DFT, molecular docking and molecular dynamics simulation studies on some recent natural products revealing their EGFR tyrosine kinase inhibition potential

Phytochemicals are important chemical compounds in pharmaceutical chemistry. These natural compounds have interesting biological activities, including anticancer, as well as many other functions. EGFR (epidermal growth factor receptor) tyrosine kinase inhibition is emerging as one of the accepted methods in the treatment of cancer. On the other hand, computer-aided drug design has become an increasingly important field of study due to its many important advantages such as efficient use of time and other resources. In this study, fourteen phytochemicals which have triterpenoid structure and have recently entered the literature were investigated computationally for their potential as EGFR tyrosine kinase inhibitors. In the study, DFT (density functional theory) calculations, molecular docking, molecular dynamics simulations, binding free energy calculations with the use of MM-PBSA (molecular mechanics Poisson-Boltzmann Surface Area) method, and ADMET predictions were performed. The obtained results were compared to the results obtained for reference drug Gefitinib. Results showed that the investigated natural compounds are promising structures for EGFR tyrosine kinase inhibition.Communicated by Ramaswamy H. Sarma.

Controlled synthesis and computational analysis of gold nanostars for the treatment of Fusarium oxysporum

Fusarium oxysporum (F. oxysporum) is linked to the widespread fusarium wilt in plants affecting the quality and yield of food crops. Management of fusarium wilt by synthetic fertilizers poses safety concerns. Safer-by-design nanomaterials synthesized with a greener approach can meet the needs of commercial antifungal drug resistance. Herein, a simple aqueous reduction method has been adopted for the synthesis of anisotropic gold nanostars (AuNSs) using quercetin-para aminobenzoic acid (QPABA) as both a reducing and stabilizing agent at room temperature for the treatment of F. oxysporum. QPABA was used to control the growth of Au³⁺ star-shaped nanoparticles at increasing concentrations in the ratio of 2 : 1 (QPABA : Au³⁺ ions) respectively. Transmission electron microscopy (TEM) analysis of the as-prepared gold nanoparticles confirmed the formation of nanostars with sizes of 40 ± 2 nm. The formation of anisotropic gold nanoparticles was evaluated by UV-vis characterizations which showed longitudinal surface plasmon modes at 540 and 800 nm. The gold nanoparticles exhibit excellent antifungal activity against F. oxysporum with the minimum inhibitory concentration (MIC) of 100 μg mL^-1 using an agar well-diffusion assay. AuNSs proved to be efficacious in controlling F. oxysporum, as shown in the SEM analysis with a disintegrated cell membrane upon treatment. Computational analysis was performed to determine the specific binding sites on the QPABA ligand for gold ion interactions using the DFT B3LYP method, with a 6-31+G(d) basis set. Results showed that the interaction between Au³⁺ and QPABA at the 4 and 3 positions yielded the highest stability and formation of gold nanostars. The results suggest that the synthesized AuNSs act as a promising antifungal agent with great potential in treating frequent fungal infections that affect agricultural production.

Probing some recent natural compounds from Phellinus baumii, Colletotrichum sp. and Ligustrum lucidum as heat shock protein 90 inhibitors

Heat shock protein 90 (HSP90) is one of the most attractive targets for research on cancer treatment, and nowadays, many studies carried out for the development of effective HSP90 inhibitors. In the current study, recently published ten natural compounds have been investigated using computer aided drug design (CADD) approach. The study consists of three parts; (1) density functional theory (DFT) calculations including geometry optimizations, vibrational analyses, and molecular electrostatic potential (MEP) map calculations, (2) molecular docking and molecular dynamics (MD) simulations, and (3) binding energy calculations. In DFT calculations, Becke three-parameter hybrid functional with Lee-Yang-Parr correlation functional (B3LYP) and 6-31 + G(d,p) basis set were used. After performing molecular docking calculations, top-scoring ligand-receptor complexes were subjected to MD simulations for 100 ns to investigate the stability of the ligand-receptor complexes and the interactions in more detail. Finally, in binding energy calculations molecular mechanics with Poisson-Boltzmann surface area (MM-PBSA) method was used. The results showed that five of the investigated ten natural compounds have higher binding affinity to HSP90α than that of reference drug Geldanamycin, and could be promising compounds for future studies.Communicated by Ramaswamy H. Sarma.

