Computational Molecular Modeling Research Articles

Molecular self-assembled helix peptide nanotubes based on some amino acid molecules and their dipeptides: molecular modeling studies.

The paper considers the features of the structure and dipole moments of several amino acids and their dipeptides which play an important role in the formation of the peptide nanotubes based on them. The influence of the features of their chirality (left L and right D) and the alpha-helix conformations of amino acids are taken into account. In particular, amino acids with aromatic rings, such as phenylalanine (Phe/F), and branched-chain amino acids (BCAAs)-leucine (Leu/L) and isoleucine (Ile/I)-as well as corresponding dipeptides (diphenylalanine (FF), dileucine (LL), and diisoleucine (II)) are considered. The main features and properties of these dipeptide structures and peptide nanotubes (PNTs), based on them, are investigated using computational molecular modeling and quantum-chemical semi-empirical calculations. Their polar, piezoelectric, and photoelectronic properties and features are studied in detail. The results of calculations of dipole moments and polarization, as well as piezoelectric coefficients and band gap width, for different types of helical peptide nanotubes are presented. The calculated values of the chirality indices of various nanotubes are given, depending on the chirality of the initial dipeptides-the results obtained are consistent with the law of changes in the type of chirality as the hierarchy of molecular structures becomes more complex. The influence of water molecules in the internal cavity of nanotubes on their physical properties is estimated. A comparison of the results of these calculations by various computational methods with the available experimental data is presented and discussed. The main tool for molecular modeling of all studied nanostructures in this work was the HyperChem 8.01 software package. The main approach used here is the Hartree-Fock (HF) self-consistent field (SCF) with various quantum-chemical semi-empirical methods (AM1, PM3, RM1) in the restricted Hartree-Fock (RHF) and in the unrestricted Hartree-Fock (UHF) approximations. Optimization of molecular systems and the search for their optimal geometry is carried out in this work using the Polak-Ribeire algorithm (conjugate gradient method), which determines the optimized geometry at the point of their minimum total energy. For such optimized structures, dipole moments D and electronic energy levels (such as EHOMO and ELUMO), as well as the band gap Eg = ELUMO - EHOMO, were then calculated. For each optimized molecular structure, the volume was calculated using the QSAR program implemented also in the HyperChem software package.

Development, characterization, and evaluation of withaferin-A and artesunate-loaded pH-responsive acetal-dextran polymeric nanoparticles for the management of malaria

Artemisinin and its derivatives have been commonly used to treat malaria. However, the emergence of resistance against artemisinin derivatives has posed a critical challenge in malaria management. In the present study, we have proposed a combinatorial approach, utilizing pH-responsive acetal-dextran nanoparticles (Ac-Dex NPs) as carriers for the delivery of withaferin-A (WS-3) and artesunate (Art) to improve treatment efficacy of malaria. The optimized WS-3 and Art Ac-Dex NPs demonstrated enhanced pH-responsive release profiles under parasitophorous mimetic conditions (pH 5.5). Computational molecular modeling reveals that Ac-Dex's polymeric backbone strongly interacts with merozoite surface protein-1 (MSP-1), preventing erythrocyte invasion. In-vitro antimalarial activity of drug-loaded Ac-Dex NPs reveals a 1–1.5-fold reduction in IC50 values compared to pure drug against the 3D7 strain of Plasmodium falciparum. Treatment with WS-3 Ac-Dex NPs (100 mg/kg) and Art Ac-Dex NPs (30 mg/kg) to Plasmodium berghei-infected mice resulted in 78.11 % and 100 % inhibition of parasitemia. Notably, the combination therapy comprised of Art and WS-3 Ac-Dex NPs achieved complete inhibition of parasitemia even at a half dose of Art, indicating the synergistic potential of the combinations. However, further investigations are necessary to confirm the safety and effectiveness of WS-3 and Art Ac-Dex NPs for their successful clinical implications.

Synthesis and Molecular Dynamic Simulation of Novel Cationic and Non-cationic Pyrimidine Derivatives as Potential G-quadruplex-ligands.

