A pilot study of the antiviral activity of anionic and cationic polyamidoamine dendrimers against the Middle East respiratory syndrome coronavirus.

The Middle East respiratory syndrome coronavirus (MERS-CoV) is an emerging virus that causes infection with a potentially fatal outcome. Dendrimers are highly branched molecules that can be added to antiviral preparations to improve their delivery, as well as their intrinsic antiviral activity. Studies on identifying anti-MERS-CoV agents are few. Three types of polyanionic dendrimers comprising the terminal groups sodium carboxylate (generations 1.5, 2.5, 3.5, and 4.5), hydroxyl (generations 2, 3, 4, and 5), and succinamic acid (generations 2, 3, 4, and 5) and polycationic dendrimers containing primary amine (generations 2, 3, 4, and 5) were used to assess their antiviral activity with the MERS-CoV plaque inhibition assay. The hydroxyl polyanionic set showed a 17.36% to 29.75% decrease in MERS-CoV plaque formation. The most potent inhibition of MERS-CoV plaque formation was seen by G(1.5)-16COONa (40.5% inhibition), followed by G(5)-128SA (39.77% inhibition). In contrast, the cationic dendrimers were cytotoxic to Vero cells. Polyanionic dendrimers can be added to antiviral preparations to improve the delivery of antivirals, as well as the intrinsic antiviral activity.

Paeonol Attenuates Methotrexate-Induced Cardiac Toxicity in Rats by Inhibiting Oxidative Stress and Suppressing TLR4-Induced NF-κB Inflammatory Pathway.

Methotrexate (MTX) is a commonly used chemotherapeutic agent. Oxidative stress and inflammation have been proved in the development of MTX toxicity. Paeonol is a natural phenolic compound with various pharmacological activities including antioxidant and anti-inflammatory properties. The aim of the present study was to evaluate the protective effect of paeonol against MTX-induced cardiac toxicity in rats and to evaluate the various mechanisms that underlie this effect. Paeonol (100 mg/kg) was administered orally for 10 days. MTX cardiac toxicity was induced at the end of the fifth day of the experiment, with or without paeonol pretreatment. MTX-induced cardiac damage is evidenced by a distortion in the normal cardiac histological structure, with significant oxidative and nitrosative stress shown as a significant increase in NADPH oxidase-2, malondialdehyde, and nitric oxide levels along with a decrease in reduced glutathione concentration and superoxide dismutase activity compared to the control group. MTX-induced inflammatory effects are evidenced by the increased cardiac toll-like receptor 4 (TLR4) mRNA expression and protein level as well as increased cardiac tumor necrosis factor- (TNF-) α and interleukin- (IL-) 6 levels along with increased nuclear factor- (NF-) κB/p65 immunostaining. MTX increased apoptosis as shown by the upregulation of cardiac caspase 3 immunostaining. Paeonol was able to correct the oxidative and nitrosative stress as well as the inflammatory and apoptotic parameters and restore the normal histological structure compared to MTX alone. In conclusion, paeonol has a protective effect against MTX-induced cardiac toxicity through inhibiting oxidative and nitrosative stress and suppressing the TLR4/NF-κB/TNF-α/IL-6 inflammatory pathway, as well as causing an associated reduction in the proapoptotic marker, caspase 3.

Metabolic drug targets of the cytosine metabolism pathways in the dromedary camel (Camelus dromedarius) and blood parasite Trypanosoma evansi.

Trypanosomiasis is a major illness affecting camels in tropical and subtropical regions. Comparisons of camel and Trypanosoma evansi genomes can lead to the discovery of new drug targets for treating Trypanosoma infections. The synthesis pathways of cytosine, cytidine, cytidine monophosphate (CMP), cytidine diphosphate (CDP), cytidine triphosphate (CTP) deoxycytidine, deoxycytidine monophosphate (dCMP), deoxycytidine diphosphate (dCDP), and deoxycytidine triphosphate (dCTP) were compared in the dromedary camel (Camelus dromedarius) and T. evansi. None of the enzymes involved in cytosine pathway were detected in camels and T. evansi. Notably, cytidine kinase (CK) and 5'-nucleotidase, which interconverts cytidine to CMP, were not detected in T. evansi but were present in camels. UMP/CMP kinase was not predicted in T. evansi. Therefore, the presence of enzymes involved in the CTP synthesis cascade was not predicted in T. evansi. CMP synthesis might also be encoded by other enzymes, e.g., purine nucleotides kinases. Both camel and T. evansi share an efficient enzyme system for converting CDP to CTP. In conclusion, CTP synthase is important for homeostasis of cytosine nucleotides in T. evansi and could be a potential drug target against the parasite. In addition, the inhibition of UMP synthesis might contribute to parasite death as it is a shared source for CTP synthesis.

