Right-handed Conformation Research Articles

Cytotoxic Peptaibols from Trichoderma strigosum.

Five new lipopeptaibols (1-5) and eight new 19-residue peptaibols (8-15) along with two known lipopeptaibols, lipovelutibols C (6) and D (7) were isolated from Trichoderma strigosum. The planar structures of the newly discovered peptaibols (1-5, 8-15) were elucidated using 1D and 2D NMR, and UPLC-MS/MS data. The absolute configurations for new peptaibols (1-5, 8-15) were elucidated using the advanced Marfey's method and GITC (2,3,4,6-tetra-O-acetyl-β-d-glucopyranosyl isothiocyanate) derivatization. Through analysis of CD spectra, these peptabols were found to have right-handed helical conformations. While most of the new compounds were significantly more active than the positive control, 9, 10, 12, and 15 containing Ser and Leu at positions 10 and 11, respectively, were the most cytotoxic against MDA-MB-231, SNU449, SKOV3, DU145, and HCT116 cancer cell lines, and the 19-residue peptaibols were generally more potent than lipopeptaibols.

Characterization of a novel gammapartitivirus infecting the phytopathogenic fungus Pyricularia oryzae.

In this study, we identified a novel double-strand RNA (dsRNA) mycovirus in Pyricularia oryzae, designated "Magnaporthe oryzae partitivirus 4" (MoPV4). The genome of MoPV4 consists of a dsRNA-1 segment encoding an RNA-dependent RNA polymerase (RdRP) and a dsRNA-2 segment encoding a capsid protein (CP). Phylogenetic analysis indicated that MoPV4 belongs to the genus Gammapartitivirus within family Partitiviridae. The particles of MoPV4 are isometric with a diameter of about 32.4 nm. Three-dimensional structure predictions indicated that the RdRP of MoPV4 forms a classical right-handed conformation, while the CP has a reclining-V shape.

Abstract 3731: Spliceosome: A gatekeeper for necroptosis

Abstract Small cell lung cancer (SCLC) is the most aggressive type of lung cancer with a 5-year overall survival of approximately 5%. SCLC has high prevalence of somatic mutations, yet express low to zero neoantigen. Despite promising advances in immunotherapy, highly metastatic SCLC remains a devastating disease and only a small fraction of SCLC patients respond to immunotherapy. These poor survival and lack of therapy options stresses the unmet need to identify novel and effective targeted therapies for metastatic SCLC. Here, we demonstrate that targeting the splicing core component, SF3B1, in SCLC, is a molecular trigger for tumor killing and viral mimicry.SF3B1 inhibition through the small molecule Pladienolide B (PlaB) induces the accumulation of immunogenic double-stranded RNAs (dsRNAs), including right-handed dsRNA conformation (A-RNA), provoking a tumor-intrinsic innate immune response and tumor cell death in SCLC preclinical models. Strikingly, we discovered that PlaB treatment also induces the formation of Z-form nucleic acids (Z-NAs), which are unique, left-handed nucleic acids and necroptosis-activating ligands for the host sensor ZBP1.These endogenous A-RNAs and Z-NAs initiate tumor-intrinsic antiviral interferon (IFN) signaling in SCLC cells leading to tumor-intrinsic immunogenicity and apoptosis. Notably, we also found that Z-NAs derived from spliceosome inhibition trigger the activation of ZBP1, inducing RIPK3-mediated MLKL activation and eventual necroptosis, a highly immunogenic cell-death pathway, in ‘necroptosis competent’ cells, including mouse embryonic fibroblasts (MEFs). This opens unexplored strategies for spliceosome inhibitors to activate anti-tumor immune pathways not only in tumor cells themselves, but also in cells of the Tumor Microenvironment (TME), which too can break tolerance and enhance anti-tumor T cell responses which is crucial to enhance cancer immunotherapy responses. These findings demonstrate a unique and novel spliceosome-targeted mechanism to remodel the immunosuppressive TME of SCLCs. Also, our study suggests that SF3B1 inhibitors and potentially other spliceosome inhibitors might be used not only to selectively kill tumor cells, but also as compounds to generate Z-NAs in tumor cells and cells of the TME and trigger on-demand necroptosis without need for an active virus infection. Citation Format: Xinpei Jiang, Xueying Ma, Siddharth Balachandran, Israel Cañadas. Spliceosome: A gatekeeper for necroptosis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3731.