Drug resistance has been a problem in cancer chemotherapy, which often causes shortterm effectiveness. Further, the literature indicates that telomere G-quadruplex could be a promising anti-cancer target. We synthesized and characterized two new pyrimidine derivatives as ligands for G-quadruplex DNA. The interaction of novel non-cationic and cationic pyrimidine derivatives (3a, b) with G-quadruplex DNA (1k8p and 3qsc) was explored by circular dichroism (CD) and ultraviolet-visible spectroscopy and polyacrylamide gel electrophoresis (PAGE) methods. The antiproliferative activity of desired compounds was evaluated by the MTT assay. Apoptosis induction was assessed by Propidium iodide (P.I.) staining and flow cytometry. Computational molecular modeling (CMM) and molecular dynamics simulation (MD) were studied on the complexes of 1k8p and 3qsc with the compounds. The van der Waals, electrostatic, polar solvation, solventaccessible surface area (SASA), and binding energies were calculated and analyzed. The experimental results confirmed that both compounds 3a and 3b interacted with 1k8p and 3qsc and exerted cytotoxic and proapoptotic effects on cancer cells. The number of hydrogen bonds and the RMSD values increased in the presence of the ligands, indicating stronger binding and suggesting increased structural dynamics. The electrostatic contribution to binding energy was higher for the cationic pyrimidine 3b, indicating more negative binding energies. Both experimental and MD results confirmed that 3b was more prone to form a complex with DNA G-quadruplex (1k8p and 3qsc), inhibit cell growth, and induce apoptosis, compared to the non-cationic pyrimidine 3a.

Guest-Responsive Near-Infrared-Luminescent Metal-Organic Cage Organized by Porphyrin Dyes and Yb(III) Complexes.

Metal-organic cages (MOCs) with luminophores have significant advantages for the facile detection of specific molecules based on turn-on or turn-off luminescence changes induced by host-guest complexation. One important challenge is the development of turn-on-type near-infrared (NIR)-luminescent MOCs. In this study, we synthesized a novel MOC consisting of two porphyrin dyes linked by four Yb(III) complexes, which exhibit bimodal red and NIR fluorescence signals upon photoexcitation of the porphyrin π system. Single-crystal X-ray structural analysis and computational molecular modeling revealed that planar aromatic perfluorocarbons were intercalated into the MOC. The tight packing between the MOC and guests enhanced the NIR fluorescence of Yb(III) by suppressing energy transfer from the photoexcited porphyrin to oxygen molecules. Guest-responsive turn-on NIR fluorescence changes in an MOC were successfully demonstrated.

Chitin-glucan improves important pathophysiological features of irritable bowel syndrome.