In-silico investigation of some recent natural compounds for their potential use against SARS-CoV-2: a DFT, molecular docking and molecular dynamics study

Since its first appearance in December 2019, SARS-CoV-2 has infected many people all over the world, causing serious health problems in many people and causing many deaths, but no specific drug has been developed yet. SARS-CoV-2 main protease (SARS-CoV-2 M^pro) has an important role in viral replication and transcription, so inhibition of this enzyme is proposed to be an attractive route for the treatment of COVID-19. Natural compounds have been used in the treatment of many diseases throughout the history. In this study, it was aimed to investigate SARS-CoV-2 M^pro inhibition abilities, thus the therapeutic potentials of some novel phytochemicals which have recently been entered the literature. For this purpose, eleven novel phytochemicals obtained from various natural resources have been investigated for their potential antiviral activity against SARS-CoV-2 with the use of in silico methods. In the first part of the study, DFT (density functional theory) calculations were performed on the investigated compounds. In this part, geometry optimizations, vibrational analyses, and MEP (molecular electrostatic potential) map calculations were performed. In the second part, molecular docking calculations and then molecular dynamics (MD) simulations were performed to investigate how these natural compounds interact with SARS-CoV-2 M^pro which is a promising target for COVID-19 treatments. In this part, MM-PBSA (molecular mechanics with Poisson-Boltzmann surface area) calculations were also performed to determine the binding free energies of the investigated compounds. Results showed that most of the investigated compounds interacted with SARS-CoV-2 M^pro effectively and can be promising structures for drug development studies for COVID-19.Communicated by Ramaswamy H. Sarma.

DFT, molecular docking and molecular dynamics simulation studies on some newly introduced natural products for their potential use against SARS-CoV-2

Throughout the history, natural products always give new paths to develop new drugs. As with many other diseases, natural compounds can be helpful in the treatment of COVID-19. SARS-CoV-2 main protease enzyme has an important role in viral replication and transcription. Therefore, inhibiting this enzyme may be helpful in the treatment of COVID-19. In this study, it is aimed to investigate eight natural compounds which have recently entered the literature, computationally for their potential use against SARS-CoV-2. For this purpose, first, density functional theory (DFT) calculations were performed on the investigated compounds, and energy minimizations, geometry optimizations, vibrational analyses, molecular electrostatic potential map calculations were carried out. After DFT calculations, geometry optimized structures were subjected to molecular docking calculations with the use of SARS-CoV-2 main protease (pdb id: 5r80) and top-scoring ligand-receptor complexes were obtained. In the next part of the study, molecular dynamics (MD) simulations were performed on the top-scoring ligand-receptor complexes to investigate the stability of the ligand-receptor complexes and the interactions between ligands and receptor in more detail. Additionally, in this part of the study, binding free energies are calculated with the use of molecular mechanics with Poisson-Boltzmann surface area (MM-PBSA) method. Results showed that, all ligand-receptor complexes remain stable during the MD simulations and most of the investigated compounds but especially two of them showed considerably high binding affinity to SARS-CoV-2 main protease. Finally, in the study, ADME (adsorption, desorption, metabolism, excretion) predictions and drug-likeness analyses were performed on the investigated compounds.

Aspirin 300 mg/day is effective for treating aspirin-exacerbated respiratory disease

BACKGROUND

Aspirin desensitization (AD) treatment at doses of up to 1300 mg/day improves outcomes in aspirin-exacerbated respiratory disease (AERD). The aim of this study was to investigate the efficacy of aspirin 300 mg/day in the treatment of patients with AERD.

METHODS

The study included 40 patients diagnosed in our clinic as AERD that were desensitized and treated with aspirin 300 mg/day between December 2005 and December 2012. Changes from the baseline status were analyzed at 1 year and at 3 years of follow-up.

RESULTS

Of the 40 patients included, 24 (60%) were female and median (interquartile range [IQR]) age was 45 (40-51) years. Median (IQR) duration of AD was 31.5 (10.5-48.5) months. In total, 29 patients continued treatment for at least 1 year and 18 patients for at least 3 years. The annual rate of use of systemic corticosteroid regimens, episodes of sinusitis, and surgery was significantly lower both at 1 year (P = 0.002, P = 0.01, and P < 0.001, respectively) and at 3 years (P = 0.001, P = 0.03, and P = 0.002, respectively). Significant improvement was observed in the nasal congestion score (P = 0.01) and sense of smell score (P = 0.05) at 1 year and in the postnasal drainage score (P = 0.01) at 3 years.

CONCLUSION

Daily treatment with aspirin 300 mg had beneficial effects in patients with AERD, especially for the control of upper airway disease.

Comparision of inflammatory biomarkers for detection of coronary stenosis in patients with stable coronary artery disease

BACKGROUND

The objective of the current study was to evaluate the role of various inflammatory biomarkers in detection of coronary stenosis in patients with stable coronary artery disease (CAD) and healthy people.

METHODS

A total of 111 patients with stable coronary artery disease, and 66 healthy subjects were enrolled in the study. Serum levels of lipoprotein-associated-phospholipase A2 (Lp-PLA2), high-sensitivity C-reactive protein (hs-CRP), and myeloperoxidase (MPO) were measured to compare patient and control groups.