The synergy of artificial intelligence and personalized medicine for the enhanced diagnosis, treatment, and prevention of disease.

INTRODUCTION: The completion of the Human Genome Project in 2003 marked the beginning of a transformative era in medicine. This milestone laid the foundation for personalized medicine, an innovative approach that customizes healthcare treatments. CONTENT: Central to the advancement of personalized medicine is the understanding of genetic variations and their impact on drug responses. The integration of artificial intelligence (AI) into drug response trials has been pivotal in this domain. These technologies excel in handling large-scale genomic datasets and patient histories, significantly improving diagnostic accuracy, disease prediction and drug discovery. They are particularly effective in addressing complex diseases such as cancer and genetic disorders. Furthermore, the advent of wearable technology, when combined with AI, propels personalized medicine forward by offering real-time health monitoring, which is crucial for early disease detection and management. SUMMARY: The integration of AI into personalized medicine represents a significant advancement in healthcare, promising more accurate diagnoses, effective treatment plans and innovative drug discoveries. OUTLOOK: As technology continues to evolve, the role of AI in enhancing personalized medicine and transforming the healthcare landscape is expected to grow exponentially. This synergy between AI and healthcare holds great promise for the future, potentially revolutionizing the way healthcare is delivered and experienced.

Camel Proteins and Enzymes: A Growing Resource for Functional Evolution and Environmental Adaptation.

In less agroecological parts of the Asian, Arabian, and African deserts, Camelus dromedarius play an important role in human survival. For many years, camels have been employed as a source of food, a tool of transportation, and a means of defense. They are becoming increasingly important as viable livestock animals in many desert climates. With the help of camel genetics, genomics and proteomics known so far, this review article will summarize camel enzymes and proteins, which allow them to thrive under varied harsh environmental situations. An in-depth study of the dromedary genome revealed the existence of protein-coding and fast-developing genes that govern a variety of metabolic responses including lipid and protein metabolism, glucoamylase, flavin-containing monooxygenase and guanidinoacetate methyltransferase are other metabolic enzymes found in the small intestine, liver, pancreas, and spleen. In addition, we will discuss the handling of common medications by camel liver cytochrome p 450, which are different from human enzymes. Moreover, camels developed several paths to get optimum levels of trace elements like copper, zinc, selenium, etc., which have key importance in their body for normal regulation of metabolic events. Insulin tolerance, carbohydrate and energy metabolism, xenobiotics metabolizing enzymes, vimentin functions, behavior during the rutting season, resistance to starvation and changes in blood composition and resistance to water loss were among the attractive aspects of camel enzymes and proteins peculiarities in the camels. Resolving the enigma of the method of adaptation and the molecular processes linked with camel life is still a developing repository full of mysteries that need additional exploration.

Discovery of New Potent anti-MERS CoV Fusion Inhibitors.

Middle East respiratory syndrome coronavirus (MERS-CoV), capable of zoonotic transmission, has been associated with emerging viral pneumonia in humans. In this study, a set of highly potent peptides were designed to prevent MERS-CoV fusion through competition with heptad repeat domain 2 (HR2) at its HR1 binding site. We designed eleven peptides with stronger estimated HR1 binding affinities than the wild-type peptide to prevent viral fusion with the cell membrane. Eight peptides showed strong inhibition of spike-mediated MERS-CoV cell-cell fusion with IC50 values in the nanomolar range (0.25-2.3 µM). Peptides #4-6 inhibited 95-98.3% of MERS-CoV plaque formation. Notably, peptide four showed strong inhibition of MERS-CoV plaques formation with EC50 = 0.302 µM. All peptides demonstrated safe profiles without cytotoxicity up to a concentration of 10 µM, and this cellular safety, combined with their anti-MERS-CoV antiviral activity, indicate all peptides can be regarded as potential promising antiviral agents.

Analysis of preferred codon usage in the coronavirus N genes and their implications for genome evolution and vaccine design.

