond further revealed that S195 maintained close hydrogen bond distances across both rotameric regions, whereas T195 exhibited longer and more variable His57 to hydroxyl distances with reduced distance based occupancy. Analysis of the local environment showed that the additional T195 methyl group was associated with redistributed protein contacts. Additional rotamer conditioned analyses demonstrated differences in local packing within corresponding conformational states. Furthermore, solvent accessibility and water contact analyses revealed that the effects of the substitution on the catalytic side chain environment depend on rotameric conformation. Together, these findings demonstrate that two complementary simulation approaches converge on similar conformational preferences and suggest that the S195T substitution alters the rotameric free energy landscape in association with changes in catalytic geometry, local packing, and solvation. These results provide insight into the evolutionary preference for serine over threonine at the catalytic position of thrombin.

biophysics↗

bioRxiv2026

Differential Behavior of Uncleaved gp160 Human Immunodeficiency Virus Type 1 (HIV-1) Envelope (Env) Glycoproteins

The envelope glycoprotein (Env) of human immunodeficiency virus type 1 (HIV-1) plays important roles in viral entry by coordinating host-cell receptor recognition and membrane fusion. Env is synthesized as a homotrimeric precursor, gp160, which is cleaved into gp120 and gp41 subunits. Although the cleaved form of Env is required for fusion, uncleaved Env remains plentiful on the surface of HIV-1-infected cells. Previous studies have suggested that uncleaved Env is conformationally more flexible than the cleaved form making its dynamics important for understanding the broader structural landscape of HIV-1 Env. In this study, we employed microsecond-long all-atom molecular dynamics (MD) simulations to characterize the dynamics of two structures of uncleaved HIV-1 Env that have been previously assigned to the same conformational state. Our results reveal differences in their conformational behavior, including differences in collective motions, FRET distributions, and trimer symmetry. These findings provide molecular-level insight into the structural plasticity of uncleaved HIV-1 Env and highlight that different structures within the same conformational state can exhibit distinct dynamic behavior.

biophysics↗

bioRxiv2026

Cholesterol-Dependent Structure and Dynamics of Curved Lipid Vesicles Revealed by Dry MARTINI Simulations

Cholesterol is a key regulator of membrane structure and dynamics, yet its effects on large curved vesicles under implicit-solvent coarse-grained conditions remain incompletely understood. Equilibrating large Dry MARTINI vesicles is challenging because transient membrane deformations can arise during the early stages of equilibration. Here, we developed a leaflet-specific restrained-equilibration protocol that preserves vesicle geometry while allowing local lipid relaxation. All restraints were removed before production simulations, and all reported results were obtained from unbiased trajectories. Using this protocol together with the Dry MARTINI force field and the TS2CG membrane builder, we simulated [~]50 nm DOPC vesicles containing 0-40 mol% cholesterol in three independent 20 {micro}s production simulations for each membrane composition. Increasing cholesterol concentration produced a consistent structural reorganization of the membrane, characterized by increased membrane thickness and lipid-tail ordering, and decreased species-specific Voronoi area per lipid, lipid-tail interdigitation, solvent-accessible surface area, and vesicle shape anisotropy. Cholesterol flip-flop increased progressively with cholesterol concentration, whereas DOPC flip-flop exhibited a reproducible non-monotonic dependence with a maximum near 20 mol% cholesterol. Comparison with our previous explicit-solvent MARTINI simulations showed that the major cholesterol-dependent structural trends were preserved across both solvent representations, whereas species-specific lipid packing, lipid-tail interdigitation, and the absolute magnitude of lipid flip-flop remained sensitive to the solvent representation. Overall, Dry MAR-TINI combined with the restrained-equilibration protocol provides an efficient framework for studying large curved cholesterol-containing vesicles.

bioengineering↗

bioRxiv2026

Protonation- and substrate-regulated dimer opening couples brain-type creatine kinase to vesicular and actin-remodeling membranes

