Constituent Fragments Research Articles

Towards antimicrobial agents: Design and antibacterial activity of a hybrid fluorophore where porphyrin and Rose Bengal moieties are linked through the hydroxyl group of a xanthene dye

The axial complex of Sn(IV)-tetra(4-sulfophenyl)porphyrin (SnP) with Rose Bengal (RB) was obtained where RB axial binding is realized through the hydroxyl groups of the xanthene dye [SnP(RB)2]. The luminescent properties of the SnP(RB)2 (fluorescence and ability to generate singlet oxygen at room temperature) in aqueous media with additives of surfactant cetylpyridinium chloride (CPC) and ε-poly-l-lysine (EPL) were studied. It was found that nature of the medium (surfactant additives of different concentrations) determines the effectiveness of the photoinduced energy transfer from the RB fragment to the SnP fragment of the hybrid fluorophore (HF). It has been established that the ability of the HF to generate singlet oxygen in D2O and D2O-micellar media is higher than that of its constituent fragments. The dark and photodynamic antibacterial activity of the HF against two microorganisms [Pseudomonas aeruginosa (P. aeruginosa) and Staphylococcus aureus (S. aureus)] was determined and analyzed. It was shown how the antibacterial activity of the HF depends on the nature of the bacteria, the micellar environment and radiation dose.

Варианты генов Mycobacterium tuberculosis, ассоциированные с лекарственной устойчивостью к фторхинолонам (обзор литературы)

Background: The spread of M. tuberculosis drug resistance to fluoroquinolones poses a threat to their long-term clinical efficacy. Understanding the mechanisms of formation of drug resistance to fluoroquinolones, based on information on genes associated with drug resistance of M. tuberculosis, is important for optimizing TB chemotherapy regimens. The aim of the study: To study the available literature data on the most significant variants of M. tuberculosis genes associated with drug resistance to fluoroquinolones. Materials and methods: To achieve this goal, the task was to analyze the sources of domestic and foreign literature on this priority issue over the past 5 years. The databases of scientific electronic libraries PubMed, Elibriary were used. Results: Mycobacterial resistance to fluoroquinolones is associated with mutations in the gyrA and gyrB genes, encoding the GyrA and GyrB subunits of DNA gyrase, the main target of fluoroquinolones. In the fluoroquinolone-binding pocket of the “DNA-gyrase + DNA” catalytic center, the fluoroquinolone molecule is supported by the gyrA and gyrB regions, which determine resistance to fluoroquinolones (QRDR-A and QRDR-B). Modification of any of the constituent fragments of these regions affects the level of resistance to fluoroquinolones. Small quinolone molecules (nalidixic acid) have a high MIC against Mtb and other bacteria, while larger PC molecules (sparfloxacin, sitafloxacin, gatifloxacin, levofloxacin and moxifloxacin) are tightly adjacent to the fluoroquinolone-binding pocket and have a lower MIC. Modification of the DNA structure can change the spatial structure of the pocket itself, which leads to destabilization of the fluoroquinolone inside it. Thus, the presence of heteroresistance of the tuberculosis pathogen to fluoroquinolones indicates the active development of its resistance to this group of drugs in modern conditions. Conclusion: Analysis of modern studies shows the dependence of drug resistance of mycobacteria on fluoroquinolone compounds, while most often resistance to a decrease in the concentration of fluoroquinolones is associated with substitutions in the gyrB gene, as well as mutations in the gyrA gene. It has also been established that in addition to the main studied regions of the gyrA and gyrB genes associated with phenotypic drug resistance to fluoroquinols, there are regions that have not been sufficiently studied so far. These areas cannot be diagnosed in the clinical work of bacteriological laboratories of anti-tuberculosis institutions.

Predicting Emission Wavelengths in Benzobisoxazole-Based OLEDs with Gradient Boosted Ensemble Models.

