Unique Conformation Research Articles

Evaluating the Importance of Conformers for Understanding the Vacuum-Ultraviolet Spectra of Oxiranes: Experiment and Theory.

Vacuum-ultraviolet (VUV) absorption spectroscopy enables electronic transitions that offer the unambiguous identification of molecules. As target molecules become more complex, multifunctional species present a great challenge to both experimental and computational spectroscopy. This research reports both experimental and theoretical studies of oxiranes. Computationally, the nuclear ensemble approach has been used to accurately predict experimental spectra for a variety of molecules. However, this approach incurs great computational cost, as ensembles generally consist of thousands of geometries. The present study aims to drastically reduce the ensemble by evaluating the significance of the conformers to the predicted spectra. This approach was applied to 11 substituted oxiranes using the Conformer Rotamer Ensemble Sampling Tool (CREST) of Grimme to generate an ensemble of unique conformers determined by their Boltzmann populations. Five TD-DFT functionals (BMK, CAM-B3LYP, M06-2X, MN15, ωB97X-D) and EOM-CCSD were used to simulate the spectrum of each substituted oxirane ensemble. Computed spectra were then compared to the experiment using both qualitative and quantitative metrics. Based on these metrics, it was observed that certain conformers may not be necessary to characterize this set of oxiranes despite the temperature (323 K) of the experiment. A single conformer can then be used with TD-DFT and EOM-CCSD to replicate the experimental spectra of these medium-sized combustion species.

Unveiling molecular mechanism underlying inhibition of human islet amyloid polypeptide fibrillation by benzene carboxylic acid-peptide conjugate

Type 2 diabetes (T2D) is linked to the apoptosis of insulin-producing β-cells due to the aberrant fibrillation of the human islet amyloid polypeptide (hIAPP or amylin) to cytotoxic aggregates. Profit et al. generated conjugates (C1–C7) by appending benzene carboxylic acids of varying charges to the N-terminal of hIAPP22-29 fragment peptide NFGAILSS to modulate hIAPP fibrillation and cytotoxicity. C5 (4 µM) derived by conjugating low-cost, commercially available benzene-1,2,4,5-tetracarboxylic acid known as pyromellitic acid to NFGAILSS completely abolishes the hIAPP (40 µM) self-assembly as noted in the thioflavin T (ThT) fluorescence assay. The circular dichroism (CD) spectra highlighted that C5 stabilized hIAPP in a distinctive conformation and blocked its conformational switching to amyloidogenic β-sheet structure. C5 possessing a charge-dense pyromellitic acid moiety appended on the N-terminal region of self-recognition hIAPP fragment sequence NFGAILSS created significant interest as it effectively inhibited hIAPP fibrillation and possessed lower molecular mass, smaller size, and charge as compared to hIAPP aggregation inhibitor EEEENFGAILSS (P10). However, it remains unclear how C5 traps hIAPP into a unique conformation that abolishes its self-aggregation propensity. Thus, molecular dynamics (MD) simulations have been employed to illuminate the conformational transitions and structural changes in hIAPP on the inclusion of C5. C5 displayed high-affinity binding interactions to hIAPP (ΔGbinding = −37.11 ± 3.72 kcal/mol) with major contributions from the van der Waals and electrostatic interactions. Furthermore, residue-specific binding free energy analysis depicted high-affinity binding interactions of C5 with Phe15, His18, Asp21, and Tyr37 of hIAPP that play a crucial role in hIAPP fibrillation. The negatively charged carboxylate groups of pyromellitic acid moiety of C5 displayed interactions with the key residues of hIAPP as noted in the conformational clustering analysis. Notably higher sampling of helix from 24.00 ± 0.84 % in hIAPP to 34.20 ± 1.92 % in hIAPP–C5 is consistent with the CD studies, which depicted that C5 trapped hIAPP monomer in a conformation that blocked its self-association. MD simulations illuminated the molecular mechanism and atomistic details of the C5 interactions with hIAPP, which are responsible for its inhibitory activity against hIAPP fibrillation and alleviating hIAPP aggregates-induced cytotoxicity.

