In-silico study: docking simulation and molecular dynamics of peptidomimetic fullerene-based derivatives against SARS-CoV-2 Mpro

COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, has become a global pandemic resulting in significant morbidity and mortality. This study presents 12 new peptidomimetic fullerene-based derivatives in three groups that are investigated theoretically as SARS-CoV-2 M^pro inhibitors to increase the chance of treating COVID-19. Studied compounds are designed and optimized at B88-LYP/DZVP method. Molecular descriptors results show the stability and reactivity of the compounds with M^pro, especially in the 3rd group (Ser compounds). However, Lipinski's Rule of Five values indicates that the compounds are not suitable as oral drugs. Furthermore, molecular docking simulations are carried out to investigate the binding affinity and interaction modes of the top five compounds (compounds 1, 9, 11, 2, and 10) with the M^pro protein, which have the lowest binding energy. Molecular dynamics simulations are also performed to evaluate the stability of the protein-ligand complexes with compounds 1 and 9 and compare them with natural substrate interaction. The analysis of RMSD, H-bonds, Rg, and SASA indicates that both compounds 1 (Gly-α acid) and 9 (Ser-α acid) have good stability and strong binding affinity with the M^pro protein. However, compound 9 shows slightly better stability and binding affinity compared to compound 1.

Novel inhibitors against wild-type and mutated HCV NS3 serine protease: an in silico study

In 2011, the FDA approved boceprevir as a hepatitis C virus (HCV) NS3 serine protease inhibitor. The sustained virological response rate for treatment with this approved compound is considerably low. Patients have not responded as much as expected to boceprevir therapy. In this in silico study, modified boceprevir compounds are suggested and tested on wild-type HCV NS3 protease and 19 mutated HCV NS3 proteases using molecular docking. Results reveal the superiority of two of the proposed modified compounds to boceprevir. One of which appears to be more potent than boceprevir itself concerning activity against wild-type NS3 and most of the examined mutated NS3 proteases.

Evaluation of the expression of the stromal cell-derived factor-1 alpha (CXCL 12) in psoriatic patients after treatment with Methotrexate

BACKGROUND

CXCL12 has an important role in skin homeostasis and inflammation.

OBJECTIVE

In this work, the expression of CXCL12 was evaluated in psoriasis vulgaris, psoriatic arthritis (PsA) patients in relation to disease activity and methotrexate (MTX) therapy.

METHODS

Skin biopsies were obtained from 10 psoriasis vulgaris patients, 10 PsA patients, and 20 controls. The biopsies were repeated 6 weeks after MTX therapy. The biopsies were stained immunohistochemically by stromal dermal factor 1 alpha (CXCL 12) antibody.

RESULTS

Psoriatic arthritis showed significantly more expression of CXCL 12 than psoriasis vulgaris patients before treatment but not after treatment. There was significant decrease in CXCL 12 expression in the keratinocytes of psoriasis vulgaris patients after MTX therapy than before treatment, P-value was 0.009. There was no significant difference between pre- and post-treatment in the CXCL 12 expression of keratinocytes of PsA patients, P-value was 0.093. The percentage decrease of PASI score after treatment showed a moderate correlation with the percentage decrease of CXCL12 expression of the keratinocytes of the total psoriasis patients, r = 0.484, P-value was 0.015.

CONCLUSION

CXCL12 might be involved in the progression of psoriasis vulgaris to PsA. MTX therapy downregulated the expression of CXCL12 of the keratinocytes of psoriasis patients. This downregulation was paralleled by decrease in the PASI score. CXCL12 can be used as a biological marker of disease severity of psoriasis patients.

