Search

Simultaneous inhibition of soluble epoxide hydrolase (sEH) and fatty acid amide hydrolase (FAAH) with a single small molecule represents a novel therapeutic approach in treating inflammatory pain, since both targets are involved in pain and inflammation processes. In this study using multi-target directed ligands methodology we designed and synthesized 7 quinolinyl-based dual sEH/FAAH inhibitors, using an optimized microwave-assisted Suzuki-Miyaura coupling reaction and tested their potency in human FAAH and human, rat, and mouse sEH inhibition assays. The structure-activity relationship study showed that quinolinyl moiety is well tolerated in the active sites of both enzymes, yielding several very potent dual sEH/FAAH inhibitors with the IC50 values in the low nanomolar range. The most potent dual inhibitor 4d was further evaluated in stability assay in human and rat plasma where it performed better than the standard Warfarin while in vivo study revealed that 1 mg/kg 4d can inhibit acute inflammatory pain in male rats to a similar degree as the traditional nonsteroidal anti-inflammatory drug ketoprofen (30 mg/kg) after intraperitoneal injection. ADMET prediction studies for this dual inhibitor show favorable pharmacokinetic properties which will guide the future in vivo evaluations.

Histone proteins form the building blocks of chromatin—nucleosomes. Incorporation of alternative histone variants instead of the major (canonical) histones into nucleosomes is a key mechanism enabling epigenetic regulation of genome functioning. In humans, H2A.J is a constitutively expressed histone variant whose accumulation is associated with cell senescence, inflammatory gene expression, and certain cancers. It is sequence-wise very similar to the canonical H2A histones, and its effects on the nucleosome structure and dynamics remain elusive. This study employed all-atom molecular dynamics simulations to reveal atomistic mechanisms of structural and dynamical effects conferred by the incorporation of H2A.J into nucleosomes. We showed that the H2A.J C-terminal tail and its phosphorylated form have unique dynamics and interaction patterns with the DNA, which should affect DNA unwrapping and the availability of nucleosomes for interactions with other chromatin effectors. The dynamics of the L1-loop and the hydrogen bonding patterns inside the histone octamer were shown to be sensitive to single amino acid substitutions, potentially explaining the higher thermal stability of H2A.J nucleosomes. Taken together, our study demonstrated unique dynamical features of H2A.J-containing nucleosomes, which contribute to further understanding of the molecular mechanisms employed by H2A.J in regulating genome functioning. [ABSTRACT FROM AUTHOR]

Here, we describe (1) the AlphaFold-based structural modeling approach to identify amino acids of the photoprotein berovin that are crucial for coelenterazine binding, and (2) the production and characterization of berovin mutants with substitutions of the identified residues regarding their effects on the ability to form an active photoprotein under physiological conditions and stability to light irradiation. The combination of mutations K90M, N107S, and W103F is demonstrated to cause a shift of optimal conditions for the conversion of apo-berovin into active photoprotein towards near-neutral pH and low ionic strength, and to reduce the sensitivity of active berovin to light. According to the berovin spatial structure model, these residues are found in close proximity to the 6-(p-hydroxy)-phenyl group of the coelenterazine peroxyanion. [ABSTRACT FROM AUTHOR]

Data are accumulating on the hydrolytic activity of serum albumin towards esters and organophosphates. Previously, with the help of the technology of proton nuclear magnetic resonance (1H NMR) spectroscopy, we observed the yield of acetate in the solution of bovine serum albumin and p-nitrophenyl acetate (NPA). Thus, we showed that albumin possesses true esterase activity towards NPA. Then, using the methods of molecular docking and molecular dynamics, we established site Sudlow I as the catalytic center of true esterase activity of albumin. In the present work, to expand our understanding of the molecular mechanisms of albumin pseudoesterase and true esterase activity, we investigated—in experiments in vitro and in silico—the interaction of anticoagulant warfarin (WRF, specific ligand of site Sudlow I) and benzodiazepine diazepam (DIA, specific ligand of site Sudlow II) with albumins of different species, and determined how the binding of WRF and DIA affects the hydrolysis of NPA by albumin. It was found that the characteristics of the binding modes of WRF in site Sudlow I and DIA in site Sudlow II of human (HSA), bovine (BSA), and rat (RSA) albumins have species differences, which are more pronounced for site Sudlow I compared to site Sudlow II, and less pronounced between HSA and RSA compared to BSA. WRF competitively inhibits true esterase activity of site Sudlow I towards NPA and does not affect the functioning of site Sudlow II. Diazepam can slow down true esterase activity of site Sudlow I in noncompetitive manner. It was concluded that site Sudlow I is more receptive to allosteric modulation compared to site Sudlow II. [ABSTRACT FROM AUTHOR]

Non-immunoglobulin-based scaffold proteins (SPs) represent one of the key therapeutic target-specific and high-affinity binders in modern medicine. Among their cellular targets are signaling receptors, in particular, receptor tyrosine kinases, whose dysfunction leads to the development of cancer and other serious diseases. Successful applications of SPs have been reported for HER receptor type 2 (HER2), a member of the human epidermal growth factor receptor family that regulates cell growth and differentiation. To extend the blood residence of SPs and prevent their high accumulation in the kidneys, these proteins are often fused with serum albumin. Promising results for HER2-binding activity were obtained for SP G3 from the DARPins (Designed Ankyrin Repeat Proteins) family fused with an albumin-binding domain (ABD). Interestingly, the detected HER2–G3 binding strongly depended on the position of the G3 module in the sequence of the constructs. Further improvement of these constructs for biomedical applications requires deciphering the molecular mechanism responsible for this effect. Here, we investigate the structural and dynamic aspects of ABD–G3 and G3–ABD chimeras using NMR spectroscopy and molecular modeling. Based on biophysical data, we come to the conclusion that extensive inter-domain contacts form in both constructs, although their binding interfaces and complex stability are somewhat different. Also, it is shown that the domain linker plays an important role—it limits the accessibility of the detected protein–protein binding sites, depending on the order of the domains in the chimeric molecules. These results create a solid structural basis for the rational design of new effective SP constructs targeting the signaling receptors in cells. [ABSTRACT FROM AUTHOR]

The circular bioeconomy is currently a promising model for repurposing natural sources; these sources include plants due to their abundance of bioactive compounds. This study evaluated the antimicrobial properties of a Chaetomorpha linum extract. Chaetomorpha linum is an invasive macroalga from the Orbetello Lagoon (Tuscany, Italy), which grows in nutrient-rich environments and has been forming extended mats since 2005. The biomass is mechanically harvested and treated as waste, consuming considerable manpower and financial resources. As a potential way to increase the value of such waste, this study found that C. linum extract (CLE) is a source of antimicrobial compounds. The phytochemical characterization of the extract revealed the predominant presence of palmitic acid, a fatty acid with known antimicrobial activity. Based on such findings, four bacterial species of high clinical relevance (Enterococcus faecalis, Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli) were tested, revealing a notable antibacterial activity of the extract on Enterococcus faecalis (MIC, 32 μg/mL). Computational analyses identified a potential Enterococcus faecalis molecular target for palmitic acid, offering molecular insights on the interaction. This study presents a comprehensive in vitro and in silico approach for drug and target discovery studies by repurposing C. linum as a source of antimicrobial bioactive compounds. [ABSTRACT FROM AUTHOR]

Advancements in computational techniques have revolutionized the field of drug design, offering a powerful arsenal of tools collectively known as in silico methods. This review provides an overview of the diverse computational techniques employed in the in silico assisted drug design process. From molecular docking and molecular dynamics simulations to Quantitative Structure-Activity Relationship (QSAR) models and artificial intelligence-based approaches, these methods play a pivotal role in expediting drug discovery and optimization. The utilization of molecular docking facilitates the prediction of ligand-receptor interactions, aiding in the identification of potential drug candidates. Molecular dynamics simulations contribute by unraveling the dynamic behavior of biomolecular complexes, offering insights into their stability and flexibility. QSAR models, relying on mathematical correlations between molecular descriptors and biological activities, enable the prediction of compound behaviors, guiding the optimization of lead compounds. The integration of machine learning and artificial intelligence further enhances drug design workflows. Deep learning algorithms, such as neural networks, have demonstrated remarkable capabilities in predicting complex biological activities and uncovering hidden patterns within large datasets. High-throughput screening, coupled with in silico methodologies, allows for the rapid exploration of vast chemical spaces, accelerating the identification of promising drug candidates. Despite these advancements, challenges persist, including the accurate representation of biological systems, the validation of computational predictions and the ethical implications of relying solely on in silico methods. This review critically evaluates the current state of computational techniques in silico assisted drug design, highlighting their strengths, limitations and potential future directions. The integration of computational techniques in drug design has significantly reshaped the landscape of pharmaceutical research. As these methods continue to evolve, bridging the gap between computational predictions and experimental validations, the synergy between in silico and in vitro approaches holds immense promise for the rapid and effective development of novel therapeutic agents. [ABSTRACT FROM AUTHOR]