We demonstrate the use of gradient-boosted ensemble models that accurately predict emission wavelengths in benzobis[1,2-d:4,5-d']oxazole (BBO) based fluorescent emitters. We have curated a database of 50 molecules from previously published data by the Jeffries-EL group using density functional theory (DFT) computed ground and excited state features. We consider two machine learning (ML) models based on (i) whole cruciform molecules and (ii) their constituent fragment molecules. Both ML models provide accurate predictions with root-mean-square errors between 30 and 36 nm, competitive with state-of-the-art deep learning models trained on orders of magnitude more molecules, and this accuracy holds even when tested on four new BBO emitters unseen by the models. We also provide an interpretable feature importance analysis and discuss the relevant relationships between DFT and changes in predicted emission wavelength.

New Perspectives on Delocalization Pathways in Aromatic Molecular Chameleons.

This study comprehensively analyzes the magnetically induced current density of polycyclic compounds labeled as "aromatic chameleons" since they can arrange their π-electrons to exhibit aromaticity in both the ground and the lowest triplet state. These compounds comprise benzenoid moieties fused to a central skeleton with 4n π-electrons and traditional magnetic descriptors are biased due to the superposition of local magnetic responses. In the S0 state, our analysis reveals that the molecular constituent fragments preserve their (anti)aromatic features in agreement with two types of resonant structures: one associated with aromatic benzenoids and the other with a central antiaromatic ring. Regarding the T1 state, a global and diatropic ring current is revealed. Our aromaticity study is complemented with advanced electronic and geometric descriptors to consider different aspects of aromaticity, particularly important in the evaluation of excited state aromaticity. Remarkably, these descriptors consistently align with the general features on the main delocalization pathways in polycyclic hydrocarbons consisting of fused 4n π-electron rings. Moreover, our study demonstrates an inverse correlation between the singlet-triplet energy difference and the antiaromatic character of the central ring in S0.

When Is a Bond Broken? The Polarizability Perspective.

AbstractThe question of when a chemical bond can be said to be broken is of fundamental chemical interest but has not been widely studied. Herein we propose that the maxima of static polarizability along bond dissociation coordinates naturally define cutoff points for bond rupture, as they represent the onset of localization of shared electron density into constituent fragments. Examples of computed polarizability maxima over the course of bond cleavage in main‐group and transition metal compounds are provided, across covalent, dative and charge‐shift bonds. The behavior along reaction paths is also considered. Overall, the static polarizability is found to be a sensitive reporter of electronic structure reorganization associated with bond stretching, and thus can serve as a metric for describing bond cleavage (or diagnose the absence of a chemical bond).

When Is a Bond Broken? The Polarizability Perspective.

The question of when a chemical bond can be said to be broken is of fundamental chemical interest but has not been widely studied. Herein we propose that the maxima of static polarizability along bond dissociation coordinates naturally define cutoff points for bond rupture, as they represent the onset of localization of shared electron density into constituent fragments. Examples of computed polarizability maxima over the course of bond cleavage in main-group and transition metal compounds are provided, across covalent, dative and charge-shift bonds. The behavior along reaction paths is also considered. Overall, the static polarizability is found to be a sensitive reporter of electronic structure reorganization associated with bond stretching, and thus can serve as a metric for describing bond cleavage (or diagnose the absence of a chemical bond).

Self-Healing of Polymers and Polymer Composites.

This review is devoted to the description of methods for the self-healing of polymers, polymer composites, and coatings. The self-healing of damages that occur during the operation of the corresponding structures makes it possible to extend the service life of the latter, and in this case, the problem of saving non-renewable resources is simultaneously solved. Two strategies are considered: (a) creating reversible crosslinks in the thermoplastic and (b) introducing a healing agent into cracks. Bond exchange reactions in network polymers (a) proceed as a dissociative process, in which crosslinks are split into their constituent reactive fragments with subsequent regeneration, or as an associative process, the limiting stage of which is the interaction of the reactive end group and the crosslink. The latter process is implemented in vitrimers. Strategy (b) is associated with the use of containers (hollow glass fibers, capsules, microvessels) that burst under the action of a crack. Particular attention is paid to self-healing processes in metallopolymer systems.