Brain-type creatine kinase (CK-BB) buffers local ATP demand through reversible phosphotransfer between ATP and phosphocreatine, yet how this soluble metabolic enzyme engages membrane compartments is unknown. Here, we combine fluorescence microscopy, DEER spectroscopy, hydrogen-deuterium exchange and native mass spectrometry, DEER- and AlphaFold-guided modeling, and long-timescale molecular dynamics to define the pH- and substrate-regulated conformational landscape governing CK-BB membrane association. Acidification promotes curvature-sensitive membrane binding and redistributes endogenous and recombinant CK-BB from diffuse cytosolic pools to punctate vesicular structures and membrane ruffles. Substrates independently promote curvature-sensitive association at neutral pH. DEER and modeling reveal an asymmetric dimer in which the convex surface remains restrained, whereas the concave catalytic-regulatory surface samples pH- and substrate-dependent intermediates. We identify progressive dimer opening as a novel regulatory mechanism whereby acidification and substrate binding increase dynamics across the convex surface and N-terminal dimer interface, generating membrane-competent conformations that facilitate curvature sensing and membrane association. Substrate binding buffers acid-induced deprotection while preserving dynamics near the His191/Ser199 regulatory interface. These findings establish CK-BB as a previously unrecognized curvature-sensitive metabolic enzyme and define dimer dynamics as a molecular switch coupling protonation and substrate occupancy to curved-membrane recognition and localized ATP regeneration, with potential relevance to neurodegeneration and cellular stress.

biophysics↗

bioRxiv2026

Interplay Between Cholesterol Concentration and Membrane Curvature in Liposomes Revealed by Molecular Dynamics Simulations

Liposomes are widely used as model membranes and nanoscale drug delivery systems, where cholesterol plays a key role in regulating bilayer structure and dynamics. However, how cholesterol concentration influences the structure and dynamics of liposome and how this influence is dependent on membrane curvature are not fully understood at the molecular level. In this work, coarse-grained molecular dynamics simulations using the MARTINI force field were employed to examine the concentration-dependent behavior of cholesterol in planar and curved membranes composed of cholesterol and unsaturated phospholipids, namely DOPC. More specifically, a planar lipid bilayer and an approximately 50-nm liposome were simulated to represent two extreme limits of small and large curvature, respectively. Increasing cholesterol concentration led to thicker membranes and reduced solvent exposure, consistent with cholesterols condensing effect. Membrane curvature enhanced interleaflet coupling and increased tail interdigitation relative to planar systems. Notably, DOPC flip-flop rate in spherical bilayers exhibited a non-monotonic dependence on cholesterol content, reflecting a balance between curvature-induced packing stress and cholesterol-driven ordering. These findings provide molecular-level insight into how cholesterol and curvature together shape the structure and dynamics of unsaturated lipid bilayers.

biophysics↗

bioRxiv2026

An Investigation of the Conformational Dynamics of ABC Exporter PCAT1 using Microsecond-Level MD Simulations

