Conformational dynamics of trypsin in the presence of caffeic acid: a spectroscopic and computational investigation.

Caffeic acid is one of the widely distributed phenolic compounds in nature and can be found in planet products. On the other hand, trypsin is a vital digestive enzyme in the intestine that plays an essential role in the immune response, blood coagulation, apoptosis and protein maturation like protein digestion. Several studies have revealed the inhibitory effects of the phenolic compound on the digestive enzyme. The present study reports functional and conformational alteration of trypsin after caffeic acid addition using multiple experimental and computational techniques for the first time. The intrinsic fluorescence of trypsin is quenched in the presence of caffeic acid via a static mechanism. The percent of secondary structures (α-helix and ß-sheet) of trypsin alter after caffeic acid addition. In the kinetic study, a reduction in the trypsin function is obtained with a lower Vmax and Kcat upon interaction with caffeic acid. The thermal study reveals an unstable structure of trypsin upon complex formation with this phenolic compound. Also, the binding sites and conformational changes of trypsin are elucidated through molecular docking and molecular dynamic simulation.Communicated by Ramaswamy H. Sarma.

The national health program for vitamin D supplementation in a developing country.

BACKGROUND: Previous studies have reported a high frequency of vitamin D deficiency (VDD) among different age groups in Iran. AIMS: In this study, the current coverage, status of vitamin D supplement taking, and program efficacy have been evaluated by the Office of Nutrition Department Society in Iran since 2014. METHODS: This study was conducted in collaboration with the International UNESCO center for Health-Related Basic Sciences and Human Nutrition and the Office of Nutrition Department Society. Sixty three medical universities were included in the current study to calculate the availability, accessibility and acceptability coverages. Furthermore, 3 medical universities including Mashhad (MUMS), Qom (QUMS) and Zahedan (ZAUMS) University of Medical Sciences were selected based on the results of the National Integrated Micronutrient Survey 2012 (NIMS-II study), in order to assess the status of vitamin D supplement intake in all age ranges. RESULTS: Quantitative analysis showed that availability coverage was 74.96% and 77.56% and accessibility was 80.70% and 83.26% in elderly and middle-aged subjects, respectively in 2018. The acceptability was approximately 43.7% and 43.9% among elderly and middle-aged participants, respectively. The availability and acceptability coverage was 80.99% and 85.0% among students in high schools. The mean vitamin D supplement uptake frequency was 27.0% (n = 387); 20.7% and 29.2% in rural and urban area, respectively (P = 0.001). The results showed that there was no significant difference in serum vitamin D levels between urban (20.41 ± 6.43 ng/ml) and rural areas, (P = 0.887). There was no significant difference in the serum vitamin D concentrations between men and women (P = 0.461). CONCLUSIONS: The frequency of taking vitamin D supplements was 27.0% in Iran in 2018. The frequency of taking of vitamin D supplements among vitamin D deficient group (serum vitamin D levels <19.99 ng/ml) was 43.6%. Lack of knowledge was the most important reason for not taking vitamin D supplement. Moreover, the serum vitamin D levels have increased in subjects aged 18-30 years old after the implementation of the vitamin D supplementary program.

The interaction mechanism of candidone with calf thymus DNA: A multi-spectroscopic and MD simulation study.

In this investigation, the effects of candidone on the structure and conformation of DNA were evaluated by spectroscopic methods, molecular dynamics simulation, and molecular docking studies. Fluorescence emission peaks, ultraviolet-visible spectra, and molecular docking exhibited the complex formation between candidone and DNA in a groove-binding mode. Fluorescence spectroscopy results also showed a static quenching mechanism of DNA in the presence of candidone. Moreover, thermodynamic parameters demonstrated that candidone spontaneously bound to DNA with a high binding affinity. The hydrophobic interactions were the dominant forces over the binding process. Based on the Fourier transform infrared data candidone tended to attach to the A-T base pairs of the minor grooves of DNA. The thermal denaturation and circular dichroism measurements displayed that candidone caused a slight change in the DNA structure, which was confirmed by the molecular dynamics simulation results. According to the obtained findings from the molecular dynamic simulation, the structural flexibility and dynamics of DNA were altered to a more extended structure.

Structural change study of pepsin in the presence of spermidine trihydrochloride: Insights from spectroscopic to molecular dynamics methods.

Spermidine is an aliphatic polyamine that directs a set of biological processes. This work aimed to use UV-Vis spectroscopy, fluorescence spectroscopy, thermal stability, kinetic methods, docking, and molecular dynamic simulations to examine the influence of spermidine trihydrochloride (SP) on the structure and function of pepsin. The results of the fluorescence emission spectra indicated that spermidine could quench pepsin's intrinsic emission in a static quenching process, resulting in the formation of the pepsin-spermidine complex. The results discovered that spermidine had a strong affinity to the pepsin structure because of its high binding constant. The obtained results from spectroscopy and molecular dynamic approaches showed the binding interaction between spermidine and pepsin, induced micro-environmental modifications around tryptophan residues that caused a change in the tertiary and secondary structure of the enzyme. FTIR analysis showed hypochromic effects in the spectra of amide I and II and redistribution of the helical structure. Moreover, the molecular dynamic (MD) and docking studies confirmed the experimental data. Both experimental and molecular dynamics simulation results clarified that electrostatic bond interactions were dominant forces.