Irritable bowel syndrome (IBS) is one of the most frequent and debilitating conditions leading to gastroenterological referrals. However, recommended treatments remain limited, yielding only limited therapeutic gains. Chitin-glucan (CG) is a novel dietary prebiotic classically used in humans at a dosage of 1.5-3.0 g/d and is considered a safe food ingredient by the European Food Safety Authority. To provide an alternative approach to managing patients with IBS, we performed preclinical molecular, cellular, and animal studies to evaluate the role of chitin-glucan in the main pathophysiological mechanisms involved in IBS. To evaluate the roles of CG in visceral analgesia, intestinal inflammation, barrier function, and to develop computational molecular models. Visceral pain was recorded through colorectal distension (CRD) in a model of long-lasting colon hypersensitivity induced by an intra-rectal administration of TNBS [15 milligrams (mg)/kilogram (kg)] in 33 Sprague-Dawley rats. Intracolonic pressure was regularly assessed during the 9 wk-experiment (weeks 0, 3, 5, and 7) in animals receiving CG (n = 14) at a human equivalent dose (HED) of 1.5 g/d or 3.0 g/d and compared to negative control (tap water, n = 11) and positive control (phloroglucinol at 1.5 g/d HED, n = 8) groups. The anti-inflammatory effect of CG was evaluated using clinical and histological scores in 30 C57bl6 male mice with colitis induced by dextran sodium sulfate (DSS) administered in their drinking water during 14 d. HT-29 cells under basal conditions and after stimulation with lipopolysaccharide (LPS) were treated with CG to evaluate changes in pathways related to analgesia (µ-opioid receptor (MOR), cannabinoid receptor 2 (CB2), peroxisome proliferator-activated receptor alpha, inflammation [interleukin (IL)-10, IL-1b, and IL-8] and barrier function [mucin 2-5AC, claudin-2, zonula occludens (ZO)-1, ZO-2] using the real-time PCR method. Molecular modelling of CG, LPS, lipoteichoic acid (LTA), and phospholipomannan (PLM) was developed, and the ability of CG to chelate microbial pathogenic lipids was evaluated by docking and molecular dynamics simulations. Data were expressed as the mean ± SEM. Daily CG orally-administered to rats or mice was well tolerated without including diarrhea, visceral hypersensitivity, or inflammation, as evaluated at histological and molecular levels. In a model of CRD, CG at a dosage of 3 g/d HED significantly decreased visceral pain perception by 14% after 2 wk of administration (P < 0.01) and reduced inflammation intensity by 50%, resulting in complete regeneration of the colonic mucosa in mice with DSS-induced colitis. To better reproduce the characteristics of visceral pain in patients with IBS, we then measured the therapeutic impact of CG in rats with TNBS-induced inflammation to long-lasting visceral hypersensitivity. CG at a dosage of 1.5 g/d HED decreased visceral pain perception by 20% five weeks after colitis induction (P < 0.01). When the CG dosage was increased to 3.0 g/d HED, this analgesic effect surpassed that of the spasmolytic agent phloroglucinol, manifesting more rapidly within 3 wk and leading to a 50% inhibition of pain perception (P < 0.0001). The underlying molecular mechanisms contributing to these analgesic and anti-inflammatory effects of CG involved, at least in part, a significant induction of MOR, CB2 receptor, and IL-10, as well as a significant decrease in pro-inflammatory cytokines IL-1b and IL-8. CG also significantly upregulated barrier-related genes including muc5AC, claudin-2, and ZO-2. Molecular modelling of CG revealed a new property of the molecule as a chelator of microbial pathogenic lipids, sequestering gram-negative LPS and gram-positive LTA bacterial toxins, as well as PLM in fungi at the lowesr energy conformations. CG decreased visceral perception and intestinal inflammation through master gene regulation and direct binding of microbial products, suggesting that CG may constitute a new therapeutic strategy for patients with IBS or IBS-like symptoms.

Computational Approach for Architecture, Tailoring, and Advancements in Perfluorinated Compounds: Synthesis, Characterization, and Future Directions in Fire Suppression Technology

The demand for effective fire extinguishants has spurred investigation into novel perfluorinated molecules due to their exceptional properties, including high thermal stability, low toxicity, and eco-friendliness. This study presents a computational framework for designing and tailoring perfluorinated compounds as potential alternatives to traditional extinguishing agents. The research centers on elucidating the synthesis, molecular architecture, and characterization of these compounds to enhance their fire suppression capabilities while mitigating environmental impact. By employing computational methods, molecular modeling, and advanced spectroscopic techniques, the structural intricacies and potential applications of perfluorinated compounds in fire suppression are investigated. Additionally, future research directions aimed at addressing challenges and advancing the development of environmentally sustainable fire extinguishants are discussed. This manuscript contributes to the ongoing efforts to replace conventional extinguishing agents with safer and more environmentally friendly alternatives.