Peptidase-containing ATP-binding cassette transporters (PCATs) couple ATP hydrolysis with proteolytic processing and export of cargo peptides across cellular membranes. Despite their importance in bacterial secretion systems, the molecular determinants governing nucleotide binding and stabilization in PCAT transporters remain incompletely understood. In particular, recent experimental observations suggest that PCAT1 may display altered nucleotide preferences compared with canonical ABC transporters. Here, we employed microsecond-scale all-atom molecular dynamics simulations combined with free energy perturbation (FEP) calculations to characterize nucleotide binding, protein stability, and conformational dynamics of PCAT1 across multiple biochemical conditions. Simulations were performed for inward-facing (IF) and outward-facing (OF) conformations in the presence or absence of Mg2+ and substrate peptides. Structural analyses reveal that substrate and Mg2+ jointly stabilize the IF conformation, reducing global structural fluctuations and enhancing nucleotide retention in the binding pockets. In contrast, systems lacking Mg2+ exhibit increased nucleotide mobility and partial dissociation events. Thermodynamic analysis using FEP calculations further demonstrates that ATP binding is strongly stabilized in the IF state, particularly in the presence of Mg2+, whereas nucleotide stability is reduced when Mg2+ coordination is absent. To identify the molecular origins of nucleotide stabilization, we introduce a residue-level free energy decomposition approach that quantifies the contribution of individual residues to nucleotide binding energetics. This analysis reveals that the Walker A residue Lys525 provides the dominant stabilizing interaction with ATP, while neighboring residues within the Walker A motif contribute additional stabilization. In contrast, acidic residues of the Walker B motif primarily participate in catalytic organization rather than direct nucleotide stabilization. Together, these results provide a comprehensive molecular description of nucleotide stabilization and conformational regulation in PCAT1. The combined structural and energetic analyses support a model in which Mg2+ coordination and substrate binding cooperatively stabilize the inward-facing state and organize the nucleotide-binding site for productive ATP hydrolysis. More broadly, this work demonstrates how residue-level free energy analysis can reveal the energetic architecture of nucleotide recognition in ABC transporters.

biophysics↗

bioRxiv2026

Predicting Binding Affinities for the Binding Domain of Hyperpolarization-Activated Cyclic Nucleotide-Gated Channel Isoforms Using Free-Energy Perturbation

Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels are are a family of voltage-gated, cyclic-nucleotide modulated Na+/K+ channels that regulate spontaneous rhythmic electrical activity in both the heart and the brain. Understanding differences in the responsiveness to cyclic adenosine monophosphate (cAMP) modulation between HCN isoforms would offer insight into the specific binding interactions that drive channel activation. Using all-atom molecular dynamics (MD) simulations and the free-energy perturbation (FEP) approach, we determined the absolute binding free energy of cAMP to the the cyclicnucleotide-binding domain (CNBD) of HCN isoforms 1-4. By studying the free-energy of ligand binding to the various isoforms of HCN, our study advances the understanding of HCN channel activation and modulation mechanisms. Overall, our work offers insight into explaining differences in channel sensitivity across the isoforms of HCN.

biophysics↗

bioRxiv2026

Characterizing the Conformational Dynamics of an Intrinsically Disordered Localization Sequence

Mitochondrial localization peptides (MLPs) play a critical role in directing proteins to mitochondria, yet how subtle sequence variations influence their conformational behavior remains poorly understood. Here, we investigate the conformational dynamics of a 15-residue MLP derived from the androgen receptor, together with a comprehensive panel of single-residue variants generated by systematic substitution at the second position. Across all variants, the peptide remains intrinsically disordered, exhibiting broad conformational heterogeneity and no stable folded state. Global measures of compactness show that single-residue substitutions induce only modest changes to overall peptide dimensions. In contrast, residue-level analysis reveals that the identity of the second residue subtly reshapes local structural preferences, particularly near the N-terminus. Small or hydrophobic substitutions enhance transient -helical sampling, whereas polar or charged substitutions favor increased disorder and {beta}- or polyprolinelike conformations. Comparison across variants further distinguishes mutations that preserve wild-type-like structural behavior from those that produce more pronounced deviations in the conformational ensemble. Enhanced sampling simulations highlight the complexity and ruggedness of the underlying free-energy landscape and demonstrate the challenges associated with achieving convergence for short intrinsically disordered peptides. Collectively, these results show that even minimal sequence changes can bias the dynamic structural ensemble of mitochondrial localization peptides, suggesting a potential mechanism by which targeting efficiency may be modulated. More broadly, this work underscores the importance of advanced sampling strategies for accurately characterizing intrinsically disordered localization signals and provides a framework for connecting sequence variation to functional targeting behavior.