Prince Rupert’s Drops: An analysis of fragmentation by thermal stresses and quench granulation of glass and bubbly glass

When volcanic eruptions involve interaction with external water (hydrovolcanism), the result is an ash-rich and energetic volcanic plume, as illustrated dramatically by the January 2022 Tonga eruption. The origin of the high explosive energy of these events remains an important question. We investigate this question by studying Prince Rupert's Drops (PRDs)-tadpole-shaped glass beads formed by dripping molten glass into water-which have long fascinated materials scientists because the great strength of the head contrasts with the explosivity of the metastable interior when the tail is broken. We show that the fragment size distribution (FSD) produced by explosive fragmentation changes systematically with PRD fragmentation in air, water, and syrup. Most FSDs are fractal over much of the size range, scaling that can be explained by the repeated fracture bifurcation observed in three-dimensional images from microcomputed tomography. The shapes of constituent fragments are determined by their position within the original PRD, with platey fragments formed from the outer (compressive) shell and blocky fragments formed by fractures perpendicular to interior voids. When molten drops fail to form PRDs, the glass disintegrates by quench granulation, a process that produces fractal FSDs but with a larger median size than explosively generated fragments. Critically, adding bubbles to the molten glass prevents PRD formation and promotes quench granulation, suggesting that granulation is modulated by heterogeneous stress fields formed around the bubbles during sudden cooling and contraction. Together, these observations provide insight into glass fragmentation and potentially, processes operating during hydrovolcanism.

Clustering a database of optically absorbing organic molecules via a hierarchical fingerprint scheme that categorizes similar functional molecular fragments.

A measure of chemical similarity is only useful if it implies similarity in some relevant property space. Typically, similarity calculations operate by assigning each molecule a chemical fingerprint: a fixed-length vector of bits where the on-bits signify the presence of a certain feature. Common fingerprinting schemes, such as extended-connectivity fingerprints, are by definition general and fail to capture much of the domain-specific theory that underpins similarity in a specific domain. In this work, a hierarchical fingerprinting scheme is developed that is bespoke to a database of ∼4500 organic molecules and their cognate optical absorption spectral properties. Our fingerprinting scheme incorporates molecular fragmentation and domain-specific chemical intuition into an algorithm that categorizes each fragment as being one of a core chemical group, a substituent, or a bridge. The algorithm is applied to every molecule in the database to generate a pool of chemically relevant fragments that are labeled according to their structural category. The fingerprint of each molecule is then composed of a nested Python dictionary specifying the unique identifiers of its constituent fragment entities and the structural links between them to give a hierarchical molecular encoding scheme. Four case studies show the application of our fingerprinting scheme to the subject database. In each case, the clustered molecules display a host of interesting chemical trends. The application that was used to develop and implement this bespoke fingerprinting scheme, referred to as ChemCluster, also exposes a host of other cheminformatics tools pertaining to this database, a selection of which is demonstrated in this work. The enhanced similarity comparisons afforded by our fingerprinting scheme, as well as the large repository of categorized fragments generated during its development, constitute the first step toward using this database in a data-driven materials discovery workflow.

Fragment-based in silico design of SARS-CoV-2 main protease inhibitors.

3CLpro is essential for SARS‐CoV‐2 replication and infection; its inhibition using small molecules is a potential therapeutic strategy. In this study, a comprehensive crystallography‐guided fragment‐based drug discovery approach was employed to design new inhibitors for SARS‐CoV‐2 3CLpro. All small molecules co‐crystallized with SARS‐CoV‐2 3CLpro with structures deposited in the Protein Data Bank were used as inputs. Fragments sitting in the binding pocket (87) were grouped into eight geographical types. They were interactively coupled using various synthetically reasonable linkers to generate larger molecules with divalent binding modes taking advantage of two different fragments' interactions. In total, 1,251 compounds were proposed, and 7,158 stereoisomers were screened using Glide (standard precision and extra precision), AutoDock Vina, and Prime MMGBSA. The top 22 hits having conformations approaching the linear combination of their constituent fragments were selected for MD simulation on Desmond. MD simulation suggested 15 of these did adopt conformations very close to their constituent pieces with far higher binding affinity than either constituent domain alone. These structures could provide a starting point for the further design of SARS‐CoV‐2 3CLpro inhibitors with improved binding, and structures are provided.