Pseudodiproline (Pro-Cyp) Oligomers Fold into Helical Polyproline Type secondary structures.

The synthesis and conformational properties of oligo-proline mimetics composed of dimeric and tetrameric Pro-Cyp constructs linked by a hydroxymethylene unit are reported. Oligomers were studied both in the solid state and in solution, unveiling right-handed helical conformation depending on the configuration of the vicinally substituted trans-cyclopentane carboxylic acid unit (Cyp). Unlike polyproline oligomers, the alternating synthetic Pro-Cyp counterparts are not stabilized by n-π* interactions but rely instead on the steric demands of the extended backbone conformation within the hydroxymethylene-linked Pro-Cyp repeating units.

"Gear-driven"-type chirality transfer of tetraphenylethene-based supramolecular organic frameworks for peptides in water.

Chirality transfer for natural chiral biomolecules can reveal the indispensable role of chiral structures in life and can be used to develop the chirality-sensing biomolecular recognition. Here, we report the synthesis and characterization of a series of achiral supramolecular organic frameworks (SOF-1, SOF-2, and SOF-3), constructed from cucurbit[8]uril (CB[8]) and tetraphenylethene (TPE) derivatives (1, 2, and 3), respectively, as chirality-sensing platforms to explore their chirality transfer mechanism for peptides in water. Given the right-handed (P) and left-handed (M) rotational conformation of TPE units and the selective binding of CB[8] to aromatic amino acids, these achiral SOFs can be selectively triggered in water by peptides containing N-terminal tryptophan (W) and phenylalanine (F) residues into their P- or M-rotational conformation, exhibiting significantly different circular dichroism (CD) spectra. Although various peptides have the same l-type chiral configuration, they can induce positive CD signals of SOF-1 and negative CD signals of SOF-2 and SOF-3, respectively. Based on the structural analysis of the linkage units between CB[8] and TPE units in these SOFs, a "gear-driven"-type chirality transfer mechanism has been proposed to visually illustrate the multiple-step chirality transfer process from the recognition site in the CB[8]'s cavity to TPE units. Furthermore, by utilizing the characteristic CD signals generated through the "gear-driven"-type chirality transfer, these SOFs can serve as chiroptical sensor arrays to effectively recognize and distinguish various peptides based on their distinctive CD spectra.

Chelerythrine, a new benzo[c]phenanthridine based converter of alternate DNA structure into conventional one: A spectroscopic exploration

Association of different polymprphic forms of DNA having alternating G-C sequences with the alkaloid Chelerythrine Chloride (CHL) was probed by using UV absorption and circular dichroism (CD) spectrometry. Spectrophotometric titration revealed that the association of CHL with right handed B-form was non-cooperative in nature with higher binding affinity (∼106 M−1) in contrast to the cooperative binding with left handed Z-form and HL-form where the intrinsic binding constants were of the order of ∼104 M−1. Further, conversion of the left-handed Z-form and the HL-form of the polymer back to the bound right-handed form by CHL has been evidenced from CD spectroscopy and under our experimental condition, the number of base pairs of Z-form and HL-form that switched to right-handed conformation by each bound CHL molecule was found to be 2–3. Moreover, kinetic measurements showed that in presence of increasing concentration of CHL, both the rate and the extent of B-form to Z-form transition were reduced.

Stapling strategy for slowing helicity interconversion of α-helical peptides and isolating chiral auxiliary-free one-handed forms

In nature, α-helical peptides adopt right-handed conformations that are dictated by L-amino acids. Isolating one-handed α-helical peptides composed of only achiral components remains a significant challenge. Here, this goal is achieved by optical resolution of the corresponding racemic (quasi-)static α-helical peptide with double stapling, which effectively freezes the interconversion between the right-handed (P)- and left-handed (M)-α-helices. An as-obtained doubly stapled analogue having an unprotected L-valine residue at the C-terminus transforms from a kinetically trapped (M)-α-helix to a thermodynamically stable (P)-α-helix upon heating. In contrast, the corresponding singly stapled α-helical peptide undergoes an acid/base-triggered and solvent-induced reversible inversion of its preferred helicity within minutes. The interconversion rates of the singly and doubly stapled α-helical peptide foldamers are approximately 106 and 1012 times slower, respectively, than that of a non-stapled dynamic helical peptide. Therefore, the enantiopure doubly-stapled (quasi-)static α-helical peptide would retain its optical activity for several years at 25 °C.