Investigating G-quadruplex structures in RPGR gene: Implications for understanding X-linked retinal degeneration

AimsThis pilot study investigates the potential pathogenic role of G-quadruplex (G4) structures in RPGR-associated retinal degeneration, starting from a case of suspected X-linked form affected family. We hypothesize that the stabilization of these structures might alter DNA replication and transcription, inducing genetic instability and influencing gene expression. Main methodsWe conducted whole genome amplification experiments and next-generation sequencing to detect the blockade of polymerase activity by G4 structures. Our specific focus was the RPGR gene, which hosts a high concentration of predicted G4-forming motifs and is implicated in most X-linked retinal degeneration cases. To understand the potential interference of G4 structures, we applied computational and 3D molecular modeling to visualize interferences in DNA replication and transcription regulation. Key findingsOur data confirmed the obstruction of DNA polymerase enzymes by G4 structures, particularly when stabilized by the compound pyridostatin. This obstruction was evident in the reduced amplification of RPGR gene regions and a shift in the start/end sites of putative G4 motifs. Moreover, the modeling indicated a potential disruption of critical promoter elements and RNA polymerase binding, which could drastically alter gene expression. SignificanceOur findings suggest that G4 formation in the RPGR gene could lead to genetic instability and affect the expression of RPGR, contributing to retinal dystrophy. Moreover, this study underscores the broader implications of G4 structures in other genetic disorders. Improved understanding of G4 structures could reveal novel therapeutic targets to combat genetic disorders, promoting the advancement of personalized medicine and precision health.

Magnetic nanoparticles loaded hydrochar for effective Cr(VI) removal from water: Batch and column studies

Chromium considered as most toxic trace metal and is essential to remove it from aqueous using influential adsorbents. Hydrochar prepared from mango peels biomass by thermal activation process was applied to produce activated hydrochr (ACH) which further prepared magnetic nano-composite activated hydrochar (Fe3O4-ACH) material as an effectual sorbent and tested for adsorption of Cr(VI) ions. SEM/EDS, BET, FTIR, VSM, and XRD instruments were utilized to evaluate the characteristics of produced Fe3O4-ACH. The obtained results revealed that the nanoparticle modification increased the surface area and improved the adsorption ability of ACH. A vibrating sample magnetometer was applied for magnetic properties in which the external magnetic field responded by saturation magnetization leading to quickly adsorbed metal ions from water. The factorial design studies were achieved to optimize the removal conditions of metal ions. Equilibrium data for isotherms (Langmuir isotherm) and kinetic mechanisms (pseudo second order) well fitted with the models. The obtained adsorption capacity for Langmuir isotherm was 174.7 mg/g under optimized conditions (dose 0.03 g, contact time 120 min, Cr(VI) solution 50 mg/L). Practical applications of real water samples were studied by fixed-bed column adsorption. The obtained results revealed that the synthesized Fe3O4-ACH was promising for Cr(VI) removal with adsorption capacity of 60.24 mg/g at optimized conditions; bed height (1.3 cm), Cr(VI) ions concentration (50 mg/L) and flow rate (12 mL/min). The experimental breakthrough curve results were compared in a fixed-bed column and were successfully fitted with kinetic models. The given results of distribution and selectivity coefficients proven that Fe3O4-ACH composite has a greater adsorption selectivity than adsorption of Cr(VI). Furthermore, computational molecular modeling was performed to evaluate the interaction types between Cr(VI), Fe3O4, and ACH. The Cr(VI) adsorption mainly carried hydrogen bonding, π–π, hydrophobic and electrostatic interactions. Desorption of chromium ions from Fe3O4-ACH composite adsorbent was more effective with 94.1% desorption efficiency. An approximate cost analysis of 3.15 USD/Kg in a week was assumed for activated hydrochar which was cheaper than the commercially available activated carbon which cost 20 USD/Kg. The obtained results indicated that the produced Fe3O4-ACH composite is a capable adsorbent to decontaminate Cr(VI) from real water samples.

Enantioseparation of organometallic compounds by electromigration techniques.