MDA-9/Syntenin, a key scaffolding protein and a molecular hub involved in a diverse range of cell signaling responses, has proved to be a challenging target for the design and discovery of small molecule probes. In this paper, we report on the design and synthesis of small molecule ligands of this key protein. Genetic algorithm-based computational design and the five–eight step synthesis of three molecules led to ligands with affinities in the range of 1–3 µM, a 20–60-fold improvement over literature reports. The design and synthesis strategies, coupled with the structure-dependent gain or loss in affinity, afford the deduction of principles that should guide the design of advanced probes of MDA-9/Syntenin. [ABSTRACT FROM AUTHOR]

Background/Objectives: Alterations in the actin cytoskeleton correlates to tumor progression and affect critical cellular processes such as adhesion, migration and invasion. Rho-associated coiled-coil-containing protein kinases (ROCK1 and ROCK2), important regulators of the actin cytoskeleton, are frequently overexpressed in various malignancies. The aim of this study was therefore to identify the key structural features of ROCK1/ROCK2 inhibitors using computer-aided drug design (CADD) approaches. In addition, new developed ROCK inhibitors provided a significant framework for the development of multitarget therapeutics—ROCK/HDAC (histone deacetylases) multitarget inhibitors. Methods: 3D-QSAR (Quantitative structure-activity relationship study) and molecular docking study were employed in order to identify key structural features that positively correlate with ROCK inhibition. MDA-MB-231, HCC1937, Panc-1 and Mia PaCa-2 cells were used for evaluation of anticancer properties of synthesized compounds. Results: C-19 showed potent anti-cancer properties, especially enhancement of apoptosis and cell cycle modulation in pancreatic cancer cell lines. In addition, C-19 and C-22 showed potent anti-migratory and anti-invasive effects comparable to the well-known ROCK inhibitor fasudil. Conclusions: In light of the results of this study, we propose a novel multi-target approach focusing on developing dual HDAC/ROCK inhibitors based on the structure of both C-19 and C-22, exploiting the synergistic potential of these two signaling pathways to improve therapeutic efficacy in metastatic tumors. Our results emphasize the potential of multi-target ROCK inhibitors as a basis for future cancer therapies. [ABSTRACT FROM AUTHOR]

This work combines experimental and computational modeling studies for the preparation of a composite of metformin and an organoclay, examining the advantages of a Tunisian clay used for drug delivery applications. The clay mineral studied is a montmorillonite-like smectite (Sm-Na), and the organoclay derivative (HDTMA-Sm) was used as a drug carrier for metformin hydrochloride (MET). In order to assess the MET loading into the clays, these materials were characterized by means of cation exchange capacity assessment, specific surface area measurement, and with the techniques of X-ray diffraction (XRD), differential scanning calorimetry, X-ray fluorescence spectroscopy, and Fourier-transformed infrared spectroscopy. Computational molecular modeling studies showed the surface adsorption process, identifying the clay–drug interactions through hydrogen bonds, and assessing electrostatic interactions for the hybrid MET/Sm-Na and hydrophobic interactions and cation exchange for the hybrid MET/HDTMA-Sm. The results show that the clays (Sm-Na and HDTMA-Sm) are capable of adsorbing MET, reaching a maximum load of 12.42 and 21.97 %, respectively. The adsorption isotherms were fitted by the Freundlich model, indicating heterogeneous adsorption of the studied adsorbate–adsorbent system, and they followed pseudo-second-order kinetics. The calculations of ΔGº indicate the spontaneous and reversible nature of the adsorption. The calculation of ΔH° indicates physical adsorption for the purified clay (Sm-Na) and chemical adsorption for the modified clay (HDTMA-Sm). The release of intercalated MET was studied in media simulating gastric and intestinal fluids, revealing that the purified clay (Sm-Na) and the modified organoclay (HDTMA-Sm) can be used as carriers in controlled drug delivery in future clinical applications. The molecular modeling studies confirmed the experimental phenomena, showing that the main adsorption mechanism is the cation exchange process between proton and MET cations into the interlayer space. [ABSTRACT FROM AUTHOR]

The synthetic peptide TAT-I24 (GRKKRRQRRRPPQCLAFYACFC) exerts antiviral activity against several double-stranded (ds) DNA viruses, including herpes simplex viruses, cytomegalovirus, some adenoviruses, vaccinia virus and SV40 polyomavirus. In the present study, in vitro profiling of this peptide was performed with the aim of characterizing and improving its properties for further development. As TAT-I24 contains three free cysteine residues, a potential disadvantageous feature, peptide variants with replacements or deletions of specific residues were generated and tested in various cell systems and by biochemical analyses. Some cysteine replacements had no impact on the antiviral activity, such as the deletion of cysteine 14, which also showed improved biochemical properties, while the cyclization of cysteines 14 and 20 had the most detrimental effect on antiviral activity. At concentrations below 20 µM, TAT-I24 and selected variants did not induce hemolysis in red blood cells (RBCs) nor modulated lipopolysaccharide (LPS)-induced release of cytokines, such as interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α), in human peripheral blood mononuclear cells (PBMCs). These data indicate that TAT-I24 or its peptide variants are not expected to cause unwanted effects on blood cells. [ABSTRACT FROM AUTHOR]

Human serum albumin (HSA) is an endogenous inhibitor of angiotensin I-converting enzyme (ACE) and, thus, plays a key role in the renin–angiotensin–aldosterone system (RAAS). However, little is known about the mechanism of interaction between these proteins, and the structure of the HSA–ACE complex has not yet been obtained experimentally. The purpose of the presented work is to apply computer modeling methods to study the interaction of HSA with ACE in order to obtain preliminary details about the mechanism of their interaction. Ten possible HSA–ACE complexes were obtained by the procedure of macromolecular docking. Based on the number of steric and polar contacts between the proteins, three leading complexes were selected, the stabilities of which were then tested by molecular dynamics (MD) simulation. Based on the results of MD simulation, the two most probable conformations of the HSA–ACE complex were selected. The analysis of these conformations revealed that the processes of oxidation of the thiol group of Cys34 of HSA and the binding of albumin to ACE can reciprocally affect each other. Known point mutations in the albumin molecules Glu82Lys, Arg114Gly, Glu505Lys, Glu565Lys and Lys573Glu can also affect the interaction with ACE. According to the result of MD simulation, the known ACE mutations, albeit associated with various diseases, do not affect the HSA–ACE interaction. A comparative analysis was performed of the resulting HSA–ACE complexes with those obtained by AlphaFold 3 as well as with the crystal structure of the HSA and the neonatal Fc receptor (FcRn) complex. It was found that domains DI and DIII of albumin are involved in binding both ACE and FcRn. The obtained results of molecular modeling outline the direction for further study of the mechanisms of HSA–ACE interaction in vitro. Information about these mechanisms will help in the design and improvement of pharmacotherapy aimed at modulation of the physiological activity of ACE. [ABSTRACT FROM AUTHOR]

Millions of years of evolution have optimized many biosynthetic pathways by use of multi‐step catalysis. In addition, multi‐step metabolic pathways are commonly found in and on membrane‐bound organelles in eukaryotic biochemistry. The fundamental mechanisms that facilitate these reaction processes provide strategies to bioengineer metabolic pathways in synthetic chemistry. Using Brownian dynamics simulations, here we modeled intermediate substrate transportation of colocalized yeast–ester biosynthesis enzymes on the membrane. The substrate acetate ion traveled from the pocket of aldehyde dehydrogenase to its target enzyme acetyl‐CoA synthetase, then the substrate acetyl CoA diffused from Acs1 to the active site of the next enzyme, alcohol‐O‐acetyltransferase. Arranging two enzymes with the smallest inter‐enzyme distance of 60 Å had the fastest average substrate association time as compared with anchoring enzymes with larger inter‐enzyme distances. When the off‐target side reactions were turned on, most substrates were lost, which suggests that native localization is necessary for efficient final product synthesis. We also evaluated the effects of intermolecular interactions, local substrate concentrations, and membrane environment to bring mechanistic insights into the colocalization pathways. The computation work demonstrates that creating spatially organized multi‐enzymes on membranes can be an effective strategy to increase final product synthesis in bioengineering systems. [ABSTRACT FROM AUTHOR]

Gene activity is tightly controlled by reversible chemical modifications called epigenetic marks, which are of various types and modulate gene accessibility without affecting the DNA sequence. Despite an increasing body of evidence demonstrating the role of oxidative-type modifications of histones in gene expression regulation, there remains a complete absence of structural data at the atomistic level to understand the molecular mechanisms behind their regulatory action. Owing to μs time-scale MD simulations and protein communication networks analysis, we describe the impact of histone H3 hyperoxidation (i.e., S-sulfonylation) on the nucleosome core particle dynamics. Our results reveal the atomic-scale details of the intrinsic structural networks within the canonical histone core and their perturbation by hyperoxidation of the histone H3 C110. We show that this modification involves local rearrangements of the communication networks and destabilizes the dyad, and that one modification is enough to induce a maximal structural signature. Our results suggest that cysteine hyperoxidation in the nucleosome core particle might favor its disassembly.