biophysics↗

bioRxiv2025

Structural dynamics of sphingosine kinase 1 regulation and inhibition

Sphingosine kinase 1 (SK1) generates sphingosine-1-phosphate, a bioactive lipid implicated in cancer and other diseases. Despite its clinical importance, the structural and dynamic basis of SK1 regulation and inhibition remains poorly understood. Using integrated spectroscopic and computational approaches, we uncover conformational transitions that govern substrate entry, catalysis, and inhibitor binding. Phosphorylation of Ser225 reconfigures the regulatory loop and reshuffles salt bridges, priming SK1 for membrane engagement and catalytic activity. We identify a previously uncharacterized catalytic intermediate with a distinct conformation and a highly dynamic lipid-binding loop 1 (LBL-1), sensitive to potent inhibitors such as PF-543. These inhibitors not only stabilize non-catalytic states but also induce LBL-mediated dimerization, blocking membrane binding and substrate access. Our findings reveal a multilayered regulatory mechanism driven by structural flexibility and establish a novel inhibitory paradigm. This framework provides critical insight into SK1 regulation and a foundation for developing next-generation SK1-targeted therapeutics.

biophysics↗

bioRxiv2025

Molecular Insights into Cholesterol Concentration Effects on Planar and Curved Lipid Bilayers for Liposomal Drug Delivery

Liposomal carriers provide a flexible and effective strategy for delivering therapeutics across a broad spectrum of diseases. Cholesterol is frequently included in these systems to improve membrane rigidity and limit permeability. Despite its widespread use, the optimal cholesterol-to-lipid proportion for achieving stable and efficient liposome performance remains to be fully determined. In this work, we apply all-atom molecular dynamics simulations to explore how different cholesterol concentrations influence the structural and dynamic characteristics of 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) bilayers, considering both planar and curved membrane geometries. Bilayers with cholesterol molar ratios of 0%, 10%, 20%, 30%, 40%, and 50% were simulated, and key biophysical parameters including area per lipid (APL), membrane thickness, leaflet interdigitation, and deuterium order parameters (SCD) were analyzed. In planar bilayers, increasing cholesterol concentration led to a progressive decrease in APL from approximately 60 {degrees}A2 to 40 {degrees}A2, accompanied by increased membrane thickness and lipid ordering, consistent with cholesterols classical condensing effect. In contrast, curved bilayers exhibited a cholesterol-induced expansion effect, particularly in the inner leaflet, where APL increased from approximately 60 {degrees}A2 to 90 {degrees}A2 with rising cholesterol levels. SCD profiles showed that cholesterol enhanced tail ordering up to 40% concentration, beyond which the effect plateaued or slightly declined, suggesting structural saturation or packing frustration. Membrane thickness displayed a monotonic increase in planar bilayers but followed a nonlinear trend in curved systems due to curvature-induced stress. These findings highlight that cholesterols influence on membrane properties is highly dependent on bilayer geometry and asymmetry. While planar bilayers exhibit predictable responses, curved systems reveal nonclassical behaviors that challenge traditional models of cholesterol-lipid interactions. This work provides molecular-level insights and establishes a computational framework for the rational design of liposomal systems, emphasizing the need to account for curvature and asymmetry in membrane engineering.

biophysics↗

bioRxiv2025

A conserved differentiation program facilitates inhibitory neuron production in the developing mouse and human cerebellum

Understanding the molecular mechanisms driving lineage decisions and differentiation during development is challenging in complex systems with a diverse progenitor pool, such as the mammalian cerebellum. Importantly, how different transcription factors cooperate to generate neural diversity and the gene regulatory mechanisms that drive neuron production, especially during the late stages of cerebellar development are poorly understood. Here, we used single cell RNA-sequencing (scRNA-seq) to investigate the developmental trajectories of Nestin-expressing progenitors (NEPs) in the neonatal mouse cerebellum. We identified FOXO1 as a key regulator of NEP-to-inhibitory neuron differentiation, acting directly downstream of ASCL1. Genome occupancy and functional experiments using primary NEPs showed that both ASCL1 and FOXO1 regulate neurogenesis genes during differentiation while independently regulating proliferation and survival, respectively. Furthermore, we demonstrated that WNT signalling promotes the transition from an ASCL1+ to a FOXO1+ cellular state. Finally, we showed that the role of WNT signalling in promoting neuron production via FOXO1 is conserved in primary human NEPs. By resolving how cerebellar interneurons differentiate, our findings could have implications for cerebellar disorders such as spinocerebellar ataxia, where cerebellar interneurons are overproduced.