Cathelicidin (LL-37) level in the scalp hair of patients with tinea capitis

Antimicrobial peptides (AMPs) are considered an important first line of defense against pathogens. Cathelicidin LL-37 was upregulated in response to fungal infection. In this work we aimed to evaluate cathelicidin LL-37 in the hair of tinea capitis and compare it to normal controls. Hair samples were collected from 30 children and 30 controls aged from 2 to10 years old, and the level of cathelicidin LL-37 in the hair was detected by quantitative real-time PCR. The 30 patients were further subdivided into three subgroups according to their clinical type. Ten patients were scaly type, 10 patients were black dots type, and 10 patients were kerion type. Cathelicidin level in patients ranged from 6.0 to 17.5 with mean ± SD (11.3 ± 2.3) and in control ranged from 1.02 to 6.2, with mean ± SD (2.8 ± 1.5). There was a significant difference between the patients and controls regarding the cathelicidin level; P value was 0. The mean cathelicidin level was lowest in the kerion type10.73 ± 2.6 and highest in the black dot type 12.05 ± 2.76. However, there was no significant difference between the cathelicidin level of the different clinical types of tinea capitis; P value was 0.58. In conclusion, the level of cathelicidin LL-37 in hair specimens of human tinea capitis was significantly higher than controls.

Structure-based drug design of novel peptidomimetic cellulose derivatives as HCV-NS3 protease inhibitors

Hepatitis C Virus (HCV) represents a global health threat not only due to the large number of reported worldwide HCV infections, but also due to the absence of a reliable vaccine for its prevention. HCV NS3 protease is one of the most important targets for drug design aiming at the deactivation of HCV. In the present work, molecular docking simulations are carried out for suggested novel NS3 protease inhibitors applied to the Egyptian genotype 4. These inhibitors are modifications of dimer cellulose by adding a hexa-peptide to the cellulose at one of the positions 2, 3, 6, 2', 3' or 6'. Results show that the inhibitor compound with the hexa-peptide at position 6 shows significantly higher simulation docking score with HCV NS3 protease active site. This is supported by low total energy value of docking system, formation of two H-bonds with HCV NS3 protease active site residues, high binding affinity and increased stability in the interaction system.

The QSAR and docking calculations of fullerene derivatives as HIV-1 protease inhibitors

The inhibition of HIV-1 protease is considered as one of the most important targets for drug design and the deactivation of HIV-1. In the present work, the fullerene surface (C60) is modified by adding oxygen atoms as well as hydroxymethylcarbonyl (HMC) groups to form 6 investigated fullerene derivative compounds. These compounds have one, two, three, four or five O atoms+HMC groups at different positions on phenyl ring. The effect of the repeating of these groups on the ability of suggested compounds to inhibit the HIV protease is studied by calculating both Quantitative Structure Activity Relationship (QSAR) properties and docking simulation. Based on the QSAR descriptors, the solubility and the hydrophilicity of studied fullerene derivatives increased with increasing the number of oxygen atoms+HMC groups in the compound. While docking calculations indicate that, the compound with two oxygen atoms+HMC groups could interact and binds with HIV-1 protease active site. This is could be attributed to the active site residues of HIV-1 protease are hydrophobic except the two aspartic acids. So that, the increase in the hydrophilicity and polarity of the compound is preventing and/or decreasing the hydrophobic interaction between the compound and HIV-1 protease active site.

Structural and electronic properties of new fullerene derivatives and their possible application as HIV-1 protease inhibitors

Density functional theory (DFT) calculations have been carried out at the hybrid Becke 3-Lee-Yang-Parr; B3LYP/3-21G** level of theory to study two series of hydroxy-chalca-acetic acid-(4-pyrrolidin-1-yl-phenyl) ester [C(60)-C(2)H(4)N-(4-XCOCH(2)OH)C(6)H(4)] and hydroxy-chalcoacetic acid-[2-(2-hydroxy-acetylchalcanyl)-4-pyrrolidin-1-yl-phenyl] ester[C(60)-C(2)H(4)N-(3,4-XCOCH(2)OH)C(6)H(4)]. The X atom is O, S or Se for the two series. The vibrational spectra, physical, chemical, thermodynamics and Quantitative Structure Activity Relationship (QSAR) properties of the studied molecules are calculated and discussed. We have evaluated these molecules as HIV-1 protease inhibitors based on the hydrogenation interaction between the hydroxymethylcarbonyl (HMC) groups and the two aspartic acid of the HIV-1 protease active site. Results show that some of the investigated fullerene-based derivatives can be considered promising as HIV-1 protease inhibitors.