How viable is password cracking in digital forensic investigation? Analyzing the guessability of over 3.9 billion real-world accounts

Passwords have been and still remain the most common method of authentication in computer systems. These systems are therefore privileged targets of attackers, and the number of data breaches in the last few years attests to that. A detailed analysis of such data can provide insight on password trends and patterns users follow when they create a password. To this end, this paper presents the largest and most comprehensive analysis of real-world passwords to date – associated with over 3.9 billion accounts from Have I Been Pwned. This analysis includes statistics on use and most common patterns found in passwords and innovates with a breakdown of the constituent fragments that make each password. Furthermore, a classification of these fragments according to their semantic meaning, provides insight on the role of context in password selection. Finally, we provide an in-depth analysis on the guessability of these real-world passwords.

Molecular structure and vibrational spectra of isolated nucleosides at low temperatures (Review article)

The application of various action spectroscopy and absorption spectroscopy methods for studying the structure of biological molecules and their constituent fragments in an isolated state is considered. The main attention is paid to the results achieved in the study of the nucleosides which are the structural units of DNA and RNA. It has been demonstrated that modern low-temperature spectroscopy methods allow registration the vibrational spectra of isolated nucleosides in neutral or ionized form. It was shown that most of the nucleosides can be converted into the gas phase by prolonged evaporation from the Knudsen cell without thermal decomposition. Cooling molecules to cryogenic temperatures plays an important role in these studies. The conformational equilibrium of the gas phase between syn and anti subsets of nucleosides is maintained due to fast cooling when frozen in inert matrices. Within these subsets, interconversion processes between conformers can occur during cooling if the conformers are separated by low energy barriers. In inert gas matrices at 6 K, subsets of the syn-conformers of deoxyribonucleosides are mainly frozen with the C2′-endo structure of the deoxyribose ring. The structures of molecular ions of nucleosides are very different from their neutral forms. In particular protonation leads to the domination of the enol forms of thymidine, as well as syn-conformations of adenosine, stabilized by the intramolecular hydrogen bond N3H+•••O5.

Toward Drug-Like Multispecific Antibodies by Design.

The success of antibody therapeutics is strongly influenced by their multifunctional nature that couples antigen recognition mediated by their variable regions with effector functions and half-life extension mediated by a subset of their constant regions. Nevertheless, the monospecific IgG format is not optimal for many therapeutic applications, and this has led to the design of a vast number of unique multispecific antibody formats that enable targeting of multiple antigens or multiple epitopes on the same antigen. Despite the diversity of these formats, a common challenge in generating multispecific antibodies is that they display suboptimal physical and chemical properties relative to conventional IgGs and are more difficult to develop into therapeutics. Here we review advances in the design and engineering of multispecific antibodies with drug-like properties, including favorable stability, solubility, viscosity, specificity and pharmacokinetic properties. We also highlight emerging experimental and computational methods for improving the next generation of multispecific antibodies, as well as their constituent antibody fragments, with natural IgG-like properties. Finally, we identify several outstanding challenges that need to be addressed to increase the success of multispecific antibodies in the clinic.

Self-Learning Molecular Design for High Lithium-Ion Conductive Ionic Liquids using Maze Game.

A self-learning artificial intelligence system for an autonomous molecular search was recently utilized in place of laborious material development processes by humans. In this approach, because the evaluation of unsuitable or unrealistic candidates considerably decreases the search efficiency, prior knowledge of the chemistry and engineering requirements should be embedded into the molecular-generative algorithm. However, when using naive rule-based restrictions, one must implement the complex rule logic into the code each time, depending on the materials and potential applications. Herein, we propose a molecular-generative method using a maze game to control the allowable constituent fragments of molecules, which improves the flexibility and consistency to implement the rules. We performed an autonomous search for optimized cation structures of high Li-ion conductive ionic liquids evaluated by molecular dynamics simulations, in its practically reasonable scope defined by the maze game. From the search, we discover that acyl ammonium cations are favorable for high Li-ion conductivity because of the high association between the cations and Li ions. These results broaden our existing insight owing to the ability to explore beyond our practical experiences.