developmental biology↗

bioRxiv2025

Lipid-Mediated Modulation of mGluR2 Embedded in Micelle and Bilayer Environments: Insights from Molecular Dynamics

Metabotropic glutamate receptor 2 (mGluR2), a subclass C member of the G protein-coupled receptor (GPCR) superfamily, is essential for regulating neurotransmitter signaling and facilitating synaptic adaptability in the central nervous system. This receptor, like other GPCRs, is highly sensitive to its surrounding lipid environment, where specific lipid compositions can influence its stability, conformational dynamics, and function. In particular, cholesteryl hemisuccinate (CHS) plays a critical role in stabilizing mGluR2 and modulating its structural states within cellular membranes and micellar environments. However, the molecular basis for this lipid-mediated modulation remains largely unexplored. To investigate the effects of CHS and lipid composition on mGluR2, we employed all-atom molecular dynamics simulations of mGluR2 embedded in both detergent micelles (BLMNG and CHS) and a POPC lipid bilayer containing 0%, 10%, and 25% CHS. These simulations were conducted for both active and inactive states of the receptor. Our findings reveal that CHS concentration modulates mGluR2s structural stability and conformational behavior, with a marked impact observed within transmembrane helices TM1, TM2, and TM3, which constitute the core of the receptors transmembrane domain. In micelle environments, mGluR2 displayed unique conformational dynamics influenced by CHS, underscoring the receptors sensitivity to its lipid surroundings. Notably, a CHS concentration of 10% elicited more pronounced conformational changes than either cholesterol-depleted (0%) or cholesterol-enriched (25%) systems, indicating an optimal CHS range for maintaining structural stability. Our study provides atomistic insights into how lipid composition and CHS concentration impact mGluR2s conformational landscape in distinct micelle and bilayer environments. These findings advance our understanding of lipid-mediated modulation in GPCR function, highlighting potential avenues for receptor-targeted drug design, particularly in cases where lipid interactions play a significant role in therapeutic efficacy.

biophysics↗

bioRxiv2024

Molecular dynamics investigation of the influenza hemagglutinin conformational changes in acidic pH

The surface protein hemagglutinin (HA) of the influenza virus plays a pivotal role in facilitating viral infection by binding to sialic acid receptors on host cells. Its conformational state is pH-sensitive, impacting its receptor-binding ability and evasion of the host immune response. In this study, we conducted extensive equilibrium microsecond-level all-atom molecular dynamics (MD) simulations of the HA protein to explore the influence of low pH on its conformational dynamics. Specifically, we investigated the impact of protonation on conserved histidine residues (His1062) located in the hinge region of HA2. Our analysis encompassed comparisons between non-protonated (NP), partially protonated (1P, 2P), and fully-protonated (3P) conditions. Our findings reveal substantial pH-dependent conformational alterations in the HA protein, affecting its receptor-binding capability and immune evasion potential. Notably, the non-protonated form exhibits greater stability compared to protonated states. Conformational shifts in the central helices of HA2 involve outward movement, counterclockwise rotation of protonated helices, and fusion peptide release in protonated systems. Disruption of hydrogen bonds between the fusion peptide and central helices of HA2 drives this release. Moreover, HA1 separation is more likely in the fully-protonated system (3P) compared to non-protonated systems (NP), underscoring the influence of protonation. These insights shed light on influenza virus infection mechanisms and may inform the development of novel antiviral drugs targeting HA protein and pH-responsive drug delivery systems for influenza.

