Substitution Pattern Research Articles

The Potential Role of Genic-SSRs in Driving Ecological Adaptation Diversity in Caragana Plants.

Caragana, a xerophytic shrub genus widely distributed in northern China, exhibits distinctive geographical substitution patterns and ecological adaptation diversity. This study employed transcriptome sequencing technology to investigate 12 Caragana species, aiming to explore genic-SSR variations in the Caragana transcriptome and identify their role as a driving force for environmental adaptation within the genus. A total of 3666 polymorphic genic-SSRs were identified across different species. The impact of these variations on the expression of related genes was analyzed, revealing a significant linear correlation (p < 0.05) between the length variation of 264 polymorphic genic-SSRs and the expression of associated genes. Additionally, 2424 polymorphic genic-SSRs were located in differentially expressed genes among Caragana species. Through weighted gene co-expression network analysis, the expressions of these genes were correlated with 19 climatic factors and 16 plant functional traits in various habitats. This approach facilitated the identification of biological processes associated with habitat adaptations in the studied Caragana species. Fifty-five core genes related to functional traits and climatic factors were identified, including various transcription factors such as MYB, TCP, ARF, and structural proteins like HSP90, elongation factor TS, and HECT. The roles of these genes in the ecological adaptation diversity of Caragana were discussed. Our study identified specific genomic components and genes in Caragana plants responsive to heterogeneous habitats. The results contribute to advancements in the molecular understanding of their ecological adaptation, lay a foundation for the conservation and development of Caragana germplasm resources, and provide a scientific basis for plant adaptation to global climate change.

A gem‐Dibromocyclopropane Ring‐Expansion/Mizoroki‐Heck Cyclisation Route to Tetrahydrodibenzofurans

AbstractReadily accessible, oxygenated 6,6‐dibromobicyclo[3.1.0]hexanes react with isovanillin in the presence of silver salts and an inorganic base to afford ring‐expanded/nucleophilic trapping products of various regio‐ and stereo‐chemical forms. Most such products undergo efficient, intramolecular Mizoroki‐Heck reactions to give the corresponding tetrahydrodibenzofurans. In certain cases, simple variations in the first step of such reaction sequences enables the preparation distinct ring‐expansion products that also cyclise to give tetrahydrodibenzofurans embodying alternative substitution patterns.

Oligo-Condensation Reactions of Silanediols with Conservation of Solid-State-Structural Features.

Oligo- and polysiloxanes are usually prepared by condensation reactions in solvents without control of stereochemistry. Here we present a solventless thermal condensation of stable organosilanols. We investigated the condensation reactions of organosilanediols with different organic substituents, having in common at least one aromatic group. The condensation kinetics of the precursors observed by NMR spectroscopy revealed a strong dependence on temperature, time, and substitution pattern at the silicon atom. SEC measurements showed that chain length increases with increasing condensation temperature and time and lower steric demand of the substituents, which also influences the glass transition temperatures (Tg) of the resulting oligo- or polymers. X-ray diffraction studies of the crystalline silanediols and their condensation products revealed a structural correlation between the substituent location in the crystalline precursors and the formed macromolecules induced by the hydrogen bonding pattern. In certain cases, it is possible to carry out topotactic polymerization in the solid-state, which has its origin in the crystal structure.

Design and Synthesis of Novel 3-Nitro-1H-1,2,4-triazole-1,2,3-triazole-1,4-disubstituted Analogs as Promising Antitrypanosomatid Agents: Evaluation of In Vitro Activity against Chagas Disease and Leishmaniasis.