Ambidexterity and Left-Handedness Induced by Geminally Disubstituted γ Amino Acid Residues in Chiral 310 Helices.

Chirality is an omnipresent feature in nature's architecture starting from simple molecules like amino acids to complex higher-order structures viz. proteins, DNA, and RNA. The L configuration of proteinogenic amino acids gives rise to right-handed helices. Ambidexterity is as rare in organisms as in molecules. There are only a few reports of ambidexterity in single-peptide molecules composed of either mixed L and D or achiral residues. Here, we report, for the first time, the ambidextrous and left-handed helical conformations in the chiral nonapeptides P1-P3 (Boc-LUVUγx,xULUV-OMe where U = Aib, x,x = 2,2/3,3/4,4), containing chiral L α amino acid residues, in addition to the usually observed right-handed helical conformation. The centrally located achiral γ residue, capable of adopting both left and right-handed helical conformations, induces its handedness on the neighboring chiral and achiral residues, leading to the observation of both left and right-handed helices in P2 and P3. The presence of a single water molecule proximal to the γ residue induces the reversal of helix handedness by forming distinct and stable water-mediated hydrogen bonds. This gives rise to ambidextrous helices as major conformers in P1 and P2. The absence of the observation of ambidexterity in P3 might be due to the inability of γ4,4 in the recruitment of a water molecule. Experiments (NMR, X-ray, and CD) and density functional theory (DFT) calculations suggest that the position of geminal disubstitution is crucial for determining the population of the amenable helical conformations (ambidextrous, left and right-handed) in these chiral peptides.

Supramolecular Helical Polymer Formed Via Complementary Dimerization of Bisporphyrin Cleft

We have been developing supramolecular polymers directed by unique host-guest motifs.1,2 During study, a tetrakisporphyrin monomer was discovered to form the supramolecular helical polymers.3,4 A lack of chirality resulted in the racemic mixture of the supramolecular helical polymers. In this presentation, we report that the chirally-twisted pseudo macrocyclic tetrakisporphyrin monomer is self-assembled to form the one-handed helical supramolecular structures. Two amino acid side chains were installed at the termini of a tetrakisporphyrin monomer. The intramolecular antiparallel hydrogen bonding between the amino acid side chains resulted in the pseudo macrocyclic conformation, which was chirally-twisted. The right-handed and left-handed conformations of the pseudo macrocyclic monomer are determined by the absolute configuration of the stereogenic centers. The chirally-twisted pseudo macrocyclic monomer was self-assembled to result in the one-handed helical structures with very high association constants. The well-developed supramolecular chains generated entangled polymer solution, which suggests the formation of the well-developed long supramolecular polymer chains. Atomic force microscopy visualized the long supramolecular polymer chains with the length more than 100 nm. The right-handed helical morphology was formed from the D-amino acid side chains.

Modulating Lipid Membrane Morphology by Dynamic DNA Origami Networks.

Membrane morphology and its dynamic adaptation regulate many cellular functions, which are often mediated by membrane proteins. Advances in DNA nanotechnology have enabled the realization of various protein-inspired structures and functions with precise control at the nanometer level, suggesting a viable tool to artificially engineer membrane morphology. In this work, we demonstrate a DNA origami cross (DOC) structure that can be anchored onto giant unilamellar vesicles (GUVs) and subsequently polymerized into micrometer-scale reconfigurable one-dimensional (1D) chains or two-dimensional (2D) lattices. Such DNA origami-based networks can be switched between left-handed (LH) and right-handed (RH) conformations by DNA fuels and exhibit potent efficacy in remodeling the membrane curvatures of GUVs. This work sheds light on designing hierarchically assembled dynamic DNA systems for the programmable modulation of synthetic cells for useful applications.