Multifunctional Binuclear Ln(III) Complexes Obtained viaIn SituTandem Reactions: Multiple Photoresponses to Volatile Organic Solvents and Anticounterfeiting and Magnetic Properties

The design and synthesis of simple lanthanide complexes with multiple functions have been widely studied and have faced certain challenges. Herein, we successfully synthesized the series of binuclear lanthanide complexes [Ln2(L1)2(NO3)4] (HL1 = 2-amino-1,2-bis(pyridin-2-yl)ethanol; Ln = Dy (Dy2), Tb (Tb2), Ho (Ho2) Er (Er2)) via the in situ self-condensation of Ln(NO3)3·6H2O-catalyzed 2-aminomethylpyridine (16 steps) under solvothermal conditions. Dy2 was mixed with different volatile organic solvents, and photoluminescence tests demonstrated that it showed an excellent selective photoresponse to chloroform (CHCl3). Sensing Tb2 on different organic solvents under the same conditions showed that it exhibited excellent selective photoresponse to methanol (CH3OH). Even under EtOH conditions, Tb2 could selectively respond to small amounts of CH3OH. To the best of our knowledge, achieving a selective photoresponse to various volatile organic compounds by changing the metal center of the complex is difficult. Furthermore, we performed anticounterfeiting tests on Tb2, and the results showed significant differences between the anticounterfeiting marks under white light and ultraviolet light conditions. The alternating current susceptibilities of Dy2 suggested that it was a typical single-molecule magnet (SMM) (Ueff = 93.62 K, τ0 = 1.19 × 10-5 s) under a 0 Oe dc field. Ab initio calculations on Dy2 indicated that the high degrees of axiality of the constituent mononuclear Dy fragments are the main reasons for the existence of SMM behavior.

Complexity Reduction in Density Functional Theory Calculations of Large Systems: System Partitioning and Fragment Embedding.

With the development of low order scaling methods for performing Kohn-Sham density functional theory, it is now possible to perform fully quantum mechanical calculations of systems containing tens of thousands of atoms. However, with an increase in the size of the system treated comes an increase in complexity, making it challenging to analyze such large systems and determine the cause of emergent properties. To address this issue, in this paper, we present a systematic complexity reduction methodology which can break down large systems into their constituent fragments and quantify interfragment interactions. The methodology proposed here requires no a priori information or user interaction, allowing a single workflow to be automatically applied to any system of interest. We apply this approach to a variety of different systems and show how it allows for the derivation of new system descriptors, the design of QM/MM partitioning schemes, and the novel application of graph metrics to molecules and materials.

Modelling the binding mode of macrocycles: Docking and conformational sampling

Drug discovery is increasingly tackling challenging protein binding sites regarding molecular recognition and druggability, including shallow and solvent-exposed protein-protein interaction interfaces. Macrocycles are emerging as promising chemotypes to modulate such sites. Despite their chemical complexity, macrocycles comprise important drugs and offer advantages compared to non-cyclic analogs, hence the recent impetus in the medicinal chemistry of macrocycles. Elaboration of macrocycles, or constituent fragments, can strongly benefit from knowledge of their binding mode to a target. When such information from X-ray crystallography is elusive, computational docking can provide working models. However, few studies have explored docking protocols for macrocycles, since conventional docking methods struggle with the conformational complexity of macrocycles, and also potentially with the shallower topology of their binding sites. Indeed, macrocycle binding mode prediction with the mainstream docking software GOLD has hardly been explored. Here, we present an in-depth study of macrocycle docking with GOLD and the ChemPLP scores. First, we summarize the thorough curation of a test set of 41 protein-macrocycle X-ray structures, raising the issue of lattice contacts with such systems. Rigid docking of the known bioactive conformers was successful (three top ranked poses) for 92.7% of the systems, in absence of crystallographic waters. Thus, without conformational search issues, scoring performed well. However, docking success dropped to 29.3% with the GOLD built-in conformational search. Yet, the success rate doubled to 58.5% when GOLD was supplied with extensive conformer ensembles docked rigidly. The reasons for failure, sampling or scoring, were analyzed, exemplified with particular cases. Overall, binding mode prediction of macrocycles remains challenging, but can be much improved with tailored protocols. The analysis of the interplay between conformational sampling and docking will be relevant to the prospective modelling of macrocycles in general.

