Synthetic heparan sulfate standards and machine learning facilitate the development of solid-state nanopore analysis.

The application of solid-state (SS) nanopore devices to single-molecule nucleic acid sequencing has been challenging. Thus, the early successes in applying SS nanopore devices to the more difficult class of biopolymer, glycosaminoglycans (GAGs), have been surprising, motivating us to examine the potential use of an SS nanopore to analyze synthetic heparan sulfate GAG chains of controlled composition and sequence prepared through a promising, recently developed chemoenzymatic route. A minimal representation of the nanopore data, using only signal magnitude and duration, revealed, by eye and image recognition algorithms, clear differences between the signals generated by four synthetic GAGs. By subsequent machine learning, it was possible to determine disaccharide and even monosaccharide composition of these four synthetic GAGs using as few as 500 events, corresponding to a zeptomole of sample. These data suggest that ultrasensitive GAG analysis may be possible using SS nanopore detection and well-characterized molecular training sets.

Enzymatic Polymerization of Poly(glycerol-1,8-octanediol-sebacate): Versatile Poly(glycerol sebacate) Analogues that Form Monocomponent Biodegradable Fiber Scaffolds.

A family of poly(glycerol sebacate) (PGS) analogues were synthesized by Candida antarctica lipase B (CALB) catalysis to tailor biomaterial properties. Different fractions of glycerol (G) units in PGS were replaced by 1,8-octanediol (O) units. Poly(glycerol-1,8-octanediol-sebacate), PGOS, synthesized by CALB catalysis with a 1:3 molar ratio of G to O units has Mn and Mw values of 9500 and 92,000, respectively. PGS undergoes fiber fusion during electrospinning, and cross-linked PGS rapidly resorbs when implanted. By decreasing the molar ratio of glycerol-to-octanediol from 1:1 to 1:4, the peak melting temperature (Tm) increased from 27 to 47 °C. PGOS with 1:3 G to O units was electrospun into nanofibers without the need for a second component. The copolymer is semicrystalline and, when cross-linked, undergoes slow in vitro mass loss (3.5 ± 1.0% in 31 days) at pH 7.4 and 37 °C. Furthermore, PGOS cross-linked films have an elastic modulus of 106.1 ± 18.6 MPa, which is more than 100 times that of cross-linked PGS. New PGOS polymers showed tunable molecular weights, better thermal properties, and excellent electrospinnability. This work expanded PGS analogues' function, making these suitable biodegradable polymers for various biomedical applications.

Hybrid heterogeneous phantoms for biomedical applications: a demonstration to dosimetry validation.

Phantoms simultaneously mimicking anatomical and optical properties of real tissues can play a pivotal role for improving dosimetry algorithms. The aim of the paper is to design and develop a hybrid phantom model that builds up on the strengths of solid and liquid phantoms for mimicking various anatomical structures for prostate cancer photodynamic therapy (PDT) dosimetry validation. The model comprises of a photosensitizer-embedded gelatin lesion within a liquid Intralipid prostate shape that is surrounded by a solid silicone outer shell. The hybrid phantom was well characterized for optical properties. The final assembled phantom was also evaluated for fluorescence tomographic reconstruction in conjunction with SpectraCure's IDOSE software. The developed model can lead to advancements in dosimetric evaluations. This would improve PDT outlook as a clinical treatment modality and boost phantom based standardization of biophotonic devices globally.

In silico screening of herbal phytochemicals to develop a Rasayana for immunity against Nipah virus.

BACKGROUND: The first emergence of the Nipah virus (NiV) in 1998 from Malaysia became a major concern when it came to light and resurfaced on different occasions thereafter. NiV is a bat-borne zoonotic and pleomorphic virus that causes severe infection in human and animal hosts. Studies revealed fruit bats are the major reservoirs as natural hosts and pigs as intermediate hosts for the spread of this infection. This became a major concern as the disease was characterized by high pathogenicity varying from 40% to 80% depending on its acuteness. Moreover, the solemnity lies in the fact that the infection transcends from being a mere mild illness to an acute respiratory infection leading to fatal encephalitis with a reportedly high mortality rate. Currently, there is no treatment or vaccine available against the NiV. Many antiviral drugs have been explored and developed but with limited efficacy. METHODOLOGY: In search of high-affinity ayurvedic alternatives, we conducted a pan-proteome in silico exploration of the NiV proteins for their interaction with the best-suited phytoconstituents. The toxicity prediction of thirty phytochemicals based on their LD50 value identified thirteen potential candidates. Molecular docking studies of those thirteen phytochemicals with five important NiV proteins identified Tanshinone I as the potential compound with a high binding affinity. RESULTS: The pharmacokinetics and pharmacodynamics studies also aided in determining the absorption, distribution, metabolism, excretion, and toxicity of the selected phytoconstituent. Interestingly, docking studies also revealed Rosmariquinone as a potent alternative to the antiviral drug Remdesivir binding the same pocket of RNA-dependent RNA polymerase of the NiV. A molecular dynamics simulation study of the surface glycoprotein of NiV against Tanshinone I showed a stable complex formation and significant allosteric changes in the protein structure, implying that these phytochemicals could be a natural alternative to synthetic drugs against NiV. CONCLUSION: This study provides preliminary evidence based on in silico analysis that the herbal molecules showed an effect against NiV. However, it is essential to further evaluate the efficacy of this approach through cell-based experiments, organoid models, and eventually clinical trials.

Exploring the pharmacological aspects of natural phytochemicals against SARS-CoV-2 Nsp14 through an in silico approach.