A series of 28 compounds, 3-nitro-1H-1,2,4-triazole, were synthesized by click-chemistry with diverse substitution patterns using medicinal chemistry approaches, such as bioisosterism, Craig-plot, and the Topliss set with excellent yields. Overall, the analogs demonstrated relevant in vitro antitrypanosomatid activity. Analog 15g (R1 = 4-OCF3-Ph, IC50 = 0.09 μM, SI = >555.5) exhibited an outstanding antichagasic activity (Trypanosoma cruzi, Tulahuen LacZ strain) 68-fold more active than benznidazole (BZN, IC50 = 6.15 μM, SI = >8.13) with relevant selectivity index, and suitable LipE = 5.31. 15g was considered an appropriate substrate for the type I nitro reductases (TcNTR I), contributing to a likely potential mechanism of action for antichagasic activity. Finally, 15g showed nonmutagenic potential against Salmonella typhimurium strains (TA98, TA100, and TA102). Therefore, 3-nitro-1H-1,2,4-triazole 15g is a promising antitrypanosomatid candidate for in vivo studies.

B(OH)3‐Catalyzed Dual Friedel‐Crafts Type Reaction of Anilines and Aldehydes to Access Di‐ or Triarylmethanes (TRAMs)

AbstractThe catalytic influences of boric acid have been introduced on dual Friedel‐Crafts reaction between arylamines and aldehydes to install the Csp3‐center that leads to the formation of di‐ or tri‐substituted methanes. The described reaction conditions have directed the transformation to favor the para‐para substitution pattern to deliver the major products rather than the corresponding ortho‐para functionalization process. The devised transformation was examined by DFT calculation, which shows the favorable activation energy of transition states (TS) for the generation of highly substituted molecular scaffolds. The method was applicable over diversely substituted aldehydes and arylamines to afford the final products in excellent yields (60‐92 %) and selectivity. The proposed mechanism is supported by suitable control experiments, GC‐MS studies, and DFT calculations.

Polymerase gene mutation pattern in patients of chronic Hepatitis B treatment in Prof. Dr. W.Z. Johannes Hospital, Kupang, Indonesia

Abstract. Djuma AW, Dewu S, Kambuno NT, Banunu A, Silaen OSM. 2024. Polymerase gene mutation pattern in patients of chronic Hepatitis B treatment in Prof. Dr. W.Z. Johannes Hospital, Kupang, Indonesia. Biodiversitas 25: 150-155. Hepatitis B virus (HBV) infection is a significant global health concern, impacting over two billion people worldwide. Among them, more than 240 million individuals develop chronic HBV infection, placing them at a high risk of developing severe liver conditions such as cirrhosis, liver failure, and Hepatocellular Carcinoma (HCC). In 2013, Nusa Tenggara Timur (NTT) emerged as one of the Indonesian provinces with a high incidence of hepatitis cases. Long-term therapy has proven effective in halting disease progression but may also lead to the emergence of resistant mutations. This study aims to analyze mutation patterns in the Polymerase (P) gene as indicators of viral resistance to nucleotide analogs (NUCs) in HBV patients at RSUD Prof. Dr. W.Z. Johannes Kupang, a previously unreported case. The research was conducted at the Hematology-Oncology Medical Laboratory Division, Faculty of Medicine, Universitas Indonesia, RS. Dr. Cipto Mangunkusumo, Department of Internal Medicine, Jakarta. A total of 28 individual samples with positive Hepatitis B surface Antigen (HBsAg) were subjected to PCR sequencing, resulting in 23 positive samples. Mutation profiles were analyzed by comparing them with the reference sequence M54923. Sequencing of the Polymerase (P) gene region was successfully carried out for 14 samples. Among these, 12 (85.71%) exhibited nucleotide substitutions, while the remaining two (9.14%) did not show any mutations. The most prevalent substitution patterns in the P gene included rtQ228H, rtS127R, rtM135L, rtV243I, rtL257A, rtS127A, rtK323N, rtL326R, rtV214I, rtT312S, rtV281E, rtF290Y, rtM299I, rtQ306H, and rtK308N. No mutations associated with antiviral resistance were detected. The use of NUCs in chronic hepatitis B treatment is considered safe for patients at Prof. Dr. W.Z. Johannes Kupang Hospital.