A comprehensive insight into the effects of caffeic acid (CA) on pepsin: Multi-spectroscopy and MD simulations methods.

The interaction between caffeic acid (CA) and pepsin was investigated using multi-spectroscopy approaches and molecular dynamic simulations (MDS). The effects of CA on the structure, stability, and activity of pepsin were studied. Fluorescence emission spectra and UV-vis absorption peaks all represented the static quenching mechanism of pepsin by CA. Moreover, the fluorescence spectra displayed that the interaction of CA exposed the tryptophan chromophores of pepsin to a more hydrophilic micro-environment. Consistent with the simulation results, thermodynamic parameters revealed that CA was bound to pepsin with a high binding affinity. The Van der Waals force and Hydrogen bond interaction were the dominant driving forces during the binding process. The circular dichroism (CD) spectroscopy analysis showed that the CA binding to pepsin decreased the contents of α-Helix and Random Coil but increased the content of ß-sheet in the pepsin structure. Accordingly, MD simulations confirmed all the experimental results. As a result, CA is considered an inhibitor with adverse effects on pepsin activity.

Investigation of the interaction behavior between quercetin and pepsin by spectroscopy and MD simulation methods.

The ability of a therapeutic compound to bind to proteins is critical for characterizing its therapeutic impacts. We have selected quercetin (Qu), a most common flavonoid found in plants and vegetables among therapeutic molecules that are known to have anti-inflammatory, antioxidant, anti-genotoxic, and anti-cancer effects. The current study aimed to see how quercetin interacts with pepsin in an aqueous environment under physiological conditions. Absorbance and emission spectroscopy, circular dichroism (CD), and kinetic methods, as well as molecular dynamic (MD) simulation and docking, were applied to study the effects of Qu on the structure, dynamics, and kinetics of pepsin. Stern-Volmer (Ksv) constants were computed for the pepsin-quercetin complex at three temperatures, showing that Qu reduces enzyme emission spectra using a static quenching. With Qu binding, the Vmax and the kcat/Km values decreased. UV-vis absorption spectra, fluorescence emission spectroscopy, and CD result indicated that Qu binding to pepsin leads to microenvironmental changes around the enzyme, which can alter the enzyme's secondary structure. Therefore, quercetin caused alterations in the function and structure of pepsin. Thermodynamic parameters, MD binding, and docking simulation analysis showed that non-covalent reactions, including the hydrophobic forces, played a key role in the interaction of Qu with pepsin. The findings conclude of spectroscopic experiments were supported by molecular dynamics simulations and molecular docking results.

Identification of SARS-CoV-2 surface therapeutic targets and drugs using molecular modeling methods for inhibition of the virus entry.

Although COVID-19 emerged as a major concern to public health around the world, no licensed medication has been found as of yet to efficiently stop the virus spread and treat the infection. The SARS-CoV-2 entry into the host cell is driven by the direct interaction of the S1 domain with the ACE-2 receptor followed by conformational changes in the S2 domain, as a result of which fusion peptide is inserted into the target cell membrane, and the fusion process is mediated by the specific interactions between the heptad repeats 1 and 2 (HR1 and HR2) that form the six-helical bundle. Since blocking this interaction between HRs stops virus fusion and prevents its subsequent replication, the HRs inhibitors can be used as anti-COVID drugs. The initial drug selection is based on existing molecular databases to screen for molecules that may have a therapeutic effect on coronavirus. Based on these premises, we chose two approved drugs to investigate their interactions with the HRs (based on docking methods). To this end, molecular dynamics simulations and molecular docking were carried out to investigate the changes in the structure of the SARS-CoV-2 spike protein. Our results revealed, cefpiramide has the highest affinity to S protein, thereby revealing its potential to become an anti-COVID-19 clinical medicine. Therefore, this study offers new ways to re-use existing drugs to combat SARS-CoV-2 infection.

Malachite Green, the hazardous materials that can bind to Apo-transferrin and change the iron transfer.