IN SILICO BASED RE-ENGINEERING OF A COMPUTATIONALLY DESIGNED BIOSENSOR WITH ALTERED SIGNALLING MODE AND IMPROVED DYNAMIC RANGE.

A current challenge in the rational design of biomolecular sensors is the ability to custom design binding affinities and detection mode in silico. To this end, we re-engineered a previously reported computationally-designed fluorescent maltooligosaccharide (MOS)-detecting biosensor to both alter its ligand-binding affinity and to analyse the underlying sensing mechanism. The dynamic range of the biosensor was expanded through the computer aided introduction of a series of amino acid substitutions in the starting protein scaffold (MalX from Streptococcus pneumoniae), which generated a biosensor set with binding affinities spanning over five orders of magnitude. The impact of the introduced substitutions on the underlying mode of signal generation was assessed in silico using our previously reported Computational Identification of Non-disruptive Conjugation sites (CINC) pipeline. CINC utilizes molecular dynamics simulations and an in-house developed algorithm to examine and exploit the structural dynamics of a protein at amino acid-level resolution. Using CINC, we demonstrate that re-engineering of the MOS-detecting biosensor set resulted in sensors with two distinct output modes which differed based on local conformational changes at the fluorescently modified reporter position. These output modes were classified as "ligand-sensing"-type biosensors (readout based on the tool sensing a unique conformation in the ligand-bound state), and "apo-sensing"-type biosensors (readout based on the tool sensing a unique conformation in the apo state). Together, these results demonstrate that structural dynamics at the individual amino acid residue level can be used as an engineer-able feature to rationally alter the fluorescence reporting properties of a biosensing device. Moving forward, the CINC workflow can also be adapted for the rational design of protein dynamic properties maximizing its utility as an in silico design platform for custom biomolecular tools.

High-resolution crystal structure of PD-1 in complex with retifanlimab, the FDA-approved immune checkpoint blocking antibody for treating Merkel cell carcinoma

Retifanlimab is a humanized monoclonal antibody that specifically targets programmed cell death protein 1 (PD-1), an essential immune checkpoint that modulates T-cell immune responses. Several anti-PD-1 antibodies have been market-approved, marking a significant advancement in the treatment of diverse tumor types by restoring the T-cell immune response. Recently, the US FDA approved retifanlimab for treating metastatic or recurrent locally advanced Merkel cell carcinoma. We present the crystal structure of PD-1 in complex with the retifanlimab Fab at a resolution of 1.54 Å to elucidate the structural basis for the mechanism of action of this antibody. This work clarifies the detailed interactions and conformational alterations that occur upon antibody binding. The epitope of retifanlimab partially overlaps with the ligand binding site, and its binding induced unique conformations of the flexible loops within PD-1, including BC, C'D, and FG loops, thereby optimizing interactions with the antibody. A thorough analysis of its interaction with PD-1 and other FDA-approved anti-PD-1 antibodies may provide valuable insights into the rational design of enhanced therapies to regulate immune responses in cancer treatment.

Convergent evolution of berberine biosynthesis.

Berberine is an effective antimicrobial and antidiabetic alkaloid, primarily extracted from divergent botanical lineages, specifically Coptis (Ranunculales, early-diverging eudicot) and Phellodendron (Sapindales, core eudicot). In comparison with its known pathway in Coptis species, its biosynthesis in Phellodendron species remains elusive. Using chromosome-level genome assembly, coexpression matrix, and biochemical assays, we identified six key steps in berberine biosynthesis from Phellodendron amurense, including methylation, hydroxylation, and berberine bridge formation. Notably, we discovered a specific class of O-methyltransferases (NOMT) responsible for N-methylation. Structural analysis and mutagenesis of PaNOMT9 revealed its unique substrate-binding conformation. In addition, unlike the classical FAD-dependent berberine bridge formation in Ranunculales, Phellodendron uses a NAD(P)H-dependent monooxygenase (PaCYP71BG29) for berberine bridge formation, originating from the neofunctionalization of tryptamine 5-hydroxylase. Together, these findings reveal the convergence of berberine biosynthesis between Coptis and Phellodendron and signify the role of the convergent evolution in plant specialized metabolisms.