Design of Imidazo[1,2-a]pyridine-Based Donor–Acceptor Chromophores through a Multicomponent Approach

AbstractA series of donor-acceptor chromophores was synthesized bearing a 3-aminoimidazo[1,2-a]pyridine donor motive. Through DFT calculations, different combinations of the ImPy donor motive and different electron acceptors were assessed. In combination with an anthraquinone acceptor, the calculated ΔE ST values were in range to suggest that these compounds would emit via thermally activated delayed fluorescence. Based on these findings, a series of ImPy-Aq emitters with different geometries and substitution patterns was synthesized through GBB-3CR and Suzuki coupling reactions. According to preliminary experimental data, the compounds were only slightly emissive at ambient temperatures due to a combination of low radiative rates and competing non-radiative deactivation pathways.

Abstract A035: Mutation of NOTCH1 is selected within normal esophageal tissues, yet leads to selective epistasis suppressive of further evolution into cancer

Abstract Sequencing of tissues from histologically normal esophagus, among other organs, has revealed that normal tissues acquire somatic variants that are also found in cancers arising from the same tissue types. Our understanding of how somatic mutations that are commonly found in normal tissue can contribute to tumorigenesis is limited: common somatic mutations may or may not confer phenotypes compatible with oncogenesis. However, the strength of selection for somatic variants that appear in both normal and cancer tissues can be quantified in each context using evolutionary modeling approaches. We studied the evolutionary trajectory from normal esophageal tissue to esophageal squamous-cell carcinoma (ESCC) by analysis of sequencing data from previous studies on normal esophageal epithelium and ESCC to reveal the stepwise contributions of somatic mutations to increased cellular division and survival. We also analyzed pairwise selective epistasis between somatically mutated genes that may lead to stepwise substitution patterns. We found that NOTCH1 substitutions are at high prevalence in normal tissue, and scaled selection coefficients indicate that NOTCH1 mutations are highly selected in normal esophageal tissue. In contrast, there is little to no positive selection for NOTCH1 mutations in ESCC, suggesting that NOTCH1 substitutions do not drive tumorigenesis. Indeed, NOTCH1 mutations have recently been shown to favor clonal expansion in normal esophageal tissue. Furthermore, we calculate that mutations in NOTCH1 exhibit antagonistic epistasis with well-known cancer drivers, including TP53, reducing selection for progressive mutations in tumorigenesis. This antagonistic epistasis likely underlies the low likelihood of tumor progression in the presence of NOTCH1 mutations in the esophagus. Citation Format: Kira A. Glasmacher, Vincent L. Cannataro, Jeffrey D. Mandell, Mia Jackson, J. Nic Fisk, Jeffrey P. Townsend. Mutation of NOTCH1 is selected within normal esophageal tissues, yet leads to selective epistasis suppressive of further evolution into cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Cancer Evolution and Data Science: The Next Frontier; 2023 Dec 3-6; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_2):Abstract nr A035.

Utilizing Allenic Acids and Heterocyclic Diazo Compounds in the Synthesis of Polysubstituted Spirocyclic Butenolides and β-Methylidene 2-Furanones.

Herein, we report a novel approach for the assembly of spirocyclic Δα,β-butenolides and β-methylidene 2-furanones via Rh(II)-catalyzed O-H insertion of heterocyclic diazo compounds into allenic acids followed by base-promoted cyclization. Utilizing various diazo heterocycles, including α-diazo homophthalimides, 3-diazo tetramic acids, and diazo oxindoles, diverse spirocyclic scaffolds were produced. The research revealed that the allenic acid substitution pattern is decisive for the product type, enabling extraordinary target compound switching between two types of spirocyclic 2-furanones with exo- and endocyclic C═C bonds.

Nitrogen-containing heterocyclic compounds: A ray of hope in depression?