Different groups of synthetic dyes might lead to environmental pollution. The binding affinity among hazardous materials with biomolecules necessitates a detailed understanding of their binding properties. Malachite Green might induce a change in the iron transfer by Apo-transferrin. Spectroscopic studies showed malachite green oxalate (MGO) could form the apo-transferrin-MGO complex and change the Accessible Surface Area (ASA) of the key amino acids for iron transfer. According to the ASA results the accessible surface area of Tyrosine, Aspartate, and Histidine of apo-transferrin significantly were changed, which can be considered as a convincing reason for changing the iron transfer. Moreover, based on the fluorescence data MGO could quench the fluorescence intensity of apo-transferrin in a static quenching mechanism. The experimental and Molecular Dynamic simulation results represented that the binding process led to micro environmental changes, around tryptophan residues and altered the tertiary structure of apo-transferrin. The Circular Dichroism (CD) spectra result represented a decrease in the amount of the α-Helix, as well as, increase in the ß-sheet volumes of the apo-transferrin structure. Moreover, FTIR spectroscopy results showed a hypochromic shift in the peaks of amide I and II. Molecular docking and MD simulation confirmed all the computational findings.

The interaction of Naphthol Yellow S (NYS) with pepsin: Insights from spectroscopic to molecular dynamics studies.

The effects of Naphthol Yellow S (NYS) on the structure and activity of pepsin were carried out using ultraviolet-visible (UV-Vis) spectroscopy, intrinsic fluorescence spectroscopy, circular dichroism (CD), thermal stability, kinetic techniques, as well as molecular docking, and Molecular dynamic simulations (MD) technique. The experimental results from fluorescence spectroscopy showed that the changes in pepsin's tertiary structure were caused by NYS binding. The apparent binding constant Ka, the number of the binding sites, and thermodynamic parameters were computed at three different temperatures. Thermodynamic results revealed that NYS interacts with pepsin spontaneously by hydrogen bond and Van der Waals forces. The result of the circular dichroism spectral suggests the secondary structural changes. An increase in the content of the ß-sheet and ß-turn structure was shown. Kinetic parameters revealed that NYS inhibited the activity of pepsin by the mixed model. The Molecular dynamic (MD) and docking simulations supported experimental findings. The main interactions between NYS and pepsin are hydrogen bonds and Van der Waals Forces. As a result, NYS could be considered as an inhibitor with adverse effects on pepsin structure and function.

The prevalence of tropia, phoria and their types in a student population in Iran.

Purpose: The aim of this study is to determine the prevalence of tropia, phoria, and their types in Islamic Azad University students in Shahrekord, Iran.Methods: Of 826 students that were invited, 752 participated in this cross-sectional study (response rate = 91.04%). After applying exclusion criteria, statistical analyses were performed on the data of 726 individuals. All participants underwent optometric tests including measurement of visual acuity, objective and subjective refraction, as well as binocular vision and ocular health examinations. The unilateral and alternate cover tests were done to detect the tropia and phoria at 6 m and 40 cm, respectively.Results: The overall prevalence and 95% confidence interval (CI) of tropia, exotropia, and esotropia were 1.5% (0.8 to 2.7), 1.2% (0.6 to 2.4), and 0.3% (0.1 to 1.1), respectively. The prevalence of esotropia was significantly higher in older age groups (24 years old) (p = .040) . The prevalence of exotropia was significantly higher in females (0.039) and in myopic individuals (p = .001). The overall prevalence and 95% CI of phoria, exophoria, and esophoria were 12.9% (10.7 to 15.6), 11.7% (9.6 to 14.3), and 1.2% (0.6 to 2.3), respectively. There was a significant difference in the overall prevalence of exophoria according to the age (0.021). The prevalence of esophoria was significantly higher in females (p = .039). The prevalence of exophoria was significantly higher in myopic participants (p = .003). Exophoria and exotropia were the most common types of phoria and tropia, respectively.Conclusion: The prevalence of strabismus in university students was similar to the Iranian general population but lower than other countries. One in every 10 students had phoria, which was much lower than similar reports on Iranian populations; however, due to near-work activity, these students are prone to asthenopia, early visual fatigue, and decreased productivity. Therefore, it is suggested that university students also undergo screening programs to detect the cases of tropia and phoria.

Accommodative insufficiency in a student population in Iran / Insuficiencia acomodativa en una población estudiantil de Irán