The nucleocapsid (N) protein of a coronavirus plays a crucial role in virus assembly and in its RNA transcription. It is important to characterize a virus at the nucleotide level to discover the virus's genomic sequence variations and similarities relative to other viruses that could have an impact on the functions of its genes and proteins. This entails a comprehensive and comparative analysis of the viral genomes of interest for preferred nucleotides, codon bias, nucleotide changes at the 3rd position (NT3s), synonymous codon usage and relative synonymous codon usage. In this study, the variations in the N proteins among 13 different coronaviruses (CoVs) were analysed at the nucleotide and amino acid levels in an attempt to reveal how these viruses adapt to their hosts relative to their preferred codon usage in the N genes. The results revealed that, overall, eighteen amino acids had different preferred codons and eight of these were over-biased. The N genes had a higher AT% over GC% and the values of their effective number of codons ranged from 40.43 to 53.85, indicating a slight codon bias. Neutrality plots and correlation analyses showed a very high level of GC3s/GC correlation in porcine epidemic diarrhea CoV (pedCoV), followed by Middle East respiratory syndrome-CoV (MERS CoV), porcine delta CoV (dCoV), bat CoV (bCoV) and feline CoV (fCoV) with r values 0.81, 0.68, -0.47, 0.98 and 0.58, respectively. These data implied a high rate of evolution of the CoV genomes and a strong influence of mutation on evolutionary selection in the CoV N genes. This type of genetic analysis would be useful for evaluating a virus's host adaptation, evolution and is thus of value to vaccine design strategies.

Study on Genotyping Polymorphism and Sequencing of N-Acetyltransferase 2 (NAT2) among Al-Ahsa Population.

One of the well-studied phase II drug metabolizing enzymes is N-acetyltransferase 2 (NAT2) which has an essential role in the detoxification and metabolism of several environmental toxicants and many therapeutic drugs like isoniazid (antituberculosis, TB) and antimicrobial sulfonamides. According to the variability in the acetylation rate among different ethnic groups, individuals could be classified into slow, intermediate, and fast acetylators; these variabilities in the acetylation rate are a result of single nucleotide polymorphisms (SNPs) in the coding sequence of NAT2. The variety of NAT2 acetylation status is associated with some diseases such as bladder cancer, colorectal cancer, rheumatoid arthritis, and diabetes mellitus. The main objectives of this research are to describe the genetic profile of NAT2 gene among the people of the Al-Ahsa region, to detect the significant SNPs of this gene, to determine the frequency of major NAT2 alleles and genotypes, and then categorize them into fast, intermediate, and slow acetylators. Blood samples were randomly collected from 96 unrelated people from Al-Ahsa population, followed by DNA extraction then amplifying the NAT2 gene by polymerase chain reaction (PCR); finally, functional NAT2 gene (exon 2) was sequenced using the Sanger sequencing method. The well-known seven genetic variants of NAT2 gene are 191G>A, 282C>T, 341T>C, 481C>T, 590G>A, 803A>G, and 857G>A were detected with allele frequencies 1%, 35.4%, 42.7%, 41.1%, 29.2%, 51%, and 5.7%, respectively. The most common NAT2 genetic variant among Al-Ahsa population was 803A>G with a high frequency 0.510 (95% confidence interval 0.44-0.581) followed by 341T>C 0.427 (95% confidence interval 0.357-0.497). The most frequent two haplotypes of NAT2 were NAT2∗6C (25.00%) and NAT2∗5A (22.92%) which were classified as a slow acetylators. According to trimodal distribution of acetylation activity, the predicted phenotype of Al-Ahsa population was found to be 5.21% rapid acetylators, 34.38% intermediate acetylators, and 60.42% were slow acetylators. In addition, this study found four novel haplotypes NAT2∗5TB, NAT2∗5AB, NAT2∗5ZA, and NAT2∗6W which were slow acetylators. This study revealed a high frequency of the NAT2 gene with slow acetylators (60.42%) in Al-Ahsa population, which might alter the drug's efficacy and vulnerability to some diseases.

Small Molecule Inhibitors of Middle East Respiratory Syndrome Coronavirus Fusion by Targeting Cavities on Heptad Repeat Trimers.

Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is a newly emerging viral disease with fatal outcomes. However, no MERS-CoV-specific treatment is commercially available. Given the absence of previous structure-based drug discovery studies targeting MERS-CoV fusion proteins, this set of compounds is considered the first generation of MERS-CoV small molecule fusion inhibitors. After a virtual screening campaign of 1.56 million compounds followed by cell-cell fusion assay and MERS-CoV plaques inhibition assay, three new compounds were identified. Compound numbers 22, 73, and 74 showed IC50 values of 12.6, 21.8, and 11.12 µM, respectively, and were most effective at the onset of spike-receptor interactions. The compounds exhibited safe profiles against Human embryonic kidney cells 293 at a concentration of 20 µM with no observed toxicity in Vero cells at 10 µM. The experimental results are accompanied with predicted favorable pharmacokinetic descriptors and drug-likeness parameters. In conclusion, this study provides the first generation of MERS-CoV fusion inhibitors with potencies in the low micromolar range.

The structural basis of unique substrate recognition by Plasmodium thymidylate kinase: Molecular dynamics simulation and inhibitory studies.