Krabbe disease is a sphingolipidosis characterized by the genetic deficiency of the acid hydrolase β-galactosylceramidase (GALC). Most of the studies concerning the biological role of GALC performed on Krabbe patients and Galc-deficient twitcher mice (an authentic animal model of the disease) indicate that the pathogenesis of this disorder is the consequence of the accumulation of the neurotoxic GALC substrate β-galactosylsphingosine (psychosine), ignoring the possibility that this enzyme may exert a wider biological impact. Indeed, limited information is available about the effect of GALC downregulation on the cell lipidome in adult and developing organisms. The teleost zebrafish (Danio rerio) has emerged as a useful platform to model human genetic diseases, including sphingolipidoses, and two GALC co-orthologs have been identified in zebrafish (galca and galcb). Here, we investigated the effect of the competitive and irreversible GALC inhibitor β-galactose-cyclophellitol (GCP) on the lipid profile of zebrafish embryos. Molecular modelling indicates that GCP can be sequestered in the catalytic site of the enzyme and covalently binds human GALC, and the zebrafish Galca and Galcb proteins in a similar manner. Accordingly, GCP inhibits the β-galactosylceramide hydrolase activity of zebrafish in vitro and in vivo, leading to significant alterations of the lipidome of zebrafish embryos. These results indicate that the lack of GALC activity deeply affects the lipidome during the early stages of embryonic development, and thereby provide insights into the pathogenesis of Krabbe disease.

Abstract Sulfonamide derivatives as semiconductor materials for organic optoelectronic devices, including photovoltaic (PV), have received considerable interest. In the present work, the synthesis of novel pyrogallol-sulfonamide derivatives based on a molecular hybridization approach yielded N-((4-((2,3,4-trihydroxyphenyl)diazenyl)phenyl)sulfonyl)acetamide (N-DPSA). The techniques of spectroscopy, Fourier transform infrared spectroscopy (FTIR), nuclear magnetic resonance (1H NMR), and mass spectrum were utilized to identify the structural composition of the synthesized N-DPSA. The new N-DPSA was investigated by Hall-effect measurement to prove the positive charge carrier (hole mobility) with mobility and conductivity of 2.39 × 103 cm2/Vs and 1.76 × 10–1 1/Ω cm, respectively. Consequently, N-DPSA could be proposed as a strong candidate as a p-type semiconductor (hole transport layer (HTL)). The optical energy gap was computed at 2.03 eV, indicating the direct optical transition nature of N-DPSA. The elaborated molecular semiconductor's thermal features, molecular modelling, and electronic energy levels were also investigated. The new N-DPSA at various concentrations provided easy synthesis, cheap cost, high performance, and a straightforward design approach for a possible HTL in effective perovskite solar cells (PSCs). A PCE of 7.3% is shown for the N-DPSA-based PSC at its optimal concentration.

With the growing demand for hydrocarbon energy resources, there is a need to involve oil fields at deeper horizons in processing and increase the profitability of their development. Reduction of expenses on prospecting works is possible at revealing and substantiation of physicochemical markers of the naphthogenesis processes. One of the key markers is the transition metals content, which are both a measure of oil age and markers of potential associated processes in the migration and formation of hydrocarbons in the Earth's strata. The elemental composition of samples of oil and reservoir rocks of the Timan-Pechora field was studied. Based on the results of thermodynamic modeling, plausible processes of contact rock minerals transformation were proposed. Based on the results of molecular modeling the probable structure of vanadium and nickel host molecules in the heavy fraction of oils is proposed. The ratios of transition metal and sulfur contents were experimentally established, and assumptions about possible mechanisms of formation of deep hydrocarbon reservoirs were made. Analysis of the obtained ratios of transition metal contents in reservoir rocks and oil samples allowed to suggest possible processes of mantle fluids contact with the host rock and subsequent accumulation of hydrocarbons on sorption active rocks. According to the combined results of experimental and theoretical studies it was found that polymers of heavy fraction more selectively capture vanadium, which indicates the predominance of vanadium content in oil-bearing rocks in relation to the content of nickel. In this case, oil acts as a transport of transition metals, leaching them from the bedrock.

and its derivatives is one of the leaders in the development of highly promising biologically active compounds. The peculiarities of the chemical structure of the derivatives of this heterocycle provide a wide range of possibilities for chemical transformations that allow to obtain really effective drugs. The involvement of several substituents in chemical transformations simultaneously, which have the properties of highly reactive centers, additionally creates favorable conditions for the formation of rational ways to create a biologically active compound. Amino-, mercapto- or hydroxogroups often play the role of such groups in chemistry. The use of these groups as substituents of 1,2,4-triazole synthon provides multifaceted opportunities for directed chemical transformation. The ability of such structural fragments to form chemical interactions and bonds with biological targets has an additional positive effect in the sense of their involvement in chemical transformations on the way to the targeted production of a biologically active substance. Thus, the combination of a heterocyclic structure with a highly reactive chemical center is endowed with theoretically sound and practically significant meaning. The aim of the work is to preliminary determine the potential for creating a biologically active substance with antifungal action based on 1-alkyl derivatives of 3,5-dimethy-l-4-((4-nitrobenzylidene)amino)-1,2,4-triazolium bromide. Materials and methods. The toxicity of the studied compounds has been predicted using the TEST program (Toxicity Estimation Software Tool), which allowed to determine the predictive level of acute toxicity, ecotoxicity and mutagenicity. The physicochemical and pharmacokinetic parameters have been predicted, and the drug-like properties and availability of the investigated substances have been assessed using the online resource SwissADME. The determination of the most favorable spatial configuration of the ligand relative to the active site of the protein and the assessment of the strength of their interaction have been realized using the computational method of molecular docking. The ligands have been prepared using MarvinSketch 6.3.0, HyperChem 8 and AutoDock Tools-1.5.6 software. The preparation of the model enzyme has been based on the use of Discovery Studio 4.0 and AutoDock Tools-1.5.6. The practical implementation of flexible molecular docking has been carried out using the software tools of the AutoDock/Vina platform. Results. In the process of step-by-step prescreening of the formed structures of a number of 1-alkyl derivatives of 3,5-dimethyl-4-((4-nitrobenzylidene)amino)-1,2,4-triazolium bromide, a number of qualitative and quantitative indicators related to the physicochemical characteristics and pharmacokinetic parameters of the studied substances have been obtained. According to the results of the first stage of research, the group of substances under consideration can be predictively considered low-toxic, but with a high risk of mutagenic properties. The next stage of the work, which involved the analysis of physicochemical parameters, pharmacokinetic parameters, general drug-like properties and bioavailability, allowed us to identify 1-alkyl derivatives of 3,5-dimethyl-4-((4-nitrobenzylidene)amino)-1,2,4-triazolium bromide as substances with a rather positive pharmacological profile. The final stage in the form of molecular docking of the structure of the studied compounds to the active site of lanosterol 14α-demethylase allowed us to determine the nature of the chemical interaction and the type of amino acid residues that may be involved in the antifungal properties of the key ligands. The analysis of the docking results allows us to determine the privileged nature of the nonyl substituent at the first Nitrogen atom of the 1,2,4-triazole synthon in the structure of the presented series of compounds for the formation of antifungal properties. Conclusions. The general prospects for the creation of a biologically active substance with antifungal properties using 1-alkyl derivatives of 3,5-dimethyl-4-((4-nitrobenzylidene)amino)-1,2,4-triazolium bromide look quite realistic. Particular attention should be paid to 3,5-dimethyl-1-nonyl-4-((4-nitrobenzylidene)amino)-1,2,4-triazolium bromide as a substance with significant potential for antifungal properties, which allows us to recommend this compound for further more constructive and extended in vitro and in vivo studies.