biophysics↗

bioRxiv2024

Cholesterol Dependence on the Conformational Changes of Metabotropic Glutamate Receptor 1

Metabotropic glutamate receptors (mGluRs) are class C G protein-coupled receptors that function as obligate dimers in regulating neurotransmission and synaptic plasticity in the central nervous system. The mGluR1 subtype has been shown to be modulated by the membrane lipid environment, particularly cholesterol, though the molecular mechanisms remain elusive. In this study, we employed all-atom molecular dynamics simulations to investigate the effects of cholesterol on the conformational dynamics of the mGluR1 seven-transmembrane (7TM) domain in an inactive state model. Simulations were performed with three different cholesterol concentrations (0%, 10%, and 25%) in a palmitoyl-oleoyl phosphatidylcholine (POPC) lipid bilayer system. Our results demonstrate that cholesterol induces conformational changes in the mGluR1 dimer more significantly than in the individual protomers. Notably, cholesterol modulates the dynamics and conformations of the TM1 and TM2 helices at the dimer interface. Interestingly, an intermediate cholesterol concentration of 10% elicits more pronounced conformational changes compared to both cholesterol-depleted (0%) and cholesterol-enriched (25%) systems. Specific electrostatic interaction unique to the 10% cholesterol system further corroborate these conformational differences. Given the high sequence conservation of the 7TM domains across mGluR subtypes, the cholesterol-dependent effects observed in mGluR1 are likely applicable to other members of this receptor family. Our findings provide atomistic insights into how cholesterol modulates the conformational landscape of mGluRs, which could impact their function and signaling mechanisms.

biophysics↗

bioRxiv2024

Differential Behavior of Conformational Dynamics in Active and Inactive States of Cannabinoid Receptor 1 Revealed by Microsecond-Level Molecular Dynamics Simulation

Cannabinoid receptor 1 (CB1) is a G protein-coupled receptor (GPCR) that regulates critical physiological processes including pain, appetite, and cognition. Understanding the confor- mational dynamics of CB1 associated with transitions between inactive and active signaling states is imperative for developing targeted modulators. Using microsecond-level all-atom molecular dynamics (MD) simulations, we identified marked differences in the conformational ensembles of inactive and active CB1 in apo. The inactive state exhibited substantially in- creased structural heterogeneity and plasticity compared to the more rigidified active state in the absence of stabilizing ligands. Transmembrane helices TM3 and TM7 were identified as distinguishing factors modulating the state-dependent dynamics. TM7 displayed amplified fluctuations selectively in the inactive state simulations attributed to disruption of conserved electrostatic contacts anchoring it to surrounding helices in the active state. Additionally, we identified significant reorganizations in key salt bridge and hydrogen bond networks con- tributing to the CB1 activation/inactivation. For instance, D213-Y224 hydrogen bond and D184-K192 salt bridge showed marked rearrangements between the states. Collectively, these findings reveal the specialized role of TM7 in directing state-dependent CB1 dynamics through electrostatic switch mechanisms. By elucidating the intrinsic enhanced flexibility of inactive CB1, this study provides valuable insights into the conformational landscape enabling functional transitions. Our perspective advances understanding of CB1 activation mechanisms and offers opportunities for structure-based drug discovery targeting the state- specific conformational dynamics of this receptor. Graphic for manuscript O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=174 SRC="FIGDIR/small/589939v2_ufig1.gif" ALT="Figure 1"> View larger version (60K): org.highwire.dtl.DTLVardef@ade7d7org.highwire.dtl.DTLVardef@1500e0corg.highwire.dtl.DTLVardef@ca4b04org.highwire.dtl.DTLVardef@10317eb_HPS_FORMAT_FIGEXP M_FIG For Table of Contents Only C_FIG

biophysics↗

bioRxiv2024

Lipid-dependent conformational dynamics of bacterial ATP-bindingcassette transporter Sav1866