Structural insights into the ATP-dependent activation of NOD-like receptor with pyrin 3 (NLRP3) protein by molecular dynamics simulation

The inflammasome-forming NOD-like receptor containing pyrin-3 (NLRP3) protein is a critical player in the innate immune responses to cellular danger signals. New structural data of NLRP3 provide a framework to probe the conformational impact of nucleotide binding. In this study, microsecond molecular dynamics (MD) simulations were used to detail information on the unique structural conformations adopted by NLRP3 with ATP or ADP binding. Sampling convergence reflected a high degree of confidence in the MD simulations as shown by RMSD and protein-nucleotide concordance, favourable overall MM-PBSA ligand binding energies for both nucleotides and low cosine coefficients of the principal eigenvectors obtained with essential dynamics (ED) analysis. NLRP3-ADP simulations provide relatively stable conformations with few global rearrangements as shown by decreased protein RMSD, Rg, SASA, and solvent accessibility for the ADP-bound structure. In contrast, ATP binding induced increased flexibility and resulted in substantive conformational changes to the NLRP3 structure. Binding of ATP was thermodynamically favourable as shown by the ΔGsolv and MM-PBSA calculations of complex free energies, and these NLRP3-ATP simulations resulted in similar structural transitions as observed in the activated NLRC4 empirical structure. Lastly, the active conformation of NLRP3 critically depends on hinging between the HD2 and LRR domains, whereby ATP binding drives local conformational changes that are conveyed to the global structure.

3D chromatin maps of a brown alga reveal U/V sex chromosome spatial organization.

Nuclear three dimensional (3D) folding of chromatin structure has been linked to gene expression regulation and correct developmental programs, but little is known about the 3D architecture of sex chromosomes within the nucleus, and how that impacts their role in sex determination. Here, we determine the sex-specific 3D organization of the model brown alga Ectocarpus chromosomes at 2 kb resolution, by mapping long-range chromosomal interactions using Hi-C coupled with Oxford Nanopore long reads. We report that Ectocarpus interphase chromatin exhibits a non-Rabl conformation, with strong contacts among telomeres and among centromeres, which feature centromere-specific LTR retrotransposons. The Ectocarpus chromosomes do not contain large local interactive domains that resemble TADs described in animals, but their 3D genome organization is largely shaped by post-translational modifications of histone proteins. We show that the sex determining region (SDR)within the U and V chromosomes are insulated and span the centromeres andwe link sex-specific chromatin dynamics and gene expression levels to the 3D chromatin structure of the U and V chromosomes. Finally, we uncover the unique conformation of a large genomic region on chromosome 6 harboring an endogenous viral element, providing insights regarding the impact of a latent giant dsDNA virus on the host genome's 3D chromosomal folding.

The complete mitochondrial genome of Castanopsis carlesii and Castanea henryi reveals the rearrangement and size differences of mitochondrial DNA molecules

BackgroundCastanopsis carlesii is a dominant tree species in subtropical evergreen broad-leaved forests and holds significant ecological value. It serves as an excellent timber tree species and raw material for cultivating edible fungi. Henry Chinquapin (Castanea henryi) wood is known for its hardness and resistance to water and moisture, making it an exceptional timber species. Additionally, its fruit has a sweet and fruity taste, making it a valuable food source. However, the mitogenomes of these species have not been previously reported. To gain a better understanding of them, this study successfully assembled high-quality mitogenomes of C. carlesii and Ca. henryi for the first time.ResultsOur research reveals that the mitochondrial DNA (mtDNA) of C. carlesii exhibits a unique multi-branched conformation, while Ca. henryi primarily exists in the form of two independent molecules that can be further divided into three independent molecules through one pair of long repetitive sequences. The size of the mitogenomes of C. carlesii and Ca. henryi are 592,702 bp and 379,929 bp respectively, which are currently the largest and smallest Fagaceae mitogenomes recorded thus far. The primary factor influencing mitogenome size is dispersed repeats. Comparison with published mitogenomes from closely related species highlights differences in size, gene loss patterns, codon usage preferences, repetitive sequences, as well as mitochondrial plastid DNA segments (MTPTs).ConclusionsOur study enhances the understanding of mitogenome structure and evolution in Fagaceae, laying a crucial foundation for future research on cell respiration, disease resistance, and other traits in this family.