Depression is not similar to daily mood fluctuations and temporary emotional responses to day-to-day activities. Depression is not a passing problem; it is an ongoing problem. It deals with different episodes consisting of several symptoms that last for at least 2 weeks. It can be seen for several weeks, months, or years. At its final stage, or can say, in its worst condition, it can lead to suicide. Antidepressants are used to inhibit the reuptake of the neurotransmitters by some selective receptors, which increase the concentration of specific neurotransmitters around the nerves in the brain. Drugs that are currently being used for the management of various types of depression include selective serotonin reuptake inhibitors, tricyclic antidepressants, atypical antidepressants, serotonin, noradrenaline reuptake inhibitors, etc. In this review, we have outlined different symptoms, causes, and recent advancements in nitrogen-containing heterocyclic drug candidates for the management of depression. This article highlights the various structural features along with the structure-activity relationship (SAR) of nitrogen-containing heterocyclics that play a key role in binding at target sites for potential antidepressant action. The in silico studies were carried out to determine the binding interactions of the target ligands with the receptor site to determine the potential role of substitution patterns at core pharmacophoric features. This article will help medicinal chemists, biochemists, and other interested researchers in identifying the potential pharmacophores as lead compounds for further development of new potent antidepressants.

Substitution Models of Protein Evolution with Selection on Enzymatic Activity.

Substitution models of evolution are necessary for diverse evolutionary analyses including phylogenetic tree and ancestral sequence reconstructions. At the protein level, empirical substitution models are traditionally used due to their simplicity, but they ignore the variability of substitution patterns among protein sites. Next, in order to improve the realism of the modeling of protein evolution, a series of structurally constrained substitution models were presented, but still they usually ignore constraints on the protein activity. Here, we present a substitution model of protein evolution with selection on both protein structure and enzymatic activity, and that can be applied to phylogenetics. In particular, the model considers the binding affinity of the enzyme-substrate complex as well as structural constraints that include the flexibility of structural flaps, hydrogen bonds, amino acids backbone radius of gyration, and solvent-accessible surface area that are quantified through molecular dynamics simulations. We applied the model to the HIV-1 protease and evaluated it by phylogenetic likelihood in comparison with the best-fitting empirical substitution model and a structurally constrained substitution model that ignores the enzymatic activity. We found that accounting for selection on the protein activity improves the fitting of the modeled functional regions with the real observations, especially in data with high molecular identity, which recommends considering constraints on the protein activity in the development of substitution models of evolution.

Mesomorphism Modulation of Perfluorinated Janus Triphenylenes by Inhomogeneous Chain Substitution Patterns.

Two isomeric series of compounds with "inverted" chains' substitution patterns, 7,10-dialkoxy-1,2,3,4-tetrafluoro-6,11-dimethoxytriphenylene and 6,11-dialkoxy-1,2,3,4-tetrafluoro-7,10-dimethoxytriphenylene, labelled respectively p-TPFn and m-TPFn, and two non-fluorinated homologous isomers, 3,6-dibutoxy-2,7-dimethoxytriphenylene and 2,7-dibutoxy-3,6-dimethoxytriphenylene, p-TP4 and m-TP4, respectively, were synthesized in three steps and obtained in good yields by the efficient transition-metal-free, fluoroarene nucleophilic substitution via the reaction of appropriate 2,2'-dilithium biphenylenes with either perfluorobenzene, C6 F6 , to yield p-TPFn and m-TPFn, or o-difluorobenzene, C6 H4 F2 , for p-TP4 and m-TP4, respectively. The single-crystal structures of p-TPF4, m-TPF4 and p-TP4, unequivocally confirmed that the cyclization reactions occurred at the expected positions, and that the fluorinated molecules stack up into columns with short separation, a propitious situation for the emergence of columnar mesophases. The mesomorphous properties were found to be greatly affected by both chains' length and positional isomerism: a Colhex phase is found for p-TPF4 and m-TPF4, but mesomorphism vanishes in p-TPF6, and changes for the isomeric homologs m-TPFn, with the induction for n≥6 of a lamello-columnar phase, LamColrec . As expected, both non-fluorinated compounds are deprived of mesomorphism. These compounds emit blue-violet colour in solution, independently of the chains' substitution pattern, and the absolute fluorescence quantum yields can reach up to 46 %. In thin films, fluorescence is slightly redshifted.