Over time, chiral organometallic compounds have attracted great interest in several fields, with applications going across several disciplines of chemical, biological, medical, and material sciences. In the last decades, due to advancements in molecular design and computational modeling, the chemistry of chiral transition metal complexes had a remarkable flowering, with the development of new structures for applications in asymmetric synthesis, bioinorganic chemistry, and molecular recognition. In these fields, fast chiral analysis to determine the enantiomeric purity of organometallic structures prepared by asymmetric synthesis, and for high-throughput screening of analytes, catalysts, and reactions, is very important. Capillary electrophoresis and related techniques proved to be extremely versatile for chiral analysis, showing unsurpassed advantages compared to chromatography like low consumption of materials, production of limited amounts of waste, fast equilibration, and possibility to replace easily type and concentration of the chiral selector, among others. Furthermore, electromigration techniques may be useful to gain details about the stereochemistry of the enantiomers of new compounds and to study analyte-selector noncovalent interactions at molecular level. On this basis, this short review aims to provide the reader with a comprehensive view on the enantioseparation of organometallic compounds by electromigration techniques, examining the topic from the historical perspective and showing what was made in this field so far, an essential know-how for developing new and advanced applications in the next future.

σE of Streptomyces coelicolor can function both as a direct activator or repressor of transcription

σ factors are considered as positive regulators of gene expression. Here we reveal the opposite, inhibitory role of these proteins. We used a combination of molecular biology methods and computational modeling to analyze the regulatory activity of the extracytoplasmic σE factor from Streptomyces coelicolor. The direct activator/repressor function of σE was then explored by experimental analysis of selected promoter regions in vivo. Additionally, the σE interactome was defined. Taken together, the results characterize σE, its regulation, regulon, and suggest its direct inhibitory function (as a repressor) in gene expression, a phenomenon that may be common also to other σ factors and organisms.

Insights into novel inhibitors intending HCMV protease a computational molecular modelling investigation for antiviral drug repurposing

Human cytomegalovirus (HCMV) is an important opportunistic pathogen that is the most significant viral cause of congenital birth abnormalities and is responsible for a high morbidity and death rate in immunocompromised patients. HCMV's rising severity and the limitations of current vaccines in preventing infection highlight the urgent need for effective antiviral drugs. This study aimed to identify small compounds using extensive & appropriate in-silico drug design techniques, including molecular docking, Post-docking MM-GBSA, ADMET, MD simulation, PCA, and DCCM were employed in this study capable of binding to the viral protease and inhibiting its activity, thereby preventing proteolytic processing during capsid maturation. 3516 compounds from life chemical were used in molecular docking, and the top four compounds having high binding affinity and promising ADMET properties with life chemicals ID: F3407-0101 (CID: 49667672), F6559-3323 (CID: 121022124), F6456-1266 (CID: 71810903), and F3411-7969 (CID: 50785034). MD simulation was also used to assess the stability of the protein-ligand complex structure. Finally, after MD simulation, principal component analysis (PCA), and dynamic cross-correlation matrix (DCCM) analysis were performed using trajectories, and we can suggest the best drug candidate which is CID: 50785034 (N-(3-fluoro-4-methylphenyl)-2-({7-oxo-8-[(oxolan-2-yl) methyl]-5-thia-1,8,10,11-tetraazatricyclo [7.3.0.0^ {2,6}] dodeca-2(6),3,9,11-tetraen-12-yl}sulfanyl)acetamide), another two compounds CID: 121022124, and CID: 71810903 which comes after CID: 50785034. All three compounds may have the potential to be developed as a therapy option for HCMV infection.

Green synthesis, molecular structure, spectroscopic, ADME, DFT and molecular docking studies on methyl 10-trans,12-cis-octadecadienoate