Allosteric degraders induce CRL5 ASB8 mediated degradation of XPO1.

The nuclear export receptor Exportin 1 (XPO1/CRM1) is often overexpressed in cancer cells resulting in aberrant localization of many cancer-related protein cargoes. The XPO1 inhibitor and cancer drug selinexor (KPT-330), and its analog KPT-185, block XPO1-cargo binding thereby restoring cargo localization. Selinexor binding induces cullin-RING E3 ubiquitin ligase (CRL) substrate receptor ASB8-mediated XPO1 degradation. Here we reveal the mechanism of inhibitor-XPO1 engagement by CRL5ASB8. Cryogenic electron microscopy (cryo-EM) structures show ASB8 binding to a large surface of selinexor/KPT-185-XPO1 that includes a three-dimensional degron unique to the drug-bound exportin. The structure explains weak XPO1-ASB8 binding in the absence of selinexor/KPT-185 that is unproductive for proteasomal degradation, and the substantial affinity increase upon selinexor/KPT-185 conjugation, which results in CRL5 ASB8 -mediated XPO1 ubiquitination. In contrast to previously characterized small molecule degraders, which all act as molecular glues, selinexor/KPT-185 binds extensively to XPO1 but hardly contacts ASB8. Instead, selinexor/KPT-185 binds XPO1 and stabilizes a unique conformation of the NES/inhibitor-binding groove that binds ASB8. Selinexor/KPT-185 is an allosteric degrader. We have explained how drug-induced protein degradation is mediated by a CRL5 system through an allosteric rather than a molecular glue mechanism, expanding the modes of targeted protein degradation beyond the well-known molecular glues of CRL4.

Potential allosteric pockets identification of glucagon receptor based on molecular dynamics simulations

Glucagon receptor (GCGR) is an important target for the treatment of type 2 diabetes mellitus. Although several small molecules with antagonistic activity have been discovered, so far, only one small molecule binding site has been resolved. To discover more novel allosteric pockets and allosteric molecules, we started with the unique full-length inactive conformation of GCGR and applied all-atom molecular dynamics (MD) simulations to obtain extensive dynamic conformations of the GCGR/glucagon complex. For the first time, MDpocket, FTMove and FTMap were used to detect allosteric pockets in simulation trajectories, selecting 4 stable pockets with a total of 14 structures as templates for virtual screening. From the results of virtual screening, 14 compounds were ultimately selected after a series of filtering steps. The cAMP accumulation assay indicated that compound gs6 has antagonistic activity, and MD simulations further revealed the allosteric mechanism of gs6. We are the first to identify new allosteric pockets and allosteric molecules in simulation trajectories of the GCGR/glucagon complex, providing a reference for research on other G-protein-coupled receptors (GPCR). However, there is still considerable room for improvement, such as using more simulation methods to obtain a richer set of dynamic conformations.

Identification of novel and potent inhibitors of SARS-CoV-2 main protease from DNA-encoded chemical libraries.

In vitro screening of large compound libraries with automated high-throughput screening is expensive and time-consuming and requires dedicated infrastructures. Conversely, the selection of DNA-encoded chemical libraries (DECLs) can be rapidly performed with routine equipment available in most laboratories. In this study, we identified novel inhibitors of SARS-CoV-2 main protease (Mpro) through the affinity-based selection of the DELopen library (open access for academics), containing 4.2 billion compounds. The identified inhibitors were peptide-like compounds containing an N-terminal electrophilic group able to form a covalent bond with the nucleophilic Cys145 of Mpro, as confirmed by x-ray crystallography. This DECL selection campaign enabled the discovery of the unoptimized compound SLL11 (IC50 = 30 nM), proving that the rapid exploration of large chemical spaces enabled by DECL technology allows for the direct identification of potent inhibitors avoiding several rounds of iterative medicinal chemistry. As demonstrated further by x-ray crystallography, SLL11 was found to adopt a highly unique U-shaped binding conformation, which allows the N-terminal electrophilic group to loop back to the S1' subsite while the C-terminal amino acid sits in the S1 subsite. MP1, a close analog of SLL11, showed antiviral activity against SARS-CoV-2 in the low micromolar range when tested in Caco-2 and Calu-3 (EC50 = 2.3 µM) cell lines. As peptide-like compounds can suffer from low cell permeability and metabolic stability, the cyclization of the compounds will be explored in the future to improve their antiviral activity.