Abstract Ubiquitin-specific peptidase 7 (USP7) is a deubiquitinating enzyme that mediates the stability and activity of numerous proteins. At basal expression levels, USP7 stabilizes p53 protein, even in the presence of excess MDM2. However, its overexpression leads to the deubiquitination of MDM2 at a rate faster than p53, leading to p53 degradation and pro-tumorigenic roles. Consequently, it is an attractive target for anticancer drug discovery via the modulation of its allosteric site from which the protein is activated. In this study, molecular modeling techniques and cheminformatics approaches were employed to unravel the potential of eighty compounds to serve as its allosteric site modulators. The compounds were initially subjected to virtual screening. Subsequently, the binding free energies of the top four compounds with the highest binding affinities were calculated, and their drug-likeness, and pharmacokinetic and toxicity profiles were evaluated. Ultimately, the complexes of the protein and hit compounds were subjected to a 100 nanoseconds (ns) molecular dynamics simulation. The results of the study revealed eight compounds from the compound library with docking scores ranging from − 7.491 to -11.43 kcal/mol, compared to P217564, which exhibited a docking score of -5.671 kcal/mol. The top four compounds with the highest affinities possessed drug-like properties, and good pharmacokinetic and toxicity profiles, and their predicted inhibitory potentials showed they will be effective at minimal concentration. Also, molecular dynamics simulation confirmed the stability of the protein-ligand complexes. Conclusively, the compounds identified in this study are worthy of further evaluation for the development of allosteric site modulators of USP7.

Iron delivery to the plasma is closely coupled to erythropoiesis, the production of red blood cells, as this process consumes most of the circulating plasma iron. In response to hemorrhage and other erythropoietic stresses, increased erythropoietin stimulates the production of the hormone erythroferrone (ERFE) by erythrocyte precursors (erythroblasts) developing in erythropoietic tissues. ERFE acts on the liver to inhibit bone morphogenetic protein (BMP) signaling and thereby decrease hepcidin production. Decreased circulating hepcidin concentrations then allow the release of iron from stores and increase iron absorption from the diet. Guided by evolutionary analysis and Alphafold2 protein complex modeling, we used targeted ERFE mutations, deletions, and synthetic ERFE segments together with cell-based bioassays and surface plasmon resonance to probe the structural features required for bioactivity and BMP binding. We define the ERFE active domain and multiple structural features that act together to entrap BMP ligands. In particular, the hydrophobic helical segment 81 to 86 and specifically the highly conserved tryptophan W82 in the N-terminal region are essential for ERFE bioactivity and Alphafold2 modeling places W82 between two tryptophans in its ligands BMP2, BMP6, and the BMP2/6 heterodimer, an interaction similar to those that bind BMPs to their cognate receptors. Finally, we identify the cationic region 96-107 and the globular TNFα-like domain 186-354 as structural determinants of ERFE multimerization that increase the avidity of ERFE for BMP ligands. Collectively, our results provide further insight into the ERFE-mediated inhibition of BMP signaling in response to erythropoietic stress.

The COVID-19 pandemic, instigated by the emergence of the novel coronavirus, SARS-CoV-2, created an incomparable global health crisis. Due to its highly virulent nature, identifying potential therapeutic agents against this lethal virus is crucial. PLpro is a key protein involved in viral polyprotein processing and immune system evasion, making it a prime target for the development of antiviral drugs to combat COVID-19. To expedite the search for potential therapeutic candidates, this review delved into computational studies. Recent investigations have harnessed computational methods to identify promising inhibitors targeting PLpro, aiming to suppress the viral activity. Molecular docking techniques were employed by researchers to explore the binding sites for antiviral drugs within the catalytic region of PLpro. The review elucidates the functional and structural properties of SARS-CoV-2 PLpro, underscoring its significance in viral pathogenicity and replication. Through comprehensive all-atom molecular dynamics (MD) simulations, the stability of drug–PLpro complexes was assessed, providing dynamic insights into their interactions. By evaluating binding energy estimates from MD simulations, stable drug–PLpro complexes with potential antiviral properties were identified. This review offers a comprehensive overview of the potential drug/lead candidates discovered thus far against PLpro using diverse in silico methodologies, encompassing drug repurposing, structure-based, and ligand-based virtual screenings. Additionally, the identified drugs are listed based on their chemical structures and meticulously examined according to various structural parameters, such as the estimated binding free energy (ΔG), types of intermolecular interactions, and structural stability of PLpro–ligand complexes, as determined from the outcomes of the MD simulations. Underscoring the pivotal role of targeting SARS-CoV-2 PLpro in the battle against COVID-19, this review establishes a robust foundation for identifying promising antiviral drug candidates by integrating molecular dynamics simulations, structural modeling, and computational insights. The continual imperative for the improvement of existing drugs and exploring novel compounds remains paramount in the global efforts to combat COVID-19. The evolution and management of COVID-19 hinge on the symbiotic relationship between computational insights and experimental validation, underscoring the interdisciplinary synergy crucial to this endeavor.

Abstract In this body of work, a chemical known as 2-cyano-N-(4-morpholino benzyl dine) acetohydrazide (CMBAH) is explored for its ability to suppress the carbidic austempered ductile iron (CADI) corrosion in 1M H2SO4. Density functional theory was used in experiments and theoretical investigations to investigate the inhibiting impact. The corrosion of CADI alloys in 1M H2SO4 produced a corrosion resistance superior to that of CADI heat treatment (H.T.). As-cast carbidic ductile iron (CDI) 4 alloy with 1.5%t Cr-Nb has a corrosion rate (C.R.) of 11.69 mm/year, which drops to 5.31 mm/year at HT-275 °C and 6.13 mm/year at HT-375 °C. When describing the adsorption of inhibitors, the Langmuir adsorption isotherm is the most effective method. The findings of the Gads show that the inhibition was induced mainly by the physisorption on the surface CADI alloys. In addition to this, it was found that the results of the experiments and the hypotheses were largely harmonious with one another. The formation of protective layers on the CADI surfaces is also visible in the images captured by the SEM. In 1M H2SO4, these Schiff base inhibitors effectively prevent corrosion caused by CADI. However, the combination of inhibitors leads to a fine microstructure with ausferrite and narrow ferrite needles, promoting corrosion resistance. The CADI needles rated an upper ausferritic microstructure with wide ferrite needles.

Guanine-rich sequences of nucleic acids, including DNA and RNA, are known to fold into non-canonical structures named G-quadruplexes (G4s). Such arrangements of these macromolecular polymers are mainly located in telomeres and in promoter regions of oncogenes and, for this reason, they represent a potential target for compounds with therapeutic applications. In fact, the ligand-mediated stabilization of G4s inhibits telomerase and the activity of transcriptional machinery and counteracts cancer cell immortalization. Flavonoids, along with other classes of small molecules, have been previously tested for their ability to stabilize G4s, but the mechanism of their interaction has not been fully elucidated. In the current work, we report a multi-technique investigation on the binding of tosylated isoflavones obtained by the B-ring modification of compounds from Maclura pomifera to a telomeric DNA sequence. Our study demonstrates that such derivatization leads to compounds showing lower binding affinity but with an increased selectivity toward G4 with respect to double-stranded DNA. The binding mode to the macromolecular target G4 was studied by combining results from electrospray mass spectrometry binding studies, nuclear magnetic resonance experiments and computational simulations. Overall, our findings show that tosylation influences the selectivity toward the macromolecular target by affecting the interaction mode with the nucleic acid.

Abstract In recent years computational methods for molecular modeling have become a prime focus of computational biology and cheminformatics. Many dedicated systems exist for modeling specific classes of molecules such as proteins or small drug-like ligands. These are often heavily tailored toward the automated generation of molecular structures based on some meta-input by the user and are not intended for expert-driven structure assembly. Dedicated manual or semi-automated assembly software tools exist for a variety of molecule classes but are limited in the scope of structures they can produce. In this work we present BuildAMol, a highly flexible and extendable, general-purpose fragment-based molecular assembly toolkit. Written in Python and featuring a well-documented, user-friendly API, BuildAMol empowers researchers with a framework for detailed manual or semi-automated construction of diverse molecular models. Unlike specialized software, BuildAMol caters to a broad range of applications. We demonstrate its versatility across various use cases, encompassing generating metal complexes or the modeling of dendrimers or integrated into a drug discovery pipeline. By providing a robust foundation for expert-driven model building, BuildAMol holds promise as a valuable tool for the continuous integration and advancement of powerful deep learning techniques. Scientific contribution BuildAMol introduces a cutting-edge framework for molecular modeling that seamlessly blends versatility with user-friendly accessibility. This innovative toolkit integrates modeling, modification, optimization, and visualization functions within a unified API, and facilitates collaboration with other cheminformatics libraries. BuildAMol, with its shallow learning curve, serves as a versatile tool for various molecular applications while also laying the groundwork for the development of specialized software tools, contributing to the progress of molecular research and innovation.