Interfacial Adsorption of a Monoclonal Antibody and Its Fab and Fc Fragments at the Oil/Water Interface.

The physical stability of a monoclonal antibody (mAb) solution for injection in a prefilled syringe may in part depend on its behavior at the silicone oil/water interface. Here, the adsorption of a mAb (termed COE-3) and its fragment antigen-binding (Fab) and crystallizable (Fc) at the oil/water interface was measured using neutron reflection. A 1.4 ± 0.1 μm hexadecane oil film was formed on a sapphire block by a spin-freeze-thaw process, retaining its integrity upon contact with the protein solutions. Measurements revealed that adsorbed COE-3 and its Fab and Fc fragments retained their globular structure, forming layers that did not penetrate substantially into the oil phase. COE-3 and Fc were found to adsorb flat-on to the interface, with denser 45 and 42 Å inner layers, respectively, in contact with the oil and a more diffuse 17-21 Å outer layer caused by fragments adsorbing in a tilted manner. In contrast, Fab fragments formed a uniform 60 Å monolayer. Monolayers were formed under all conditions studied (10-200 ppm, using three isotopic contrasts), although changes in packing density across the COE-3 and Fc layers were observed. COE-3 had a higher affinity to the interface than either of its constituent fragments, while Fab had a lower interfacial affinity consistent with its higher net surface charge. This study extends the application of high-resolution neutron reflection measurements to the study of protein adsorption at the oil/water interface using an experimental setup mimicking the protein drug product in a siliconized prefilled syringe.

Isolation, Purification, Characterization and Direct Conjugation of the Lipid A-Free Lipopolysaccharide of Vibrio cholerae O139.

The lipopolysaccharide (LPS) of Vibrio cholerae O139, strain CIRS245, was isolated conventionally, and the lipid A was removed by mild acid hydrolysis (0.1 m NaOAc buffer containing 1 % SDS, pH 4.2, 95 °C, 8 h). The crude product was a complex mixture consisting mainly of constituent fragments of the O-specific polysaccharide-core (OSPc). The OSPc was only a minor component in the mixture. Two-stage purification of the crude OSPc by HPLC gave pure OSPc fragment of the LPS, as shown by NMR spectroscopy, analytical HPLC and ESI-MS. This material is the purest OSPc fragment of the LPS from Vibrio cholerae O139 reported to date. The purified OSPc was readily converted to the corresponding methyl squarate derivative and the latter was conjugated to BSA. The conjugate, when examined by ELISA, showed immunoreactivity with sera from patients in Bangladesh recovering from cholera caused by V. cholerae O139, but not O1.

Structural analysis of the A\u03b2(11\u201342) amyloid fibril based on hydrophobicity distribution

The structure of the Aβ(11–42) amyloid available in PDB makes possible the molecular analysis of the specificity of amyloid formation. This molecule (PDB ID 2MVX) is the object of analysis. This work presents the outcome of in silico experiments involving various alternative conformations of the Aβ(11–42) sequence, providing clues as to the amylodogenecity of its constituent fragments. The reference structure (PDB) has been compared with folds generated using I-Tasser and Robetta—the strongest contenders in the CASP challenge. Additionally, a polypeptide which matches the Aβ(11–42) sequence has been subjected to folding simulations based on the fuzzy oil drop model, which favors the production of a monocentric hydrophobic core. Computer simulations yielded 15 distinct structural forma (five per software package), which, when compared to the experimentally determined structure, allow us to study the role of structural elements which cause an otherwise globular protein to transform into an amyloid. The unusual positions of hydrophilic residues disrupting the expected hydrophobic core and propagating linearly along the long axis of fibril is recognized as the seed for amyloidogenic transformation in this polypeptide. This paper discusses the structure of the Aβ(11–42) amyloid fibril, listed in PDB under ID 2MXU (fragment od Aβ(1–42) amyloid).