Two new flavonoids from Retama raetam

Two new flavones were isolated from the aerial parts of Retama raetam subsp. raetam. Their structures were established as luteolin 4'-O-neohesperidoside (1) and 5,4'-dihydroxy-(3",4"-dihydro-3", 4"-dihydroxy)-2",2"-dimethylpyrano-(5",6":7,8)-flavone (2) by means of spectroscopic methods. Also present was ephedroidin (4',5, 7-trihydroxy-8-(2-hydroxy-3-butenyl)-flavone).

New flavonoids from Avicennia marina

In addition to luteolin 7-O-methylether, chrysoeriol 7-O-glucoside and isorhamnetin 3-O-rutinoside, the methanol extract of the aerial parts of Avicennia marina yielded two new flavonoids identified as luteolin 7-O-methylether 3'-O-beta-D-glucoside and its galactoside analogue 2.

Quercetin triglycoside from Capparis spinosa

In addition to rutin, quercetin 3-O-glucoside and quercetin 3-O-glucoside-7-O-rhamnoside, the methanolic extract of the aerial parts of Capparis spinosa yielded the new flavonoid quercetin 3-O-[6'"-alpha-L-rhamnosyl-6"-beta-D-glucosyl]-beta-D-glucoside (1).

Four flavonoid glycosides from Peganum harmala

The aerial parts of Peganum harmala yielded four new flavonoids: acacetin 7-O-rhamnoside, 7-O-[6"-O-glucosyl-2"-O-(3'''-acetylrhamnosyl)glucoside and 7-O-(2'''-O-rhamnosyl-2"-O-glucosylglucoside), and the glycoflavone 2'''-O-rhamnosyl-2"-O-glucosylcytisoside.

Biochemical changes associated with acute phosphorus poisoning (in humans)

1. Thirty patients with acute phosphorus poisoning (APP) were chosen from the poison control centre, Cairo (PCCC), Ain Shams University, and classified into three groups according to the amount of ingested inorganic phosphorus (Pi). 2. Group I recorded high mortality rate (90%) with liver failure as a main cause of death. This group also showed hepatorenal failure, hypoglycemia and severe effect on the heart function. 3. Groups II and III recorded no mortality, but their patients showed an effect on the liver, which was severe in group II and mild in group III.

Antibacterial activity of selected tropones and tropolones

The antibacterial activity of 33 substituted and unsubstituted seven-member ring tropones and tropolones was examined on 14 reference strains representing Gram-positive and Gram-negative bacteria. It was shown that the chemical character and position of the substituent plays a distinct role in the biological activity of investigated compounds. Depending on the substituent the antibacterial effect may be either increased or diminished. C-1 thio and C-2 nitro derivatives of tropone are significantly more active than tropone. The dibenzotropone derivatives display no antibacterial activity. Hydroxymethyl derivatives of tropolone are more active than tropolone, while hydroxy-, isopropyl-, methyl- as well as tropolone acetates are equipotent.

New inhibitors for aminoglycoside-adenylyltransferase

Two hydroxymethyltropolones and two tropolone acetate derivatives were found to inhibit an aminoglycoside-adenylyltranferase in a gentamicin-resistant Escherichia coli strain. The inhibitory effect of tropolones depends on the nature of the aminoglycoside antibiotic subject to adenylation. Combinations of hydroxymethyltropolones with tobramycin were more active compared with tropolone acetates against gentamicin-resistant strains displaying adenylyltransferase activity. On the contrary a combination of the investigated acetate with gentamicin was of lower activity. It could be shown that these inhibitors inhibit, to a varying degree, the transfer of radioactive ATP to different aminoglycoside molecules.

UDP-Glucose: Cyanidin 3-O-glucosyltransferase from cell cultures of Haplopappus gracilis

From cell cultures of Haplopappus gracilis, an enzyme, catalyzing the glucosylation of cyanidin at the 3 position using uridine diphosphate-D-glucose (UDPG) as glucosyl-donor, has been isolated and purified 50-fold. The enzyme was not specific for cyanidin alone, but also glucosylated other anthocyanidins and flavonols in position 3. However, apigenin, luteolin, naringenin and dihydroquercetin were not glucosylated. The reaction has an optimum pH of approximately 8, and the apparent K m values for UDPG and cyanidin were 0.5 and 0.33 mM respectively. The enzyme reaction is strongly inhibited by cyanidin (above 0.25 mM).