Abstract We present a methodology for the synthesis of inorganic-organic Janus-type molecules based on mono-T8 and difunctionalized double-decker silsesquioxanes (DDSQs) via hydrosilylation reactions, achieving exceptionally high yields and selectivities. The synthesized compounds were extensively characterized using various spectroscopic techniques, and their sizes and spatial arrangements were predicted through molecular modelling and density functional theory (DFT) calculations. Quantum chemical calculations were employed to examine the interactions among four molecules of the synthesized compounds. These computational results allowed us to determine the propensity for molecular aggregation, identify the functional groups involved in these interactions, and understand the changes in interatomic distances during aggregation. Understanding the aggregation behaviour of silsesquioxane molecules is crucial for tailoring their properties for specific applications, such as nanocomposites, surface coatings, drug delivery systems, and catalysts. Through a combination of experimental and computational approaches, this study provides valuable insights into the design and optimization of silsesquioxane-based Janus-type molecules for enhanced performance across various fields.

Abstract An automated pipeline for comprehensive calculation of intermolecular interaction energies based on molecular force-fields using the Tinker molecular modelling package is presented. Starting with non-optimized chemically intuitive monomer structures, the pipeline allows the approximation of global minimum energy monomers and dimers, configuration sampling for various monomer–monomer distances, estimation of coordination numbers by molecular dynamics simulations, and the evaluation of differential pair interaction energies. The latter are used to derive Flory–Huggins parameters and isotropic particle–particle repulsions for Dissipative Particle Dynamics (DPD). The computational results for force fields MM3, MMFF94, OPLS-AA and AMOEBA09 are analyzed with Density Functional Theory (DFT) calculations and DPD simulations for a mixture of the non-ionic polyoxyethylene alkyl ether surfactant C10E4 with water to demonstrate the usefulness of the approach. Scientific Contribution To our knowledge, there is currently no open computational pipeline for differential pair interaction energies at all. This work aims to contribute an (at least academically available, open) approach based on molecular force fields that provides a robust and efficient computational scheme for their automated calculation for small to medium-sized (organic) molecular dimers. The usefulness of the proposed new calculation scheme is demonstrated for the generation of mesoscopic particles with their mutual repulsive interactions.

Natural curcumin is composed of three curcuminoids, namely curcumin (CUR), deme-thoxycurcumin (DMC) and bis-demethoxycurcumin (BDMC). These compounds are utilized in various biophotonics applications, including photodynamic therapy (PDT). This work aimed to evaluate the photodynamic action (alternative to antibiotics) of synthetic curcuminoids against Staphylococcus aureus. Herein, we evaluated an optimal proportion of the three curcuminoids mixed in solution to improve photoinactivation effects. Therefore, a set of computational calculations was carried out to understand the photodynamic action (stability and mechanism) of curcuminoids. Regarding computational analysis, the curcuminoid molecules were optimized using DFT with the hybrid exchange–correlation functional M06-2X, which includes long-range correction, and the 6-311++G(d,p) basis set. DMC and BDMC were more effective as photosensitizers than curcumin at a very low concentration of 0.75 µM, inactivating more than five orders of magnitude of S. aureus. Theoretical UV-vis absorption spectra showed that at maximum absorption wavelengths, electronic transitions of the π→π* type originated from H→L excitations. The BDMC was more stable than the other two curcuminoids after photobleaching, and the fluorescence emission was also higher, which could lead to its usage as a fluorescence dye to track bacteria. In fact, the results of electronic structure calculations proved that the stability order of curcuminoids is CUR < DMC < BDMC. The mixture of synthetic curcuminoids was more effective in the inactivation of S. aureus compared to curcumin by itself; for all proposed mixtures, an equal or superior reduction was achieved.

Abstract Based on a structural family of thirty-two NR2B-selective N-Methyl-D-Aspartate receptor (NMDAR) antagonists, two phenylpiperazine derivatives labeled C37 and C39 were conceived thanks to molecular modeling techniques, as novel NMDAR inhibitors exhibiting the highest analgesic activities (of pIC50 order) against neuropathic pain, with excellent ADME-toxicity profiles, and good levels of molecular stability towards the targeted protein of NMDA receptor. Initially, the quantitative structure-activity relationships (QSARs) models were developed using multiple linear regression (MLR), partial least square regression (PLSR), multiple non-linear regression (MNLR), and artificial neural network (ANN) techniques, revealing that analgesic activity was strongly correlated with dipole moment, octanol/water partition coefficient, Oxygen mass percentage, electronegativity, and energy of the lowest unoccupied molecular orbital, whose the correlation coefficients of generated models were: 0.860, 0.758, 0.885 and 0.977, respectively. The predictive capacity of each model was evaluated by an external validation with correlation coefficients of 0.703, 0.851, 0.778, and 0.981 respectively, followed by a cross-validation technique with the leave-one-out procedure (CVLOO) with Q2 cv of 0.785, more than Y-randomization test, and applicability domain (AD), in addition to Fisher’s and Student’s statistical tests. Thereafter, ten novel molecules were designed based on MLR QSAR model, then predicted with their ADME-Toxicity profiles and subsequently examined for their similarity to the drug candidates. Finally, two of the most active compounds (C37 and C39) were chosen for molecular docking and molecular dynamics (MD) investigations during 100 ns of MD simulation time in complex with the targeted protein of NMDA receptor (5EWJ.pdb).

Abstract The available Epstein Barr virus vaccine has tirelessly harnessed the gp350 glycoprotein as its target epitope, but the result has not been preventive. Right here, we designed a global multi-epitope vaccine for EBV; with special attention to making sure all strains and preventive antigens are covered. Using a robust computational vaccine design approach, our proposed vaccine is armed with 6–16 mers linear B-cell epitopes, 4–9 mer CTL epitopes, and 8–15 mer HTL epitopes which are verified to induce interleukin 4, 10 & IFN-gamma. We employed deep computational mining coupled with expert intelligence in designing the vaccine, using human Beta defensin-3—which has been reported to induce the same TLRs as EBV—as the adjuvant. The tendency of the vaccine to cause autoimmune disorder is quenched by the assurance that the construct contains no EBNA-1 homolog. The protein vaccine construct exhibited excellent physicochemical attributes such as Aliphatic index 59.55 and GRAVY − 0.710; and a ProsaWeb Z score of − 3.04. Further computational analysis revealed the vaccine docked favorably with EBV indicted TLR 1, 2, 4 & 9 with satisfactory interaction patterns. With global coverage of 85.75% and the stable molecular dynamics result obtained for the best two interactions, we are optimistic that our nontoxic, non-allergenic multi-epitope vaccine will help to ameliorate the EBV-associated diseases—which include various malignancies, tumors, and cancers—preventively.

Within the field of Philippine folkloric medicine, the utilization of indigenous plants like Euphorbia hirta (tawa-tawa), Carica papaya (papaya), and Psidium guajava (guava) as potential dengue remedies has gained attention. Yet, limited research exists on their comprehensive effects, particularly their anti-dengue activity. This study screened 2944 phytochemicals from various Philippine plants for anti-dengue activity. Absorption, distribution, metabolism, excretion, and toxicity (ADMET) profiling provided 1265 compounds demonstrating pharmacokinetic profiles suitable for human use. Molecular docking targeting the dengue virus NS2b-NS3 protease’s catalytic triad (Asp 75, Ser 135, and His 51) identified ten ligands with higher docking scores than reference compounds idelalisib and nintedanib. Molecular dynamics simulations confirmed the stability of eight of these ligand–protease complexes. Molecular Mechanics/Poisson–Boltzmann Surface Area (MM/PBSA) analysis highlighted six ligands, including veramiline (−80.682 kJ/mol), cyclobranol (−70.943 kJ/mol), chlorogenin (−63.279 kJ/mol), 25beta-Hydroxyverazine (−61.951 kJ/mol), etiolin (−59.923 kJ/mol), and ecliptalbine (−56.932 kJ/mol) with favorable binding energies, high oral bioavailability, and drug-like properties. This integration of traditional medical knowledge with advanced computational drug discovery methods paves new pathways for the development of treatments for dengue.