The methyl 10-trans, 12-cis-octadecadienoate (MOD) obtained from the methanol extract of Calotropis gigantea flowers was studied using spectroscopic, computational molecular modelling and DFT methods in the current work. The Calotropis gigantea flowers were collected from the surroundings of Tamil Nadu, India's Thiruvallur district. The preparation for extraction of bioactive compound from Plant - based green synthesis of MOD from Calatropis gigantea. The FTIR spectra of MOD have been measured between in 400 and 4000 cm−1. Density functional theory is employed to determine the geometry of the molecules, vibrational frequencies and geometrical parameters by using B3LYP/6–311++G (d, p) basis set. The identification of the modes of vibration depended on the potential energy distributions (PEDs) which have been computed. The HOMO-LUMO energies, chemical hardness, and electro negativity of the molecule have been determined via the DFT/B3LYP/6–311++G (d, p) method. The intra molecular interactions and hydrogen bonding have been interpreted using natural bond orbital analysis by NBO 3.1 program. UV–Visible absorption spectra in the wavelength range of 200–400 nm was noticed, which indicates a molecular exchange of charges inside the molecule. The time dependent density functional theory (TD-DFT) method adopted for this study to determine the excited states of the title molecule. The Argus Lab application was implemented to evaluate the molecular docking tests that were conducted to look at the anti-cancer capabilities of the MOD molecule against Caspase 3.

Charge transport in individual short base stacked single-stranded RNA molecules

Charge transport in biomolecules is crucial for many biological and technological applications, including biomolecular electronics devices and biosensors. RNA has become the focus of research because of its importance in biomedicine, but its charge transport properties are not well understood. Here, we use the Scanning Tunneling Microscopy-assisted molecular break junction method to measure the electrical conductance of particular 5-base and 10-base single-stranded (ss) RNA sequences capable of base stacking. These ssRNA sequences show single-molecule conductance values around 10^{-3}G_0 (G_0= 2e^2/h), while equivalent-length ssDNAs result in featureless conductance histograms. Circular dichroism (CD) spectra and MD simulations reveal the existence of extended ssRNA conformations versus folded ssDNA conformations, consistent with their different electrical behaviors. Computational molecular modeling and Machine Learning-assisted interpretation of CD data helped us to disentangle the structural and electronic factors underlying CT, thus explaining the observed electrical behavior differences. RNA with a measurable conductance corresponds to sequences with overall extended base-stacking stabilized conformations characterized by lower HOMO energy levels delocalized over a base-stacking mediating CT pathway. In contrast, DNA and a control RNA sequence without significant base-stacking tend to form closed structures and thus are incapable of efficient CT.

Immunoinformatics-Driven Strategies for Advancing Epitope-Based Vaccine Design for West Nile Virus

The West Nile virus (WNV) is the causative agent of West Nile disease (WND), which poses a potential risk of meningitis or encephalitis. The aim of the study was to design an epitope-based vaccine for WNV by utilizing computational analyses. The epitope-based vaccine design process encompassed WNV sequence collection, phylogenetic tree construction, and sequence alignment. Computational models identified B-cell and T-cell epitopes, followed by immunological property analysis. Epitopes were then modeled and docked with B-cell receptors, MHC I, and MHC II. Molecular dynamics simulations further explored dynamic interactions between epitopes and receptors. The findings indicated that the B-cell epitope QINHHWHKSGSSIG, along with three T-cell epitopes (FLVHREWFM for MHC I, NPFVSVATANAKVLI for MHC II, and NAYYVMTVGTKTFLV for MHC II), successfully passed the immunological evaluations. These four epitopes were further subjected to docking and molecular dynamics simulation studies. Although each demonstrated favorable affinities with their respective receptors, only NAYYVMTVGTKTFLV displayed a stable interaction with MHC II during MDS analysis, hence emerging as a potential candidate for a WNV epitope-based vaccine. This study demonstrates a comprehensive approach to epitope vaccine design, combining computational analyses, molecular modeling, and simulation techniques to identify potential vaccine candidates for WNV.