Enantiomer detection via quantum Otto cycle.

Enantiomers are chiral molecules that exist in right-handed and left-handed conformations. Optical techniques of enantiomers' detection are widely employed to discriminate between left- and right-handed molecules. However, identical spectra of enantiomers make enantiomer detection a very challenging task. Here, we investigate the possibility of exploiting thermodynamic processes for enantiomer detection. In particular, we employ a quantum Otto cycle in which a chiral molecule described by a three-level system with cyclic optical transitions is considered a working medium. Each energy transition of the three-level system is coupled with an external laser drive. We find that the left- and right-handed enantiomers operate as a quantum heat engine and a thermal accelerator, respectively, when the overall phase is the control parameter. In addition, both enantiomers act as heat engines by keeping the overall phase constant and using the laser drives' detuning as the control parameter during the cycle. However, the molecules can still be distinguished because both cases' extracted work and efficiency are quantitatively very different. Accordingly, the left- and right-handed molecules can be distinguished by evaluating the work distribution in the Otto cycle.

Structure and Formation of Z-DNA and Z-RNA.

Despite structural differences between the right-handed conformations of A-RNA and B-DNA, both nucleic acids adopt very similar, left-handed Z-conformations. In contrast to their structural similarities and sequence preferences, RNA and DNA exhibit differences in their ability to adopt the Z-conformation regarding their hydration shells, the chemical modifications that promote the Z-conformation, and the structure of junctions connecting them to right-handed segments. In this review, we highlight the structural and chemical properties of both Z-DNA and Z-RNA and delve into the potential factors that contribute to both their similarities and differences. While Z-DNA has been extensively studied, there is a gap of knowledge when it comes to Z-RNA. Where such information is lacking, we try and extend the principles of Z-DNA stability and formation to Z-RNA, considering the inherent differences of the nucleic acids.

Thermogenomic Analysis of Left-Handed Z-DNA Propensities in Genomes.

The initial discovery of left-handed Z-DNA was met with great excitement as a dramatic alternative to the right-handed double-helical conformation of canonical B-DNA. In this chapter, we describe the workings of the program ZHUNT as a computational approach to mapping Z-DNA in genomic sequences using a rigorous thermodynamic model for the transition between the two conformations (the B-Z transition). The discussion starts with a brief summary of the structural properties that differentiate Z- from B-DNA, focusing on those properties that are particularly relevant to the B-Z transition and the junction that splices a left- to right-handed DNA duplex. We then derive the statistical mechanics (SM) analysis of the zipper model that describes the cooperative B-Z transition and show that this analysis very accurately simulates this behavior of naturally occurring sequences that are induced to undergo the B-Z transition through negative supercoiling. A description of the ZHUNT algorithm and its validation are presented, followed by how the program had been applied for genomic and phylogenomic analyses in the past and how a user can access the online version of the program. Finally, we present a new version of ZHUNT (called mZHUNT) that has been parameterized to analyze sequences that contain 5-methylcytosine bases and compare the results of the ZHUNT and mZHUNT analyses on native and methylated yeast chromosome 1.

Structure and Conformation Study of the O-Antigen from the Lipopolysaccharide of Cupriavidus Metallidurans CH34

Cupriavidus metallidurans is a Gram-negative bacterium that has attracted the attention of the scientific community since its discovery back in 1976. It was initially studied as a model organism for bioremediation processes due to its ability to survive in heavy metal-rich environments. However, in recent years, there is evidence that this bacterium can be a potential pathogen for humans. How C. metallidurans can survive in such different environments is unknown and prompted the following work. Its great adaptability could be explained by the structural and conformational studies of the O-antigen portion of the lipopolysaccharide, the main constituent of the outer membrane of Gram-negative bacteria, which is the one in direct contact with the external environment. Therefore, a combination of chemical and spectroscopic analyses was used to define the O-antigen structure, disclosing that it is a polysaccharide constituted of a linear tetrasaccharide repeating unit that does not resemble other structures already reported for bacteria: [4)-α-d-GalNAc-(1→3)-α-d-Qui2NAc4NHBA-(1→3)-α-l-Rha-(1→3)-α-l-Rha-(1→]. Interestingly, the molecular dynamics studies revealed that the three-dimensional structure of the O-antigen is highly flexible: it might adopt three different right-handed helix conformations described by a two, three, or four-fold symmetry. This conformational behavior could represent the reason behind the survival of C. metallidurans in different environments.