Purpose: To determine the prevalence of accommodative insufficiency (AI) and its relation with age, gender, and refractive errors in a college-age student population in Iran. Methods: The present study was conducted cross-sectionally in 2017. All students had optometric tests including measurement of visual acuity, objective and subjective refraction, as well as binocular vision and accommodative examinations. Amplitude of accommodation was measured with the Donders¡' push-up method using the Royal Air Force (RAF) rule. Monocular accommodative facility was measured with ±2.00 diopter flipper lenses. The accommodative response was tested using dynamic retinoscopy with the monocular estimation method (MEM). Results: The prevalence of AI in the studied population was 4.07% (95% CI: 2.61-5.52). The rate was 6.04% (95% CI: 3.58-8.50) in females and 2.01% (95% CI: 0.53-3.48) in males, and logistic regression showed a significantly higher odds of AI in females (OR = 3.14, 95% CI: 1.33-7.45, p-value = 0.009). The prevalence of AI was 2.59% (95% CI: 0.55-7.56) in the 18-19-year-old age group and 4.08% (95% CI: 0.09-8.07) in the 24-25-year-old group (p-value = 0.848). The prevalence of AI among emmetropic, myopic, and hyperopic individuals was 3.74% (95% CI: 1.88-5.61), 4.44% (95% CI: 2.07-6.81), and 5.26% (95% CI: 4.79-16.32), respectively (p-value = 0.869). In the multiple regression model, only gender showed significant relationship with AI (Odds ratio = 3.14, 95% CI: 1.33-7.45; p-values = 0.009). Conclusion: The prevalence of AI in the present study is lower than the most prevalence rates reported in previous studies. In the present study, gender and AI showed a strong association, such that AI prevalence was significantly higher in females than males

Objetivo: Determinar la prevalencia de la insuficiencia acomodativa (IA) y su relación con la edad, sexo, y errores refractivos en una población universitaria de Irán. Métodos: El presente estudio se realizó de forma transversal en 2017. Se realizaron pruebas optométricas a todos los estudiantes, incluyendo medición de la agudeza visual, refracción objetiva y subjetiva, visión binocular y pruebas de acomodación. La amplitud de acomodación se midió con el método de Donders (push-up) utilizando la regla de la RAF (Royal Air Force). La flexibilidad acomodativa monocular se midió con flippers de ± 2 dioptrías. La respuesta acomodativa se evaluó mediante retinoscopía dinámica utilizando el método de estimación monocular (MEM). Resultados: La prevalencia de IA en la población de estudiantes fue de 4,07% (95%ICI: 2,61-5,52). La tasa fue de 6,04% (95%IC: 3,58-8,5) en mujeres y 2,01% (95%IC: 0,53-3,48) en varones, y la regresión logística reflejó un odds ratio significativamente superior de IA en mujeres (OR= 3,14, 95%IC: 1,33-7,45, valor p = 0,009). La prevalencia de IA fue de 2,59% (95%IC: 0,55-7,56) en el grupo de edad de 18-19 años, y de 4,08% (95%IC: 0,09-8,07) en el grupo de 24-25 años (valor p = 0,848). La prevalencia de IA entre los individuos emetrópicos, miopes e hipermétropes fue de 3,74% (95%IC: 1,88-5,61), 4,44% (95%IC: 2,07-6,81), y 5,26% (95%IC: 4,79-16,32), respectivamente (valor p=0,869). En el modelo de regresión múltiple, únicamente el sexo reflejó una relación con IA (Odds ratio = 3,14 95%IC: 1,33-7,45; valor p= 0,009). Conclusión: La prevalencia de IA en el presente estudio es inferior a la mayoría de las tasas de prevalencia reportadas en estudios previos. En el presente estudio, sexo e IA reflejaron una fuerte asociación, en el sentido de que la prevalencia de IA fue significativamente superior en las mujeres con respecto a los varones

Accommodative insufficiency in a student population in Iran.

PURPOSE: To determine the prevalence of accommodative insufficiency (AI) and its relation with age, gender, and refractive errors in a college-age student population in Iran. METHODS: The present study was conducted cross-sectionally in 2017. All students had optometric tests including measurement of visual acuity, objective and subjective refraction, as well as binocular vision and accommodative examinations. Amplitude of accommodation was measured with the Donders' push-up method using the Royal Air Force (RAF) rule. Monocular accommodative facility was measured with ±2.00diopter flipper lenses. The accommodative response was tested using dynamic retinoscopy with the monocular estimation method (MEM). RESULTS: The prevalence of AI in the studied population was 4.07% (95% CI: 2.61-5.52). The rate was 6.04% (95% CI: 3.58-8.50) in females and 2.01% (95% CI: 0.53-3.48) in males, and logistic regression showed a significantly higher odds of AI in females (OR=3.14, 95% CI: 1.33-7.45, p-value=0.009). The prevalence of AI was 2.59% (95% CI: 0.55-7.56) in the 18-19-year-old age group and 4.08% (95% CI: 0.09-8.07) in the 24-25-year-old group (p-value=0.848). The prevalence of AI among emmetropic, myopic, and hyperopic individuals was 3.74% (95% CI: 1.88-5.61), 4.44% (95% CI: 2.07-6.81), and 5.26% (95% CI: 4.79-16.32), respectively (p-value=0.869). In the multiple regression model, only gender showed significant relationship with AI (Odds ratio=3.14, 95% CI: 1.33-7.45; p-values=0.009). CONCLUSION: The prevalence of AI in the present study is lower than the most prevalence rates reported in previous studies. In the present study, gender and AI showed a strong association, such that AI prevalence was significantly higher in females than males.