RESULTS

Baseline characteristics were similar between healthy and patient groups, with the exception of age. ANCOVA and log-transformed data of inflammatory biomarkers revealed that, Lp-PLA2 (p < 0.001) and hs-CRP (p < 0.05) levels in all patient groups were significantly higher than in the control group. Conversely, there was no significant difference in MPO levels among groups.

CONCLUSIONS

In stable CAD patients, serum Lp-PLA2 levels are more compatible than hs-CRP and MPO levels in the detection of coronary stenosis.      

Recurrent parotitis as a first manifestation in a child with primary Sjogren's syndrome

Recurrent parotitis is an acute, severe inflammation of one or both parotid glands, the major salivary glands in young children. We report the case of a seven-year old boy with Primary Sjogrens syndrome (PSS) who presented with 15 episodes of painful recurrent bilateral swellings of the parotid glands over a four-year period.

Determination of preferred walking speed on treadmill may lead to high oxygen cost on treadmill walking

The energy consumption of walking relates to the intensity of physical effort and can be affected by the alterations in walking speed. Therefore, walking speed can be accepted as a crucial, determinant of energy consumption measurement for a walking test. We aimed to investigate the differences in preferred walking speed (PWS) determined both on overground and on a treadmill and, to measure walking energy expenditure and spatio-temporal parameters of gait on a treadmill at both, speeds. Participants (n=26) walked on a treadmill at two pre-determined speeds for 7 min while, indirect calorimetry measurements were being performed. Spatio-temporal parameters were collected, by video-taping during each walking session on a treadmill. The average overground preferred walking speed (O-PWS) was 85.96+/-12.82 m/min and the average treadmill preferred walking speed (T-PWS), was 71.15+/-13.85 m/min. Although T-PWS was lower, oxygen cost was statistically higher when, treadmill walking at T-PWS (0.158+/-0.02 ml/kg/m) than when the treadmill walking at O-PWS, (0.1480+/-0.02 ml/kg/m). Cadence (127+/-9.13 steps/min), stride (134.02+/-14.09 cm) and step length (67.02+/-6.90 cm) on the treadmill walking at O-PWS were significantly higher than cadence (119+/-10 steps/min), stride (117.96+/-14.38 cm) and step length (59.13+/-7.02 cm) on the treadmill walking at TPWS. In conclusion, walking on treadmill using O-PWS is more efficient than walking on treadmill using TPWS, in walking tests. Since using T-PWS for treadmill walking tests overestimates the oxygen cost of walking, O-PWS should be used for oxygen consumption measurement during treadmill walking tests.

Synthesis of thick optical thin-film filters with a layer-peeling inverse-scattering algorithm

We present an efficient and accurate method for synthesis of optical thin-film structures. The method is based on a differential inverse-scattering algorithm and considers therefore both phase and amplitude reflectance data. We apply the algorithm to the synthesis of filters with arbitrary index layers and two-material filters consisting of only high- and low-index layers. The layered structure is approximated by a stack of discrete reflectors with equal distance between all reflectors. This mirror stack is in turn determined from the desired, complex reflection spectrum by a layer-peeling inverse-scattering algorithm. The complexity of the design algorithm is approximately the same as that of the forward problem of computing the spectrum from a known structure.

Fiber mode conversion with tilted gratings in an optical fiber

The mode coupling in double-sided tilted gratings between the LP01 and LP11 modes is analyzed for three different excitation conditions. It is found that a number of modes, including various LP11q modes with different polarization states and TE01, TM01, and HE21 modes, can be formed through the mode conversion process in the gratings and with a linear combination of four different LP11 modes. Efficient single-sided and double-sided tilted gratings are demonstrated. The tilted gratings presented exhibit LP01-to-LP11 mode coupling over a spectral width as wide as 160 nm. The transmission spectra of the tilted fiber gratings agree well with the spectrum predicted by the coupled-mode analysis.

Analysis of fiber bragg gratings by a side-diffraction interference technique

A new nondestructive, noncontact, and sensitive technique for fiber Bragg grating geometry and index-fault location measurements is presented. Two plane-wave probe laser beams are incident upon the grating from the side at angles that satisfy the Bragg-reflection condition. An interference pattern is formed behind the fiber between the first-order diffracted beam (from one probe beam) and the zero-order transmitted beam (from the second probe beam). The axial grating index modulation and the grating period are functions of the fringe visibility and the fringe period, respectively. The method is sensitive and is applicable even in the case of relatively weak gratings. Unchirped and chirped Bragg gratings have been studied with the proposed technique. We demonstrate accuracies of 1 x 10(-4) for measurement of the index modulation and 0.01 nm for measurement of the period. As well as for the analysis of most already-fabricated gratings, this technique is useful for in situ analysis of a long fiber Bragg grating as such a grating is translated along its axis during the fabrication process.