Introducing the Chiral Constrained α-Trifluoromethylalanine in Aib Foldamers to Control, Quantify and Assign the Helical Screw-Sense.

Oligomers of α-aminoisobutyric acid (Aib) are achiral peptides that adopt 310 helical structures with equal population of left- and right-handed conformers. The screw-sense preference of the helical chain may be controlled by a single chiral residue located at one terminus. 1 H and 19 F NMR, X-ray crystallography and circular dichroism studies on new Aib oligomers show that the incorporation of a chiral quaternary α-trifluoromethylalanine at their N-terminus induces a reversal of the screw-sense preference of the 310 -helix compared to that of a non-fluorinated analogue having an l-α-methyl valine residue. This work demonstrates that, among the many particular properties of introducing a trifluoromethyl group into foldamers, its stereo-electronic properties are of major interest to control the helical screw sense. Its use as an easy-to-handle 19 F NMR probe to reliably determine both the magnitude of the screw-sense preference and its sign assignment is also of remarkable interest.

Peptoids as a Chiral Stationary Phase for Liquid Chromatography: Insights from Molecular Dynamics Simulations.

Peptoids are peptide regioisomers with attractive structural tunability in terms of sequence and three-dimensional arrangement. Peptoids are foreseen to have a great potential for many diverse applications, including their utilization as a chiral stationary phase in chromatography. To achieve chiral recognition, a chiral side chain is required to allow specific interactions with a given enantiomer from a racemic mixture. One of the most studied chiral stationary phases, built with (S)-N-1-phenylethyl (Nspe) units, was shown to be successful in resolving racemic mixtures of binaphthyl derivatives. However, there is currently no description at the atomic scale of the factors favoring its enantioselectivity. Here, we take advantage of steered molecular dynamics simulations to mimic the elution process at the atomic scale and present evidence that the predominantly right-handed helical conformation of Nspe peptoids and their ability to form stronger hydrogen bonds with the (S) enantiomer are responsible for the chiral recognition of the popular chiral probe 2,2'-bihydroxy-1,1'-binaphthyl.

Thermoswitching of Helical Inversion of Dynamic Polyphenylacetylenes through cis-trans Isomerization of Amide Pendants

The cis-trans isomerization of amides plays a vital role in all kinds of structural changes and biological activities, involving protein folding, protein misfolding, and even protein molecular recognition. However, the helical inversion of synthetic macromolecules arising from the cis-trans isomerization of tertiary amides, as a good mimic of natural protein, has been rarely researched. Herein, we synthesized meta-disubstituted polyphenylacetylenes (PPAs) with different N-substituted tertiary amides as one of the pendants, poly{(−)-3-methoxycarbonyl-5-[N-methyl-N-(S)-(1-phenylethyl)carbamoyl]phenylacetylene}(sP-NMe) and poly{(−)-3-methoxycarbonyl-5-[N-propyl -N-(S)-(1-phenylethyl)carbamoyl]phenylacetylene} (sP-NPr). The cis-trans isomerization of amides was investigated by a combinational analysis of 1H/13C nuclear magnetic resonance (NMR), heteronuclear multiple quantum coherence (HMQC), variable-temperature NMR, Raman spectroscopy, ultraviolet–visible (UV–vis) spectroscopy, electronic circular dichroism (ECD), vibrational circular dichroism (VCD), and computer calculations. The substituted amide of sP-NMe favors the trans isomer at low temperatures, and the polyene main chain takes the right-handed helical conformation. When increasing the temperature, the ratio of the cis isomer in sP-NMe increases, which causes helical inversion. The screw sense of the polymer backbone of sP-NMe can be thermoreversibly switched upon tuning the cis-trans isomerization equilibrium of the tertiary amide pendant. In comparison, sP-NPr has the left-handed conformation with the majority of the cis isomer owing to the bulky propyl group, and cis-trans isomerization cannot induce helical inversion upon thermal treatment. The results reveal that helical inversion caused by the cis-trans isomerization of amide groups is highly dependent on the size of N-alkyl substituents.