Assessment of intermolecular interaction of mefenamic acid (Form II) in acetone and dimethylformamide (DMF) solution using molecular modelling technique

Solvent plays an important role in the solute-solvent intermolecular interactions of crystal morphology to regulate the crystal shape. Therefore, this work aims to assess the role of functional groups of solvents on the preferential sites on mefenamic acid (Form II) crystal surfaces, namely {001}, {011}, and {010} using the computational molecular modelling interactions techniques. The crystal morphology was successfully predicted as a plate-like crystal morphology using the BFDH method, and the molecular interactions of solutesolvent were assessed using the surface-docking method via Biovia Materials Studio software. The solute and solvent interactions along with surfaces used in this study disclosed that the {001} surfaces had the most negative non-bonded energy, followed by the {010} and {011} surfaces, ranging from −2036 to −2994 kcal/mol. Meanwhile, the binding energy values of acetone on all facets of interest were stronger compared to the binding energy of DMF, which possessed the binding energy of only less than −10 kcal/mol. Nevertheless, the results showed that acetone as a small molecule interacted most strongly with all facets of mefenamic acid (Form II) crystals because it could form stronger hydrogen bonds due to its ketone functional group, hence inhibited the growth of the mefenamic acid (Form II) crystal facets.

Synthesis, DFT, in silico anticancer, ADME and toxicity prediction study of (E)-2-(2-(3,4-dihydronaphthalen-1(2H)- ylidene)hydrazineyl)-4-(4-methoxyphenyl)thiazole

In the current paper, we describe computational molecular modeling to investigate the quantum chemical, spectroscopic, MESP and in-silico Anticancer, ADME and toxicity study of (E)-2-(2-(3,4-dihydronaphthalen-1(2H)-ylidene)hydrazineyl)-4-(4-methoxyphenyl)thiazole by one pot three component reaction. DFT method with B3LYP/6-311G(d,p) level was used to optimize the geometry, molecular electrostatic potential (MESP), Mulliken charges and vibrational assignments. The UV-Vis assignments, frontier molecular orbital (FMO), electronic parameters, and global descriptor were studied using the TD-DFT method with CAM-B3LYP/6-311G(d,p) level. In-silico anticancer study revealed favorable binding interaction with an excellent docking score comparable to the anticancer drug Dasatinib. The molecular docking study found that, target 4xt2 receptor’s amino acid residues VAL422B, LEU407D, MET426D, TYR327A, GLN421B, SER424B, and LEU423D play a vital role. The title compound has the requisite toxicity and ADME profiles, and it has the potential to be therapeutic.

Antcin-B, a phytosterol-like compound from Taiwanofungus camphoratus inhibits SARS-CoV-2 3-chymotrypsin-like protease (3CLPro) activity in silico and in vitro

Despite the remarkable development of highly effective vaccines, including mRNA-based vaccines, within a limited timeframe, coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is not been entirely eradicated. Thus, it is crucial to identify new effective anti-3CLPro compounds, pivotal for the replication of SARS-CoV-2. Here, we identified an antcin-B phytosterol-like compound from Taiwanofungus camphoratus that targets 3CLPro activity. MTT assay and ADMET prediction are employed for assessing potential cytotoxicity. Computational molecular modeling was used to screen various antcins and non-antcins for binding affinity and interaction type with 3CLPro. Further, these compounds were subjected to study their inhibitory effects on 3CLPro activity in vitro. Our results indicate that antcin-B has the best binding affinity by contacting residues like Leu141, Asn142, Glu166, and His163 via hydrogen bond and salt bridge and significantly inhibits 3CLPro activity, surpassing the positive control compound (GC376). The 100 ns molecular dynamics simulation studies showed that antcin-B formed consistent, long-lasting water bridges with Glu166 for their inhibitory activity. In summary, antcin-B could be useful to develop therapeutically viable drugs to inhibit SARS-CoV-2 replication alone or in combination with medications specific to other SARS-CoV-2 viral targets.