Caffeine is an alkaloid with a purine structure and has been well known for centuries due to its presence in popular drinks—tea and coffee. However, the structural and spectroscopic parameters of this compound, as well as its chemical and biological activities, are still not fully known. In this study, for the first time, we report on the measured oxygen-17 NMR spectra of this stimulant. To support the assignment of our experimental NMR data, extensive quantum chemical calculations of NMR parameters, including nuclear magnetic shielding constants and indirect spin–spin coupling constants, were performed. In a theoretical study, using nine efficient density functionals (B3LYP, BLYP, BP86, CAM-B3LYP, LC-BLYP, M06, PBE0, TPSSh, wB97x), and in combination with a large and flexible correlation-consistent aug-cc-pVTZ basis set, the structure and NMR parameters were predicted for a free molecule of caffeine and in chloroform, DMSO and water. A polarized continuum model (PCM) was used to include a solvent effect. As a result, an optimal methodology was developed for predicting reliable NMR data, suitable for studies of known, as well as newly discovered, purines and similar alkaloids. The results of the current work could be used in future basic and applied studies, including NMR identification and intermolecular interactions of caffeine in various raw materials, like plants and food, as well as in the structural and spectroscopic characterization of new compounds with similar structures. [ABSTRACT FROM AUTHOR]

In this body of work, a chemical known as 2-cyano-N-(4-morpholino benzyl dine) acetohydrazide (CMBAH) is explored for its ability to suppress the carbidic austempered ductile iron (CADI) corrosion in 1M H2SO4. Density functional theory was used in experiments and theoretical investigations to investigate the inhibiting impact. The corrosion of CADI alloys in 1M H2SO4 produced a corrosion resistance superior to that of CADI heat treatment (H.T.). As-cast carbidic ductile iron (CDI) 4 alloy with 1.5%t Cr-Nb has a corrosion rate (C.R.) of 11.69 mm/year, which drops to 5.31 mm/year at HT-275 °C and 6.13 mm/year at HT-375 °C. When describing the adsorption of inhibitors, the Langmuir adsorption isotherm is the most effective method. The findings of the Gads show that the inhibition was induced mainly by the physisorption on the surface CADI alloys. In addition to this, it was found that the results of the experiments and the hypotheses were largely harmonious with one another. The formation of protective layers on the CADI surfaces is also visible in the images captured by the SEM. In 1M H2SO4, these Schiff base inhibitors effectively prevent corrosion caused by CADI. However, the combination of inhibitors leads to a fine microstructure with ausferrite and narrow ferrite needles, promoting corrosion resistance. The CADI needles rated an upper ausferritic microstructure with wide ferrite needles. [ABSTRACT FROM AUTHOR]

A new naturally occurring diarylheptanoid, (1E,4Z,6E)-5-hydroxy-1,7-diphenylhepta-1,4,6-trien-3-one (3), was isolated from the rhizomes of K. elegans along with six known compounds, flavokawain B (1), 5,6-dehydrokawain (2), pinocembrin (4), cardamonin (5), alpinetin (6), and crotepoxide (7), among which compound 6 had not previously been isolated from this plant species. Two chalcones, flavokawain B (1) and cardamonin (5) were active against nitric oxide (NO) radicals released from LPS-induced RAW264.7 macrophages, resulting in 91.58% and 98.68% inhibition of NO production, respectively. Furthermore, compounds 1 and 5 showed superior cytotoxicity against MCF-7 (IC50 = 23.07 and 20.84 M) and MDA-MB-231 (IC50 = 21.77 and 26.64 M) cell lines, respectively. In silico molecular modeling studies of the most active compounds 1 and 5 against epidermal growth factor receptors (EGFR) suggested that p-p interactions with residues on the EGFR protein contributed to their anticancer properties. The results suggest that cardamonin (5) could be a promising candidate for further development of anti-inflammatory and anticancer agents. [ABSTRACT FROM AUTHOR]

The COVID-19 pandemic, instigated by the emergence of the novel coronavirus, SARS-CoV-2, created an incomparable global health crisis. Due to its highly virulent nature, identifying potential therapeutic agents against this lethal virus is crucial. PLpro is a key protein involved in viral polyprotein processing and immune system evasion, making it a prime target for the development of antiviral drugs to combat COVID-19. To expedite the search for potential therapeutic candidates, this review delved into computational studies. Recent investigations have harnessed computational methods to identify promising inhibitors targeting PLpro, aiming to suppress the viral activity. Molecular docking techniques were employed by researchers to explore the binding sites for antiviral drugs within the catalytic region of PLpro. The review elucidates the functional and structural properties of SARS-CoV-2 PLpro, underscoring its significance in viral pathogenicity and replication. Through comprehensive all-atom molecular dynamics (MD) simulations, the stability of drug–PLpro complexes was assessed, providing dynamic insights into their interactions. By evaluating binding energy estimates from MD simulations, stable drug–PLpro complexes with potential antiviral properties were identified. This review offers a comprehensive overview of the potential drug/lead candidates discovered thus far against PLpro using diverse in silico methodologies, encompassing drug repurposing, structure-based, and ligand-based virtual screenings. Additionally, the identified drugs are listed based on their chemical structures and meticulously examined according to various structural parameters, such as the estimated binding free energy (ΔG), types of intermolecular interactions, and structural stability of PLpro–ligand complexes, as determined from the outcomes of the MD simulations. Underscoring the pivotal role of targeting SARS-CoV-2 PLpro in the battle against COVID-19, this review establishes a robust foundation for identifying promising antiviral drug candidates by integrating molecular dynamics simulations, structural modeling, and computational insights. The continual imperative for the improvement of existing drugs and exploring novel compounds remains paramount in the global efforts to combat COVID-19. The evolution and management of COVID-19 hinge on the symbiotic relationship between computational insights and experimental validation, underscoring the interdisciplinary synergy crucial to this endeavor. [ABSTRACT FROM AUTHOR]

Contamination of soil, water, and wastewater by pharmaceuticals, including antibiotics, is a global health problem. This work evaluated the use of a natural compound, curcumin (CUR), as a homogeneous photocatalyst, together with hydrogen peroxide (H2O2) as a benign oxidant, to promote the photodegradation of ciprofloxacin (CIP). Furthermore, we carried out theoretical calculations using density functional theory (DFT) to assess the chemical reactivity of ciprofloxacin. In addition, the intermolecular interaction patterns of two crystalline polymorphs of the antibiotic drug were analyzed through Hirshfeld surfaces. Finally, calculations using the TD-DFT formalism were carried out to understand the effects on the CIP molecule caused by the simultaneous presence of the CUR molecule and ultraviolet-visible light (UV-Vis). A photooxidative effect was observed in the presence of the CUR photocatalyst (CIP + CUR (1:0.5)), resulting in a degradation of CIP of up to 24.4%. However, increasing the concentration of the CUR photocatalyst (ciprofloxacin + curcumin (1:1)) decreased the photodegradation of CIP, which may be caused by competition between the CIP molecule and CUR for ROS generated in situ. Additionally, the calculation results showed that the electronic excitations caused by the associated CIP + CUR structures affect the CIP molecule, resulting in the effects observed experimentally. The results show that CUR, when applied as a photosensitizing catalyst, presents synergistic potential with H2O2 in the photocatalytic degradation of ciprofloxacin. This photocatalytic process can be applied to the environmental remediation of pharmaceutical micropollutants, a subject of ongoing studies. [ABSTRACT FROM AUTHOR]

Therapeutic antibodies play an important role in the public healthcare system to treat patients with a variety of diseases. Protein characterization using an array of analytical tools provides in-depth information for drug quality, safety, efficacy, and the further understanding of the molecule. A therapeutic antibody candidate MAB1 exhibits unique binding properties to both cation and anion exchange columns at neutral pH. This uniqueness disrupts standard purification processes and necessitates adjustments in manufacturing. This study identifies that the charge heterogeneity of MAB1 is primarily due to the N-terminal cyclization of glutamine to pyroglutamine and, to a lesser extent, succinimide intermediate, deamidation, and C-terminal lysine. Using three approaches, i.e., deferential chemical labeling, H/D exchange, and molecular modeling, the binding to anion exchange resins is attributed to negatively charged patches on the antibody's surface, involving specific carboxylic acid residues. The methodologies shown here can be extended to study protein binding orientation in column chromatography. [ABSTRACT FROM AUTHOR]