Synthesis and Photophysical Evaluation of 3,3’‐Nitrogen Bis‐Substituted fac‐[Re(CO)3(Diimine)Br] Complexes

AbstractThe preparations, photophysical and electrochemical properties of a series of fac‐[Re(CO)3(diimine)Br] complexes are presented. The bipyridine (bpy) based diimine ligands feature symmetrical and asymmetrical 3,3’‐diamino‐2,2’‐bipyridine substitution patterns. Photophysical and electrochemical properties of these complexes are tunable, depending on their organic diimine framework. Introduction of a distal urea bridge via the 3,3’‐substitution pattern led to prolonged phosphorescence lifetimes without a significant change in absorbance and phosphorescence emission wavelengths. Reversible electrochemical bipyridine reduction remained largely unchanged by this derivatization.

Deconstructive diversification of cyclic 1,3-diketones for accessing hydrazonylated 1,n-ketoesters

A mild base-promoted three-component deconstructive functionalization reaction of cyclic 1,3-diketones with aryl diazonium tetrafluoroborates in the presence of alcohols is reported, enabling direct ring-opening of unstrained cyclic ring systems to produce three types of skeletally diverse 1,n-ketoesters, namely, linear 1,5- and 1,4-ketoesters and ortho-ketobenzoates, with moderate to good yields. The methodology has the potential to be widely used throughout organic synthesis due to the use of easily accessible substrates, such as cyclic 1,3-diketones and aryl diazonium tetrafluoroborates, with different substitution patterns and mild reaction conditions.

Mutational signature dynamics indicate SARS-CoV-2's evolutionary capacity is driven by host antiviral molecules.

The COVID-19 pandemic has been characterised by sequential variant-specific waves shaped by viral, individual human and population factors. SARS-CoV-2 variants are defined by their unique combinations of mutations and there has been a clear adaptation to more efficient human infection since the emergence of this new human coronavirus in late 2019. Here, we use machine learning models to identify shared signatures, i.e., common underlying mutational processes and link these to the subset of mutations that define the variants of concern (VOCs). First, we examined the global SARS-CoV-2 genomes and associated metadata to determine how viral properties and public health measures have influenced the magnitude of waves, as measured by the number of infection cases, in different geographic locations using regression models. This analysis showed that, as expected, both public health measures and virus properties were associated with the waves of regional SARS-CoV-2 reported infection numbers and this impact varies geographically. We attribute this to intrinsic differences such as vaccine coverage, testing and sequencing capacity and the effectiveness of government stringency. To assess underlying evolutionary change, we used non-negative matrix factorisation and observed three distinct mutational signatures, unique in their substitution patterns and exposures from the SARS-CoV-2 genomes. Signatures 1, 2 and 3 were biased to C→T, T→C/A→G and G→T point mutations. We hypothesise assignments of these mutational signatures to the host antiviral molecules APOBEC, ADAR and ROS respectively. We observe a shift amidst the pandemic in relative mutational signature activity from predominantly Signature 1 changes to an increasingly high proportion of changes consistent with Signature 2. This could represent changes in how the virus and the host immune response interact and indicates how SARS-CoV-2 may continue to generate variation in the future. Linkage of the detected mutational signatures to the VOC-defining amino acids substitutions indicates the majority of SARS-CoV-2's evolutionary capacity is likely to be associated with the action of host antiviral molecules rather than virus replication errors.

Synthesis of 2,6-Diaminotriptycene Conjugates with Chiral Auxiliaries: Towards the Scalable Resolution of Crucial Triptycene Intermediates

Triptycenes are tridimensional molecular scaffolds with interesting properties for applications in materials science: molecular rigidity and preorganization, tailorable chromophores, and, with an appropriate substitution pattern, chirality. The separation of the two enantiomers of chiral triptycenes has been the subject of increasing interest in recent years, with limited success. Here, we report the synthesis and characterization of a series of new organic compounds, in which a chiral triptycene scaffold, derivatized in the 2 and 6 positions with amino groups, has been functionalized with different enantiopure chiral auxiliaries, forming diastereoisomeric couples. The properties of such compounds, in terms of the optimization of their chromatographic separation, are elucidated with the aid of computational calculations of preferred conformations and molecular polarities.