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), possesses an important bifunctional nonstructural protein (nsp14) with a C-terminal N7-methyltransferase (N7-MTase) domain and an N-terminal domain with exoribonuclease (ExoN) activity that is required for maintaining high-fidelity viral replication. Viruses use the error-prone replication mechanism, which results in high mutation rates, to adapt quickly to stressful situations. The efficiency with which nsp14 removes mismatched nucleotides due to the presence of ExoN activity protects viruses from mutagenesis. We investigated the pharmacological role of the phytochemicals (Baicalein, Bavachinin, Emodin, Kazinol F, Lycorine, Sinigrin, Procyanidin A2, Tanshinone IIA, Tanshinone IIB, Tomentin A, and Tomentin E) against the highly conserved nsp14 protein using docking-based computational analyses in search of new potential natural drug targets. The selected eleven phytochemicals failed to bind the active site of N7-Mtase in the global docking study, while the local docking study identified the top five phytochemicals with high binding energy scores ranging from - 9.0 to - 6.4 kcal/mol. Procyanidin A2 and Tomentin A showed the highest docking score of - 9.0 and - 8.1 kcal/mol, respectively. Local docking of isoform variants was also conducted, yielding the top five phytochemicals, with Procyanidin A1 having the highest binding energy value of - 9.1 kcal/mol. The phytochemicals were later tested for pharmacokinetics and pharmacodynamics analysis for Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) which resulted in choosing Tomentin A as a potential candidate. The molecular dynamics simulations studies of nsp14 revealed significant conformational changes upon complex formation with the identified compound, implying that these phytochemicals could be used as safe nutraceuticals which will impart long-term immunological competence in the human population against CoVs. Supplementary Information: The online version contains supplementary material available at 10.1007/s40203-023-00143-7.

Antimicrobial effects of positively charged, conductive electrospun polymer fibers.

In recent years, electrospun polymer fibers have gained attention for various antibacterial applications. In this work, the effect of positively charged polymer fiber mats as antibacterial gauze is studied using electrospun poly(caprolactone) and polyaniline nanofibers. Chloroxylenol, an established anti-microbial agent is used for the first time as a secondary dopant to polyaniline during the electrospinning process to make the surface of the polyaniline fiber positively charged. Both Gram-positive Staphylococcus aureus and Gram-negative Escherichia coli are used to investigate the antibacterial activity of the positively charged and uncharged polymer surfaces. The results surprisingly show that the polyaniline surface can inhibit the growth of both bacteria even when chloroxylenol is used below its minimum inhibitory concentration. This study provides new insights allowing the better understanding of dopant-based, intrinsically conducting polymer surfaces for use as antibacterial fiber mats.

High-Conductivity and High-Capacitance Electrospun Fibers for Supercapacitor Applications.

Electrospinning is a simple method for producing nanoscale or microscale fibers from a wide variety of materials. Intrinsically conductive polymers (ICPs), such as polyaniline (PANI), show higher conductivities with the use of secondary dopants like m-cresol. However, due to the low volatility of most secondary dopants, it has not been possible to electrospin secondary doped ICP fibers. In this work, the concept of secondary doping has been applied for the first time to electrospun fibers. Using a novel design for rotating drum electrospinning, fibers were efficiently and reliably produced from a mixture of low- and high-volatility solvents. The conductivity of electrospun PANI-poly(ethylene oxide) (PEO) fibers prepared was 1.73 S/cm, two orders of magnitude higher than the average value reported in the literature. These conductive fibers were tested as electrodes for supercapacitors and were shown to have a specific capacitance as high as 3121 F/g at 0.1 A/g, the highest value reported, thus far, for PANI-PEO electrospun fibers.

Optoelectronic, femtosecond nonlinear optical properties and excited state dynamics of a triphenyl imidazole induced phthalocyanine derivative.

A novel zinc phthalocyanine derivative [2(3), 9(10), 16(17), 23(24) tetrakis-4-((4-(1,4,5-triphenyl-1H-imidazol-2-yl)phenyl)ethynyl)phthalocyanine zinc(ii) (PBIPC)] was synthesized by incorporating a triphenyl imidazole moiety at its peripheral positions. The detailed mechanisms of absorption, emission, electrochemical, nonlinear optical (NLO) and photophysical (excited state dynamics) properties of PBIPC were explored. The absorption and emission properties of the compound were studied in different solvents. The incorporation of a triphenyl imidazole moiety at the peripheral position of the zinc phthalocyanine slightly broadened the Soret band. The emission studies revealed fluorescence quantum yields to be in the range of 0.11-0.22. The time-resolved fluorescence data established the radiative lifetimes to be in the nanosecond range. The oxidation and reduction processes were found to be ring centered, which were studied using the cyclic voltammetry (CV) technique. The energy optimized structures and HOMO-LUMO levels were calculated using DFT, TD-DFT analysis and were employed by means of hybrid functional theory (B3LYP) at 6-31G (d,p) basis set in the Gaussian 09 package. Two-photon absorption was observed in the NLO studies performed in the visible wavelength range of 600-800 nm while the nonlinear absorption was dominated by three- and four-photon absorption processes in the NIR wavelength range (1.0-1.5 µm). The molecule exhibited self-focusing behavior for all the wavelengths. Finally, the excited state dynamics of the title molecule PBIPC were investigated using femtosecond transient absorption spectroscopy and the results obtained were understood on the basis of a simple three kinetic model, for excitation wavelengths of 400 nm (Soret band) and 650 nm (Q-band). Both the spectra demonstrated a broad positive transient absorption (TA) data which overlapped with the ground state bleach (GSB), which in turn displayed a red shift over a delay of ∼2 ns. The lifetimes revealed a possibility of intersystem crossing (τ > 1 ns) owing to the triplet state transition.