Hybrid polysilane–tryptophan nanostructures with enhanced fluorescence properties through FRET mechanism

Self-assembly is a versatile approach to develop novel composite materials with unique properties. The present report describes the preparation and properties of a self-assembled hybrid material composed of tryptophan and poly[diphenyl-co-methyl(H)]silane. A modified co-precipitation method was used to obtain a stable dispersion of tryptophan–polysilane nano-aggregates with distinct internal structure and morphology. Computational molecular modeling indicates that polysilane and tryptophan can aggregate through non-covalent bonding. A combination of dedicated techniques such as FT-IR, DLS, TEM, EDX and SAED was used to characterize the composition, size, and shape of the aggregates. These aggregates have regularly shaped structures, and consist of a predominantly amino acid-containing core surrounded by a polymer layer, suggesting that the self-assembly mechanism is controlled by the template action of tryptophan. Steady-state spectroscopy of the aggregates in solution confirmed that the proximity of the components allows an efficient Förster resonance energy transfer (FRET). This study provides a valuable insight into the self-assembly mechanism of tryptophan with polysilane and opens up new possibilities for the design of novel functional materials.

Visible Light-Prompted Regioselective Synthesis of Novel 5-Aroyl/hetaroyl-2',4-dimethyl-2,4'-bithiazoles as DNA- and BSA-Targeting Agents.

Organic transformations mediated by visible light have gained popularity in recent years as they are green, renewable, inexpensive, and clean and yield excellent products. The present study describes cyclo-condensation of 2-methylthiazole-4-carbothioamide with differently substituted α-bromo-1,3-diketones achieved by utilizing a white light-emitting diode (LED) (9W) to accomplish the regioselective synthesis of novel 5-aroyl/hetaroyl-2',4-dimethyl-2,4'-bithiazole derivatives as DNA/bovine serum albumin (BSA)-targeting agents. The structure characterization of the exact regioisomer was achieved unequivocally by heteronuclear two-dimensional nuclear magnetic resonance (2D-NMR) spectroscopy [1H-13C] HMBC; [1H-13C] HMQC; and [1H-15N] HMBC. In silico toxicity studies indicated that the synthesized compounds exhibit low toxicity risks and adhere to the rules of oral bioavailability without any exception. Computational molecular modeling of the bithiazole derivatives with the dodecamer sequence of the DNA duplex and BSA identified 5-(4-chlorobenzoyl)-2',4-dimethyl-2,4'-bithiazole 7g as the most suitable derivative that can interact effectively with these biomolecules. Furthermore, theoretical results concurred with the ex vivo binding mode of the 7g with calf thymus DNA (ct-DNA) and BSA through a variety of spectroscopic techniques, viz., ultraviolet-visible (UV-visible), circular dichroism (CD), steady-state fluorescence, and competitive displacement assay, along with viscosity measurements.

Adsorption behavior, different green solvent effect and surface enhanced Raman spectra (SERS) investigation on inhibition of SARS-CoV-2 by antineoplastic drug Carmofur with silver/gold/platinum loaded silica nanocomposites: A combined computational analysis and molecular modelling approach

In recent times, extensive research has been carried out to uncover effective drug treatments for coronavirus disease (COVID-19). The Carmofur (HCFU) molecule is primarily known for its antineoplastic properties and its use in cancer treatment. Nowadays, the antineoplastic drug Carmofur has shown its effectiveness in inhibiting the SARS-CoV-2 virus. The primary objective of this article is to utilize theoretical knowledge to explore the absorption mechanism and interaction between the HCFU molecule and the noble metal (Ag/Au/Pt)-loaded silica nanocomposites (HCFU + Ag/Au/Pt…SiO2). The optimized geometry, frequency, and intensity of the vibrational bands of the HCFU molecule and its complexes were obtained from the DFT method with the LANL2DZ basis set. The SERS technique was carried out to explore the adsorption of HCFU molecule with metal (Ag/Au/Pt)-loaded silica nanocomposites. The chemical reactivity and the charge distribution within the molecule were analysed with the help of HOMO-LUMO, Molecular Electrostatic Potential (MEP), Electron Localized Function (ELF), and Localized Orbital Locator (LOL) studies. The polar protic (ethanol, methanol, and water) and polar aprotic (DMSO) solvents were used to analyse the UV–Visible spectra of the molecules using the TD-DFT method. The drug-likeness properties of the molecules were calculated utilizing Lipinski’s rule, and finally, the molecular docking prediction was carried out for the Carmofur (HCFU) and its complexes with the selected proteins.