Folic acid (FA) and its structural analog, anticancer medicine methotrexate (MTX), are known to form host/guest complexes with native cyclodextrins, of which the most stable are formed with the medium-sized β-cyclodextrin. Based on our research, proving that simple sugars (D-glucose, D-galactose, and D-mannose) can form adducts with folic acid, we envisioned that combining these two types of molecular receptors (cyclodextrin and simple carbohydrates) into one may be beneficial for the complexation of FA and MTX. We designed and obtained host/guest inclusion complexes of FA and MTX with two monoderivatives of β-cyclodextrin—substituted at position 6 with monosaccharide (glucose, G-β-CD) and disaccharide (maltose, Ma-β-CD). The complexation was proved by experimental (NMR, UV-vis, IR, TG, DSC) and theoretical methods. We proved that derivatization of β-cyclodextrin with glucose and maltose has a significant impact on the complexation with FA and MTX, as the addition of one glucose subunit to the structure of the receptor significantly increases the value of association constant for both FA/G-β-CD and MTX/G-β-CD, while further extending a pendant chain (incorporation of maltose subunit) results in no additional changes. [ABSTRACT FROM AUTHOR]

Enterovirus-D68 (EV68) has emerged as a global health concern over the last decade with severe symptomatic infections resulting in long-lasting neurological deficits and death. Unfortunately, there are currently no FDA-approved antiviral drugs for EV68 or any other non-polio enterovirus. One particularly attractive class of potential drugs are small molecules inhibitors, which can target the conserved active site of EV68-3C protease. For other viral proteases, we have demonstrated that the emergence of drug resistance can be minimized by designing inhibitors that leverage the evolutionary constraints of substrate specificity. However, the structural characterization of EV68-3C protease bound to its substrates has been lacking. Here, we have determined the substrate specificity of EV68-3C protease through molecular modeling, molecular dynamics (MD) simulations, and co-crystal structures. Molecular models enabled us to successfully characterize the conserved hydrogen-bond networks between EV68-3C protease and the peptides corresponding to the viral cleavage sites. In addition, co-crystal structures we determined have revealed substrate-induced conformational changes of the protease which involved new interactions, primarily surrounding the S1 pocket. We calculated the substrate envelope, the three-dimensional consensus volume occupied by the substrates within the active site. With the elucidation of the EV68-3C protease substrate envelope, we evaluated how 3C protease inhibitors, AG7088 and SG-85, fit within the active site to predict potential resistance mutations. [ABSTRACT FROM AUTHOR]

Chagas disease, caused by the parasitic protozoan Trypanosoma cruzi (T. cruzi), represents a worldwide public health issue. To date, there is no efficient treatment to combat this pathology, and the only drugs available are usually toxic to the patient. Through the enzyme trans-salidase, the parasite invades, infects, and multiplies intracellularly in the host cell. This protein has been considered an attractive target for developing or searching for compounds with potential trypanocidal activity. In this study, an in silico analysis was performed using a Food and Drug Administration-approved computational drug repositioning approach to identify compounds with anti-Chagas potential against two trans-sialidase proteins. Those compounds with potential inhibition were analyzed and selected through a molecular docking-based virtual screening. Forty-nine compounds were identified, of which forty-five are available on the market, and the rest were evaluated in silico. Our predicted results follow that these compounds are safe for human use and could be potential anti-trans-sialidase agents. [ABSTRACT FROM AUTHOR]

Four afatinib derivatives were designed and modeled. These derivatives were compared to the known tyrosine-kinase inhibitors in treating Chronic Myeloid Leukemia, i.e., imatinib and ponatinib. The molecules were evaluated through computational methods, including docking studies, the non-covalent interaction index, Electron Localization and Fukui Functions, in silico ADMET analysis, QTAIM, and Heat Map analysis. The AFA(IV) candidate significantly increases the score value compared to afatinib. Furthermore, AFA(IV) was shown to be relatively similar to the ponatinib profile when evaluating a range of molecular descriptors. The addition of a methylpiperazine ring seems to be well distributed in the structure of afatinib when targeting the BCR-ABL enzyme, providing an important hydrogen bond interaction with the Asp381 residue of the DFG-switch of BCR-ABL active site residue and the AFA(IV) new chemical entities. Finally, in silico toxicity predictions show a favorable index, with some molecules presenting the loss of the irritant properties associated with afatinib in theoretical predictions. [ABSTRACT FROM AUTHOR]

Alkaptonuria (AKU) is a rare autosomal recessive metabolic disorder caused by mutations in the homogentisate 1,2-dioxygenase (HGD) gene, leading to the accumulation of homogentisic acid (HGA), causing severe inflammatory conditions. Recently, the presence of serum amyloid A (SAA) has been reported in AKU tissues, classifying AKU as novel secondary amyloidosis; AA amyloidosis is characterized by the extracellular tissue deposition of fibrils composed of fragments of SAA. AA amyloidosis may complicate several chronic inflammatory conditions, like rheumatoid arthritis, ankylosing spondylitis, inflammatory bowel disease, chronic infections, neoplasms, etc. Treatments of AA amyloidosis relieve inflammatory disorders by reducing SAA concentrations; however, no definitive therapy is currently available. SAA regulation is a crucial step to improve AA secondary amyloidosis treatments. Here, applying a comprehensive in vitro and in silico approach, we provided evidence that HGA is a disruptor modulator of SAA, able to enhance its polymerization, fibril formation, and aggregation upon SAA/SAP colocalization. In silico studies deeply dissected the SAA misfolding molecular pathway and SAA/HGA binding, suggesting novel molecular insights about it. Our results could represent an important starting point for identifying novel therapeutic strategies in AKU and AA secondary amyloidosis-related diseases. [ABSTRACT FROM AUTHOR]

Guanine-rich sequences of nucleic acids, including DNA and RNA, are known to fold into non-canonical structures named G-quadruplexes (G4s). Such arrangements of these macromolecular polymers are mainly located in telomeres and in promoter regions of oncogenes and, for this reason, they represent a potential target for compounds with therapeutic applications. In fact, the ligand-mediated stabilization of G4s inhibits telomerase and the activity of transcriptional machinery and counteracts cancer cell immortalization. Flavonoids, along with other classes of small molecules, have been previously tested for their ability to stabilize G4s, but the mechanism of their interaction has not been fully elucidated. In the current work, we report a multi-technique investigation on the binding of tosylated isoflavones obtained by the B-ring modification of compounds from Maclura pomifera to a telomeric DNA sequence. Our study demonstrates that such derivatization leads to compounds showing lower binding affinity but with an increased selectivity toward G4 with respect to double-stranded DNA. The binding mode to the macromolecular target G4 was studied by combining results from electrospray mass spectrometry binding studies, nuclear magnetic resonance experiments and computational simulations. Overall, our findings show that tosylation influences the selectivity toward the macromolecular target by affecting the interaction mode with the nucleic acid. [ABSTRACT FROM AUTHOR]

To investigate the influence mechanism of the annealing treatment on the intermolecular action of waxy crude oil, this study selected the molecular models of oil, wax, resin and asphaltene, and constructed the model system to imitate instead of the waxy crude oils by using the Materials Studio software, and revealed the influence mechanism of annealing treatment. Three main findings were made: 1) The basic molecular unit structure is the premise of phase transformation, and the different annealing times are the main factors affecting the phase transformation. 2) After annealing treatment, the conformation of molecular chain gradually changes from the initial straight chain to the curly state, and the change is most obvious at the lowest energy; in terms of system energy, the changes of Eval, Enon-bond and Etotal of the three oil samples all increase in different extent during the whole thermal process. 3) In terms of the radial distribution function (RDF) between the identical types of molecules and heterogeneous molecules of waxy crude oil, the accumulation of asphaltenes plays a leading role in the annealing process of waxy crude oil system, and the van der Waals force is the main force. [ABSTRACT FROM AUTHOR]

Understanding protein function often necessitates characterizing the flexibility of protein structures. However, simulating protein flexibility poses significant challenges due to the complex dynamics of protein systems, requiring extensive computational resources and accurate modeling techniques. In response to these challenges, the CABS‐flex method has been developed as an efficient modeling tool that combines coarse‐grained simulations with all‐atom detail. Available both as a web server and a standalone package, CABS‐flex is dedicated to a wide range of users. The web server version offers an accessible interface for straightforward tasks, while the standalone command‐line program is designed for advanced users, providing additional features, analytical tools, and support for handling large systems. This paper examines the application of CABS‐flex across various structure–function studies, facilitating investigations into the interplay among protein structure, dynamics, and function in diverse research fields. We present an overview of the current status of the CABS‐flex methodology, highlighting its recent advancements, practical applications, and forthcoming challenges. [ABSTRACT FROM AUTHOR]