Single fluorogen imaging reveals distinct environmental and structural features of biomolecular condensates.

Biomolecular condensates are viscoelastic materials. Simulations predict that fluid-like condensations are defined by spatially inhomogeneous organization of the underlying molecules. Here, we test these predictions using single-fluorogen tracking and super-resolution imaging. Specifically, we leverage the localization and orientational preferences of freely diffusing fluorogens and the solvatochromic effect whereby specific fluorogens are turned on in response to condensate microenvironments. We deployed three different fluorogens to probe the microenvironments and molecular organization of different protein-based condensates. The spatiotemporal resolution and environmental sensitivity afforded by single-fluorogen imaging shows that the internal environments of condensates are more hydrophobic than coexisting dilute phases. Molecules within condensates are organized in a spatially inhomogeneous manner, and this gives rise to slow-moving nanoscale molecular clusters that coexist with fast-moving molecules. Fluorogens that localize preferentially to the interface help us map their distinct features. Our findings provide a structural and dynamical basis for the viscoelasticity of condensates.

BRCA2 C-terminal clamp restructures RAD51 dimers to bind B-DNA for replication fork stability.

Tumor suppressor protein BRCA2 acts with RAD51 in replication-fork protection (FP) and homology-directed DNA break repair (HDR). Critical for cancer etiology and therapy resistance, BRCA2 C-terminus was thought to stabilize RAD51-filaments after they assemble on single-stranded (ss)DNA. Here we determined the detailed crystal structure for BRCA2 C-terminal interaction-domain (TR2i) with ATP-bound RAD51 prior to DNA binding. In contrast to recombinogenic RAD51-filaments comprising extended ATP-bound RAD51 dimers, TR2i unexpectedly reshapes ATP-RAD51 into a unique dimer conformation accommodating double-stranded B-DNA binding unsuited for HDR initiation. Structural, biochemical, and molecular results with interface-guided mutations uncover TR2i's FP mechanism. Proline-driven secondary-structure stabilizes residue triads and spans the RAD51 dimer engaging pivotal interactions of RAD51 M210 and BRCA2 S3291/P3292, the cyclin-dependent kinase (CDK) phosphorylation site that toggles between FP during S-phase and HDR in G2. TR2i evidently acts as an allosteric clamp switching RAD51 from ssDNA to double-stranded and B-DNA binding enforcing FP over HDR.

An arabinan from Citrus grandis fruits alleviates ischemia/reperfusion-induced myocardial cell apoptosis via the Nrf2/Keap1 and IRE1/GRP78 signaling pathways

Citrus grandis fruit is a famous traditional Chinese medicine with various bioactivities, including cardioprotective effects. Polysaccharides are one of the key active ingredients responsible for its cardioprotective effects. This study aimed to investigate the structure and cardioprotective effect of a homogeneous polysaccharide from C. grandis fruit (CGP80-1) and explore its mechanism against myocardial ischemia-reperfusion (MI/R) injury. Structure analysis showed that CGP80-1 (11,917 Da) is an arabinan with compact coil chain conformation, containing →5)-α-L-Araf-(1→, →3,5)-α-L-Araf-(1→, and →2,3,5)-α-L-Araf-(1→ as the backbone, as well as →5)-α-L-Araf-(1→ and t-α-L-Araf as side-chains substituted at the C2 and C3 positions. Pharmacological experiments showed that pre-treatment with CGP80-1 could effectively alleviate MI/R injury by improving endogenous antioxidant enzymes and cardiac enzymes, reducing reactive oxygen species levels, and regulating apoptosis-related proteins such as caspase-3, Bax, and Bcl-2. The protective effects were correlated with the Nrf2/Keap1 and IRE1/GRP78 signaling pathways. Further analysis of structure-activity relationships revealed that the myocardial protection effects of CGP80-1 might be attributed to its appropriate molecular weight, high arabinose content, and unique compact coil chain conformation. Overall, our results provide insight into the chemical structure of CGP80-1 and its mechanism of action, suggesting that CGP80-1 could be a candidate drug for myocardial protection.