Mechanical and structural properties of archaeal hypernucleosomes.

Many archaea express histones, which organize the genome and play a key role in gene regulation. The structure and function of archaeal histone–DNA complexes remain however largely unclear. Recent studies show formation of hypernucleosomes consisting of DNA wrapped around an ‘endless’ histone-protein core. However, if and how such a hypernucleosome structure assembles on a long DNA substrate and which interactions provide for its stability, remains unclear. Here, we describe micromanipulation studies of complexes of the histones HMfA and HMfB with DNA. Our experiments show hypernucleosome assembly which results from cooperative binding of histones to DNA, facilitated by weak stacking interactions between neighboring histone dimers. Furthermore, rotational force spectroscopy demonstrates that the HMfB–DNA complex has a left-handed chirality, but that torque can drive it in a right-handed conformation. The structure of the hypernucleosome thus depends on stacking interactions, torque, and force. In vivo, such modulation of the archaeal hypernucleosome structure may play an important role in transcription regulation in response to environmental changes.

Optimization of lipid materials in the formulation of S-carvedilol self-microemulsifying drug-delivery systems

Objectives The blocking effect of S-carvedilol (S-CAR) on the beta-adrenoceptor is about 100 times stronger than that of the right-handed conformation. However, further development is restricted because of its poor bioavailability caused by its low solubility and high first-pass effect. In the study, S-CAR self-microemulsifying drug-delivery systems (SMEDDSs) were established, and the effects of different lipid materials on the absorption and metabolism of S-CAR were investigated. Methods Six kinds of lipid materials with different chemical structures including oleic acid, glycerol monooleate, glycerol trioleate, oleoyl macrogol-6 glycerides, soybean lecithin, and α-tocopherol were selected to be the oil phase. The S-CAR SMEDDSs were prepared by the same ratio. In vitro characteristics, in vitro release, in situ intestine absorption, and bile excretion, as well as the in vivo characteristic of relative bioavailability, were determined. Key findings The lipid structure significantly affected physical characteristics, the absorption and excretion rates of S-CAR SMEDDSs. The findings of rat-intestine perfusion experiments showed that the S-CAR SMEDDSs decreased the bile-excretion rate of S-CAR. Compared with the S-CAR group, the oleic acid and soybean lecithin groups decreased the bile excretion to 32% and 45%, respectively. Pharmacokinetic studies showed that the AUCs of these two groups were about 1.9 and 1.7 times more than that of the S-CAR group, and the mean retention time was extended. Conclusion The SMEDDS using ionic lipids (oleic acid or soybean lecithin) as oil phase can increase the oral bioavailability of S-CAR by increasing the solubility and reducing the first-pass effect.

New facets of larger Nest motifs in proteins.

The Nest is a concave-shaped structural motif in proteins formed by consecutive enantiomeric left-handed (L) and right-handed (R) helical conformation of the backbone. This important motif subsumes many turn and helix capping structures and binds electron-rich ligands. Simple Nests are either RL or LR. Larger Nests (>2 residues long) may be RLR, LRL, RLRL, and so forth, being considered as composed of overlapping simple Nests. The larger Nests remain under-explored despite their widely known contributions to protein function. In our study, we address whether the recurrence of enantiomeric geometry in the larger Nests constrains the peptide backbone such that distinct compositional and conformational preferences are seen compared to simple Nests. Our analysis reveals the critical role of the L helical torsion angle in the formation of larger Nests. This can be observed through the higher propensity of residue or secondary structure combinations in LR and LRL backbone conformation in comparison to RL or RLR, although LR/LRL is considerably lower by occurrence. We also find that the most abundant doublets and triplets in Nests have a propensity for particular secondary structures, suggesting a strong sequence-structure relationship in the larger Nest. Overall, our analysis corroborates distinct features of simple and the larger Nests. Such insights would be helpful towards in-vitro design of peptides and peptidomimetic studies.