In recent years computational methods for molecular modeling have become a prime focus of computational biology and cheminformatics. Many dedicated systems exist for modeling specific classes of molecules such as proteins or small drug-like ligands. These are often heavily tailored toward the automated generation of molecular structures based on some meta-input by the user and are not intended for expert-driven structure assembly. Dedicated manual or semi-automated assembly software tools exist for a variety of molecule classes but are limited in the scope of structures they can produce. In this work we present BuildAMol, a highly flexible and extendable, general-purpose fragment-based molecular assembly toolkit. Written in Python and featuring a well-documented, user-friendly API, BuildAMol empowers researchers with a framework for detailed manual or semi-automated construction of diverse molecular models. Unlike specialized software, BuildAMol caters to a broad range of applications. We demonstrate its versatility across various use cases, encompassing generating metal complexes or the modeling of dendrimers or integrated into a drug discovery pipeline. By providing a robust foundation for expert-driven model building, BuildAMol holds promise as a valuable tool for the continuous integration and advancement of powerful deep learning techniques. Scientific contribution BuildAMol introduces a cutting-edge framework for molecular modeling that seamlessly blends versatility with user-friendly accessibility. This innovative toolkit integrates modeling, modification, optimization, and visualization functions within a unified API, and facilitates collaboration with other cheminformatics libraries. BuildAMol, with its shallow learning curve, serves as a versatile tool for various molecular applications while also laying the groundwork for the development of specialized software tools, contributing to the progress of molecular research and innovation. [ABSTRACT FROM AUTHOR]

We present a methodology for the synthesis of inorganic-organic Janus-type molecules based on mono-T8 and difunctionalized double-decker silsesquioxanes (DDSQs) via hydrosilylation reactions, achieving exceptionally high yields and selectivities. The synthesized compounds were extensively characterized using various spectroscopic techniques, and their sizes and spatial arrangements were predicted through molecular modelling and density functional theory (DFT) calculations. Quantum chemical calculations were employed to examine the interactions among four molecules of the synthesized compounds. These computational results allowed us to determine the propensity for molecular aggregation, identify the functional groups involved in these interactions, and understand the changes in interatomic distances during aggregation. Understanding the aggregation behaviour of silsesquioxane molecules is crucial for tailoring their properties for specific applications, such as nanocomposites, surface coatings, drug delivery systems, and catalysts. Through a combination of experimental and computational approaches, this study provides valuable insights into the design and optimization of silsesquioxane-based Janus-type molecules for enhanced performance across various fields. [ABSTRACT FROM AUTHOR]

An automated pipeline for comprehensive calculation of intermolecular interaction energies based on molecular force-fields using the Tinker molecular modelling package is presented. Starting with non-optimized chemically intuitive monomer structures, the pipeline allows the approximation of global minimum energy monomers and dimers, configuration sampling for various monomer–monomer distances, estimation of coordination numbers by molecular dynamics simulations, and the evaluation of differential pair interaction energies. The latter are used to derive Flory–Huggins parameters and isotropic particle–particle repulsions for Dissipative Particle Dynamics (DPD). The computational results for force fields MM3, MMFF94, OPLS-AA and AMOEBA09 are analyzed with Density Functional Theory (DFT) calculations and DPD simulations for a mixture of the non-ionic polyoxyethylene alkyl ether surfactant C10E4 with water to demonstrate the usefulness of the approach. Scientific Contribution To our knowledge, there is currently no open computational pipeline for differential pair interaction energies at all. This work aims to contribute an (at least academically available, open) approach based on molecular force fields that provides a robust and efficient computational scheme for their automated calculation for small to medium-sized (organic) molecular dimers. The usefulness of the proposed new calculation scheme is demonstrated for the generation of mesoscopic particles with their mutual repulsive interactions. [ABSTRACT FROM AUTHOR]

Covering: 2019 to 2023. Even with the advent of modern and complementary spectroscopy techniques, comprehensive characterization of natural product continues to represent an onerous and time-consuming task, being far away to become rather "routine". Mainly due to their highly complex structures and small amount of isolated sample, in milligram or sub-milligram quantities, structural misassignment of natural products are still a recurrence theme in the modern literature. Since the seminal paper from Nicolau and Snider, in 2005, evaluating the various cases of reassignment of natural products, from the present era, in which NMR parameters calculations play such an important role in the structural elucidation of natural products, helping to uncover and ultimately revise the structure of previously reported compounds, a pertinent question arises: are we still chasing molecules that were never there? In this minireview, we intent to discuss the current state of computational NMR parameter calculations, with a particular focus on their application in the structural determination of natural products. Additionally, we have conducted a comprehensive survey of the literature spanning the years 2019-2023, in order to select and discuss recent noteworthy cases of incorrectly assigned structures that were revised through NMR calculations. Therefore, our main goal is to show what can be done through computational simulations of NMR parameters, currently user-friendly and easily implemented by non-expert users with basic skills in computational chemistry, before venturing into complex and time-consuming total synthesis projects. In conclusion, we anticipate a promising future for NMR parameter calculations, fueled by the ongoing development of user-friendly tools and the integration of artificial intelligence. The emergence of these advancements is poised to broaden the applications of NMR simulations, offering a more accessible and reliable means to address the persistent challenge of structural misassignments in natural product chemistry. [ABSTRACT FROM AUTHOR]

Microbial infections pose a significant global health threat, affecting millions of individuals and leading to substantial mortality rates. The increasing resistance of microorganisms to conventional treatments requires the development of novel antimicrobial agents. Pyrroloquinoline quinone (PQQ), a natural medicinal drug involved in various cellular processes, holds promise as a potential antimicrobial agent. In the present study, our aim was, for the first time, to explore the antimicrobial activity of PQQ against 29 pathogenic microbes, including 13 fungal strains, 8 Gram-positive bacteria, and 8 Gram-negative bacteria. Our findings revealed potent antifungal properties of PQQ, particularly against Syncephalastrum racemosum, Talaromyces marneffei, Candida lipolytica, and Trichophyton rubrum. The MIC values varied between fungal strains, and T. marneffei exhibited a lower MIC, indicating a greater susceptibility to PQQ. In addition, PQQ exhibited notable antibacterial activity against Gram-positive and -negative bacteria, with a prominent inhibition observed against Staphylococcus epidermidis, Proteus vulgaris, and MRSA strains. Remarkably, PQQ demonstrated considerable biofilm inhibition against the MRSA, S. epidermidis, and P. vulgaris strains. Transmission electron microscopy (TEM) studies revealed that PQQ caused structural damage and disrupted cell metabolism in bacterial cells, leading to aberrant morphology, compromised cell membrane integrity, and leakage of cytoplasmic contents. These findings were further affirmed by shotgun proteomic analysis, which revealed that PQQ targets several important cellular processes in bacteria, including membrane proteins, ATP metabolic processes, DNA repair processes, metal-binding proteins, and stress response. Finally, detailed molecular modeling investigations indicated that PQQ exhibits a substantial binding affinity score for key microbial targets, including the mannoprotein Mp1P, the transcriptional regulator TcaR, and the endonuclease PvuRTs1I. Taken together, our study underscores the effectiveness of PQQ as a broad-spectrum antimicrobial agent capable of combating pathogenic fungi and bacteria, while also inhibiting biofilm formation and targeting several critical biological processes, making it a promising therapeutic option for biofilm-related infections. [ABSTRACT FROM AUTHOR]

Human terminal deoxynucleotidyl transferase (TdT) can catalyze template-independent DNA synthesis during the V(D)J recombination and DNA repair through nonhomologous end joining. The capacity for template-independent random addition of nucleotides to single-stranded DNA makes this polymerase useful in various molecular biological applications involving sequential stepwise synthesis of oligonucleotides using modified dNTP. Nonetheless, a serious limitation to the applications of this enzyme is strong selectivity of human TdT toward dNTPs in the order dGTP > dTTP ≈ dATP > dCTP. This study involved molecular dynamics to simulate a potential impact of amino acid substitutions on the enzyme's selectivity toward dNTPs. It was found that the formation of stable hydrogen bonds between a nitrogenous base and amino acid residues at positions 395 and 456 is crucial for the preferences for dNTPs. A set of single-substitution and double-substitution mutants at these positions was analyzed by molecular dynamics simulations. The data revealed two TdT mutants—containing either substitution D395N or substitutions D395N+E456N—that possess substantially equalized selectivity toward various dNTPs as compared to the wild-type enzyme. These results will enable rational design of TdT-like enzymes with equalized dNTP selectivity for biotechnological applications. [ABSTRACT FROM AUTHOR]