Aqueous extractable nonfibrillar and sarkosyl extractable fibrillar Alzheimer’s disease tau seeds have distinct properties

Pathological tau fibrils in progressive supranuclear palsy, frontotemporal dementia, chronic traumatic encephalopathy, and Alzheimer’s disease each have unique conformations, and post-translational modifications that correlate with unique disease characteristics. However, within Alzheimer’s disease (AD), both fibrillar (sarkosyl insoluble (AD SARK tau)), and nonfibrillar (aqueous extractable high molecular weight (AD HMW tau)) preparations have been suggested to be seed-competent. We now explore if these preparations are similar or distinct in their in vivo seeding characteristics. Using an in vivo amplification and time-course paradigm we demonstrate that, for AD HMW and AD SARK tau species, the amplified material is biochemically similar to the original sample. The HMW and SARK materials also show different clearance, propagation kinetics, and propagation patterns. These data indicate the surprising co-occurrence of multiple distinct tau species within the same AD brain, supporting the idea that multiple tau conformers – both fibrillar and nonfibrillar- can impact phenotype in AD.

The assembly and comparative analysis of the first complete mitogenome of Lindera aggregata.

Lindera aggregata, a member belongs to the genus Lindera of Lauraceae family. Its roots and leaves have been used as traditional Chinese medicine or functional food for thousands of years. However, its mitochondrial genome has not been explored. Our aim is to sequence and assemble the mitogenome of L. aggregata to elucidate the genetic mechanism and evolutionary pathway. The results had shown that the mitogenome was extremely complex and had a unique multi-branched conformation with total size of 912,473 bp. Comprehensive analysis of protein coding genes of 7 related species showed that there were 40 common genes in their mitogenome. Interestingly, positive selection had become an important factor in the evolution of ccmB, ccmFC, rps10, rps11 and rps7 genes. Furthermore, our data highlighted the repeated trend of homologous fragment migrations between chloroplast and mitochondrial organelles, and 38 homologous fragments were identified. Phylogenetic analysis identified a tree that was basically consistent with the phylogeny of Laurales species described in the APG IV system. To sum up, this study will be helpful to the study of population genetics and evolution of Lindera species.

First-principles study of solvent polarity effects in the Menshutkin reaction

Quaternary ammonium salts (QASs) have been used as antimicrobial agents, surfactants, and ionic liquids in electrical double-layer capacitors, rechargeable lithium-ion batteries, and dye-sensitized solar cells. It is well known that solvents and reactants strongly affect the Menshutkin reaction. However, QASs are potentially harmful to humans and the environment. To address these issues, we report the effects of solvent polarity on the thermochemistry of two selected Menshutkin reactions, (1) trimethylamine and 1-iodopropane yielded propyltrimethylammonium, and (2) methylacetamide and 1-iodopropane yielded acetylpropylmethylammonium. We systematically constructed possible QAS unique conformers within the first-principles framework in solvents that have three various polarities: toluene, acetonitrile, and water. The polar solvent shifted both reactions toward exergonic and decreased the Gibbs free activation energy. In addition, the polar solvent changed the favorable reaction for the acetylpropylmethylammonium formation only due to an intramolecular hydrogen bond. Therefore, we suggest that selecting high solvent polarity should be considered to address the potential health and environmental effect.

Hypervalent Iodine Mediated Ring-Opening 1,3-Difluorination of Benzylidenecyclopropanes

Abstract1,3-Difluorinated compounds are characterized by their unique conformation, influenced by 1,3-dipolar minimization effects. However, their synthetic methods are relatively limited. Here, a ring-opening 1,3-difluorination of benzylidenecyclopropanes (BCPs) using HF·Py, mediated by an electron-poor hypervalent iodine reagent, which is generated in situ by the oxidation of o-nitroiodobenzene with mCPBA is described. The protocol features mild reaction conditions, good functional group tolerance, and moderate to good yields. Additionally, the synthetic utility of this method is showcased by further transformations of the olefin group and allylic fluoride motif.