Solgel-derived photosensitive germanosilicate glass monoliths

We demonstrate volume gratings written in solgel-derived, Ge-doped silica monoliths. Glass was fabricated both with and without germanium oxygen deficient center (GODC) defects. The UV absorption and UV-induced index changes of these glasses, with and without hydrogen loading, are reported. The presence of GODC defects greatly enhances the photosensitivity of Ge-doped silica with and without the presence of hydrogen.

Fiber mode coupling in transmissive and reflective tilted fiber gratings

Whereas core-mode reflection and core-mode-to-radiation-mode coupling in tilted fiber Bragg gratings is well understood, as is coupling between a core mode and higher-order core and cladding modes in untilted gratings, here we analyze in detail the coupling among core modes and cladding modes in reflective and transmissive tilted fiber gratings. We show that strong coupling between an LP(01) core mode and the exact (1m) cladding modes occurs in a transmissive tilted grating for nearly any tilt angle except angles close to 90 degrees, whereas the LP(01)-to-(lm) cladding mode coupling (l not equal 1) is appreciable only for tilt angles just below 90 degrees (approximately 88 degrees). In a reflective grating, strong coupling between the LP(01) core mode and the exact (1m) cladding modes occurs only for angles less than approximately 5 degrees, whereas coupling to (1m) cladding modes for m > 1 occurs only for angles greater than approximately 5 degrees. Coupling among bound core modes exhibits a similar behavior, except that in general the coupling is stronger. Experimentally we show coupling to both higher-order bound core modes and cladding modes in a transmissive tilted grating at visible and near-infrared wavelengths.

Dispersion control with use of long-period fiber gratings

Chirped long-period fiber gratings are analyzed for management of dispersion in optical fiber communications systems. A ray model is used to derive simple analytic expressions that describe the transmission, chromatic delay, and dispersion properties of chirped long-period fiber gratings. A numerical model based on coupled-mode theory is used to verify the accuracy of the analytic expressions and explore design issues of the chirped long-period grating. With certain reasonable restrictions, chirped long-period gratings are found to be a viable and desirable alternative to existing dispersion compensation techniques.

All-fiber wavemeter and Fourier-transform spectrometer

An all-fiber Fourier-transform spectrometer is proposed and demonstrated, based on the diffraction of light through the side of a standard optical fiber by a UV-induced fiber grating. The interference pattern, whose Fourier transform yields the optical spectrum, is formed by light diffracted from counterpropagating modes in the fiber. The device is simple and compact and functions as a wavemeter, a fiber-optic network monitor, or a tool for fabrication and testing of long fiber Bragg gratings.

Integrated-optical Mach-Zehnder add-drop filter fabricated by a single UV-induced grating exposure

A four-port bandpass filter is demonstrated with good performance by use of UV-induced Bragg gratings in P-doped channel waveguides without UV trimming. The simple, single-step fabrication procedure is experimentally and theoretically analyzed, and tolerances are calculated for achieving practical wavelength-division-multiplexed communication system performance.

Volume gratings for holographic storage applications written in high-quality germanosilicate glass

Volume holographic gratings are written with ultraviolet light in high-optical-quality, commercially available Ge-doped silica films and in Ge-doped optical-fiber preform sections loaded with molecular hydrogen. In the film samples, peak refractive-index changes exceeding 10(-2) and a sensitivity (index change/absorbed energy density) of 0.4 × 10(-7) cm(3)/J are measured. Angular multiplexing of up to 51 gratings is demonstrated in the preform samples.

Radiation-mode coupling loss in tilted fiber phase gratings

We demonstrate that grating tilt is an important adjustable parameter that can be utilized in addition to the more familiar parameters of grating length and index change to tune the spectral shapes of fiber phase gratings designed to perform demanding filter applications through guided-mode to radiation-mode coupling loss. A comparison is made between calculated transmission spectra obtained from a coupled-mode-theory analysis and measured spectra obtained from strong gratings written by ultraviolet irradiation of deuterium-sensitized fiber with grating tilt angles ranging from 0 degrees to 15 degrees . We show that good agreement is obtained between the experimental measurements and the theoretical predictions.

High-power mode-locked hybrid pulse source using two-section laser diodes

We describe a mode-locked hybrid pulse source with a two-section laser diode to obtain short mode-locked pulses (23 ps) with an average power of 7.8 mW, a high peak power of 137 mW, and a repetition rate of 2.51 GHz. The hybrid laser incorporates a two-section laser and an optical fiber cavity with an integrated Bragg reflector. The Bragg reflector controls the operating wavelength to subnanometer precision and also confines the bandwidth of the pulses so as to keep the time-bandwidth product below 1.