Sav1866, a bacterial ATP-binding cassette (ABC) exporter, plays a crucial role in cellular processes by facilitating the efflux of a diverse range of substrates, including drugs, chemotherapeutic agents, peptides, and lipids. This efflux activity significantly impacts the effectiveness of various therapies against bacterial infections. In our recent investigation, we focused on understanding the conformational dynamics of Sav1866 within different lipid environments. Specifically, we explored its behavior in environments composed of DMPC and POPE lipids, which exhibit crucial distinctions not only in their headgroup polarity but also in the length and saturation of their hydrophobic tails. Our extensive set of equilibrium microsecond-level all-atom molecular dynamics (MD) simulations revealed significant distinctions in transporter behavior influenced by these lipid compositions. We observed a rapid transition to an occluded-inward-facing (IF-occ) conformation in POPE environments, contrasting with a channel-like behavior in DMPC environments, deviating from the expected alternating access mechanism (AAM). These findings underscore the significant impact of lipid compositions on ABC transporter function, offering new perspectives on membrane transport mechanisms.

biophysics↗

bioRxiv2024

Novel Pentafluorosulfanyl-containing Triclocarban Analogs selectively kill Gram-positive bacteria.

The antibacterial and antibiofilm efficacy of our novel pentafluorosulfanyl-containing triclocarban analogs was explored against seven different Gram-positive and Gram-negative indicator strains. After initial screening, they had bactericidal and bacteriostatic activity against Gram-positive bacteria, especially Staphylococcus aureus and MRSA (methicillin-resistant staphylococcus aureus) in a very low concentration. Our results were compared with the most common antibiotic being used (Ciprofloxacin and Gentamycin); the novel components had significantly better antibacterial and antibiofilm activity in lower concentrations in comparison to the antibiotics. For instance, EBP-59 minimum inhibitory concentration was < 0.0003 mM, while ciprofloxacin 0.08 mM. Further antibacterial activity of novel components was surveyed against 10 clinical antibiotic resistance MRSA isolates. Again, novel components had significantly better antibacterial and antibiofilm activity in comparison with antibiotics. Mechanistic studies have revealed that none of these novel compounds exhibit any effect on the reduced thiol, disrupting iron sulfur clusters, or hydrogen peroxide pathways. Instead, their impact is attributed to the disruption of the Gram-positive bacterial cell membrane. Toxicity and safety testing on tissue cell culture showed promising results for the safety of components to the host.

microbiology↗

bioRxiv2023

5-MeO-DMT induces sleep-like LFP spectral signatures in the hippocampus and prefrontal cortex of awake rats

5-methoxy-N,N-dimethyltryptamine (5-MeO-DMT) is a potent classical psychedelic known to induce changes in locomotion, behaviour, and sleep in rodents. However, there is limited knowledge regarding its acute neurophysiological effects. Local field potentials (LFPs) are commonly used as a proxy for neural activity, but previous studies investigating psychedelics have been hindered by confounding effects of behavioural changes and anaesthesia, which alter these signals. To address this gap, we investigated acute LFP changes in the hippocampus (HP) and medial prefrontal cortex (mPFC) of freely behaving rats, following 5-MeO-DMT administration. 5-MeO-DMT led to an increase of delta power and a decrease of theta power in the HP LFPs, which could not be accounted for by changes in locomotion. Furthermore, we observed a dose-dependent reduction in slow (20-50 Hz) and mid (50-100Hz) gamma power, as well as in theta phase modulation, even after controlling for the effects of speed and theta power. State map analysis of the spectral profile of awake behaviour induced by 5-MeO-DMT revealed similarities to electrophysiological states observed during slow-wave sleep (SWS) and rapid-eye-movement (REM) sleep. Our findings suggest that the psychoactive effects of classical psychedelics are associated with the integration of waking behaviours with sleep-like spectral patterns in LFPs.

neuroscience↗