Targeting Monkeypox Virus Methyltransferase: Virtual Screening of Natural Compounds from Middle-Eastern Medicinal Plants.

Monkeypox is an infectious disease resulting from the monkeypox virus, and its fatality rate varies depending on the virus clade and the location of the outbreak. In monkeypox virus, methyltransferase (MTase) plays a crucial role in modifying the cap structure of viral mRNA. This alteration assists the virus in evading the host's immune system, enhances viral protein synthesis, and ultimately enables successful infection and replication within host cells. Given the significance of MTase in viral infection and spread within the host, our study aimed to identify a natural inhibitor for this enzyme using docking and molecular dynamic (MD) simulations. We collected a total of 12,971 natural compounds from 200 medicinal plants in the Middle East. After eliminating duplicate compounds, we had 5,749 unique ligand conformers, which we then subjected to high-throughput virtual screening against MTase. The most promising hits were further evaluated using the extra-precision (XP) tool. The affinity of these hits was also assessed by Prime-Molecular Mechanics/Generalized Born Surface Area (MMGBSA) tool. The analysis revealed that two standard controls (sinefungin and TO1119) and two Middle-Eastern compounds (folic acid and 1,2,4,6-tetragalloylglucose) exhibited the best XP docking scores. According to Prime MMGBSA calculations, the Middle-Eastern compounds showed higher affinities, with values of -60.61 kcal/mol for 1,2,4,6-tetragalloylglucose and -51.87 kcal/mol for folic acid, surpassing the controls (TO1119 at -35.71 kcal/mol and sinefungin at -31.51 kcal/mol). In the majority of Molecular dynamic (MD) simulations, folic acid exhibited demonstrated greater stability than sinefungin. Further investigation revealed that folic acid occupied a critical position in the active site of MTase, which reduced its interaction with the mRNA substrate. Based on these findings, it can be concluded that folic acid is a highly promising natural compound for potential use in the cost-effective treatment of monkeypox virus. The identification of folic acid as a potential antiviral agent highlights the importance of nature in providing new therapeutic uses that have significant implications for global health, particularly in regions where monkeypox viral outbreaks are prevalent. However, it is essential to note that further wet-lab validations are necessary to confirm its efficacy for treatment in a medical context.

Multiple aspects of amyloid dynamics in vivo integrate to establish prion variant dominance in yeast.

Prion variants are self-perpetuating conformers of a single protein that assemble into amyloid fibers and confer unique phenotypic states. Multiple prion variants can arise, particularly in response to changing environments, and interact within an organism. These interactions are often competitive, with one variant establishing phenotypic dominance over the others. This dominance has been linked to the competition for non-prion state protein, which must be converted to the prion state via a nucleated polymerization mechanism. However, the intrinsic rates of conversion, determined by the conformation of the variant, cannot explain prion variant dominance, suggesting a more complex interaction. Using the yeast prion system [PSI+ ], we have determined the mechanism of dominance of the [PSI+ ]Strong variant over the [PSI+ ]Weak variant in vivo. When mixed by mating, phenotypic dominance is established in zygotes, but the two variants persist and co-exist in the lineage descended from this cell. [PSI+ ]Strong propagons, the heritable unit, are amplified at the expense of [PSI+ ]Weak propagons, through the efficient conversion of soluble Sup35 protein, as revealed by fluorescence photobleaching experiments employing variant-specific mutants of Sup35. This competition, however, is highly sensitive to the fragmentation of [PSI+ ]Strong amyloid fibers, with even transient inhibition of the fragmentation catalyst Hsp104 promoting amplification of [PSI+ ]Weak propagons. Reducing the number of [PSI+ ]Strong propagons prior to mating, similarly promotes [PSI+ ]Weak amplification and conversion of soluble Sup35, indicating that template number and conversion efficiency combine to determine dominance. Thus, prion variant dominance is not an absolute hierarchy but rather an outcome arising from the dynamic interplay between unique protein conformations and their interactions with distinct cellular proteostatic niches.