Amino‐Acid Side‐Chain Nanoarchitectonics for Tuning the Chiroptical Properties and Supramolecular Structure of Pentameric Oligothiophenes

AbstractOligothiophenes with specific photophysical properties and molecular organization are of great interest, since this class of materials are used in organic electronics and bioelectronics, as well as biosensing. Herein, 8 different pentameric oligothiophenes, denoted proteophenes, with different amino acid substitution patterns at distinct positions along the thiophene backbone were investigated. Spectroscopic and microscopic studies of the ligands revealed the formation of optically active self‐assembled materials under acidic or basic conditions. The distinct photophysical characteristics, including induced circular dichroism, as well as the supramolecular structures of the assemblies deduced from light scattering and transmission electron microscopy, were highly influenced by the positioning of distinct amino acid moieties along the thiophene backbone. Proteophenes functionalized with only glutamate residues or these functionalities in combination with hydrophobic valine moieties formed fibrillar structures with excellent chiroptical properties under acidic conditions. In addition, the amino acid functionality at the β‐position of distinct thiophene moieties influenced the induced circular dichroism pattern observed from the proteophenes. Overall, the obtained results demonstrate how changes in the position of various amino acid functionalities, as well as the chemical nature of the amino acid side chain functionality greatly affect the optical properties as well as the architecture of the self‐assembled materials.

Multimodal Carbon Monoxide Photorelease from Flavonoids.

Photooxygenation of flavonoids leads to the release of carbon monoxide (CO). Our structure-photoreactivity study, employing several structurally different flavonoids, including their 13C-labeled analogs, revealed that CO can be produced via two completely orthogonal pathways, depending on their hydroxy group substitution pattern and the reaction conditions. While photooxygenation of the enol 3-OH group has previously been established as the CO liberation channel, we show that the catechol-type hydroxy groups of ring B can predominantly participate in photodecarbonylation.

Pyrroloindoles as Therapeutically Invaluable Agents: A Review on their Diverse Synthetic Methodologies

AbstractIn the realm of medicinal chemistry, heterocyclic compounds play a vital role due to their diverse pharmacological properties, especially, pyrroloindoles standing out as crucial motifs in drug development. Pyrroloindoles, which are formed by combining indole and pyrrole rings, exhibit unique characteristics and serve as integral components in numerous drugs and natural compounds. The synthesis of pyrroloindoles is challenging due to their complex ring structures and diverse substitution patterns. This comprehensive review compiles various synthetic strategies for obtaining pyrroloindole derivatives via metal‐catalyzed reactions; cyclopropanation/ ring opening/ iminium cyclization (CRI reaction); organocatalytic cascade addition‐cyclization; 1,3‐dipolar cycloaddition; Brønsted acid‐catalyzed [3+2] cyclodimerization; ring closure mechanisms; thermally‐induced ring‐opening and cyclization reactions; condensation reactions; and visible‐light photocatalytic asymmetric reactions providing a valuable resource for synthetic organic chemists and researchers interested in the synthesis of pyrroloindoles and their derivatives. These compounds play a pivotal role in drug discovery thus, making this review an indispensable reference.

Eleven highly oxygenated and anti-inflammatory guaian-8,12-olides from Hedyosmum orientale

Eleven previously undescribed guaian-8,12-olides, hedyolides A‒K (1−11) featuring a characteristic 5,7,5-fused tricyclic and possessing different degrees of unsaturation and oxygen substitution patterns, were isolated from the leaves and twigs of Hedyosmum orientale. In particular, compounds 6 and 10 are rare chlorinated guaianolides of plant origin. Their structures and absolute configurations were elucidated by a combination of spectroscopic analysis, quantum chemical calculations, DP4+ probability, and single-crystal X-ray diffraction. All compounds exhibited inhibitory effects on nitric oxide production in lipopolysaccharide-induced RAW 264.7 macrophages with IC50 values ranging from 1.22 to 6.51 μM.