Plasmodium falciparum thymidylate kinase (PfTMK) showed structural and catalytic distinctions from the host enzyme rendering it a hopeful antiprotozoal drug target. Despite the comprehensive enzymologic, structural, inhibitory and chemical synthesis approaches targeting this enzyme, the elucidation of the exact mechanism underlying the recognition of the atypical purine substrates remains to be determined. In this study, molecular dynamics (MD) simulation of a broad range of substrates and inhibitors as well as the inhibitory properties of deoxyguanosine (dG) derivatives were used to assess the PfTMK substructure molecular rearrangements. The estimated changes during the favourable binding of high affinity substrate (TMP) include lower interaction with P-loop, free residue fluctuations of the lid domain and the average RMSD value. The RMSD of TMP complex was higher and more rapidly stabilized than the dGMP complex. The lid domain flexibility is severely affected by dGMP and ß-thymidine derivatives, while being partially fluctuating with other thymidine derivatives. The TMK-purine (dGMP) complex was slowly and gradually stabilized with lower over all structure flexibility and residue fluctuations especially at the lid domain, which closes the active site during its catalytic state. Thymidine derivatives allow structure flexibility of the lid domain being highly fluctuating in α- and ß-thymidine derivatives and TMP. dG derivatives remains less efficient than thymidine derivatives in inhibiting TMK. The variations in the structural dynamics of the P-loop and lid domain in response to TMP or dGMP might favour thymidine-based compounds. The provided MD simulation strategy can be used for predicating structural changes in PfTMK during lead optimization.

In vitro and in situ inhibition of some food-borne pathogens by essential oils from date palm (Phoenix dactylifera L.) spathe.

Essential oils extracted by hydro-distillation form date palm spathe (byproduct from date palm plants) were tested for their antibacterial activity against some food-borne pathogens. Listeria monocytogenes ATCC 7644, Staphylococcus aureus ATCC 29243, Salmonella enterica subsp. enterica serovar Enteritidis ATCC 13076 and E. coli ATCC 25922 were inhibited (11-13 mm inhibition zones) by spathe essential oils (SEOs) using the agar well assay (in vitro test). Staphylococcus aureus ATCC 29243 and E. coli ATCC 25922 were not detected in chicken meat treated with 1% (v/w) SEOs and subjected to abusive storage conditions (20 °C for 18 h). When treated with 0.5% SEO, counts of S. aureus and E. coli increased by only 0.2 and 0.7 log10 cfu/g, respectively, compared to the initial inoculated level in meat samples stored at 20 °C for 18 h. SEOs possessed DPPH radical scavenging activity with IC50 of 0.61 µg/ml. Forty one compounds were major constituents detected by GC-MS analysis of SEOs. 3,4-Dimethoxytoluene (38.12%) and 5,9-Undecadien-2-one (12.45%) were major compounds in extracted oils. Density and refractive index of SEOs were 0.987 and 1.5905, respectively. SOEs are added-value products from date palm, which could be employed in food industry and pharmaceuticals. The study is the first report on antibacterial activity of SEOs against L. monocytogenes ATCC 7644 and other standard food-borne pathogens in agar diffusion assay and food model (chicken meat). DPPH radical scavenging activity of SEOs has not previously been documented.

Molecular dynamics of Middle East Respiratory Syndrome Coronavirus (MERS CoV) fusion heptad repeat trimers.

Structural studies related to Middle East Respiratory Syndrome Coronavirus (MERS CoV) infection process are so limited. In this study, molecular dynamics (MD) simulations were carried out to unravel changes in the MERS CoV heptad repeat domains (HRs) and factors affecting fusion state HR stability. Results indicated that HR trimer is more rapidly stabilized, having stable system energy and lower root mean square deviations (RMSDs). While trimers were the predominant active form of CoVs HRs, monomers were also discovered in both of viral and cellular membranes. In order to find the differences between S2 monomer and trimer molecular dynamics, S2 monomer was modelled and subjected to MD simulation. In contrast to S2 trimer, S2 monomer was unstable, having high RMSDs with major drifts above 8 Å. Fluctuation of HR residue positions revealed major changes in the C-terminal of HR2 and the linker coil between HR1 and HR2 in both monomer and trimer. Hydrophobic residues at the a and d positions of HR helices stabilize the whole system, with minimal changes in RMSD. The global distance test and contact area difference scores support instability of MERS CoV S2 monomer. Analysis of HR1-HR2 inter-residue contacts and interaction energy revealed three energy scales along HR helices. Two strong interaction energies were identified at the start of the HR2 helix and at the C-terminal of HR2. The identified critical residues by MD simulation and residues at the a and d positions of HR helix were strong stabilizers of HR recognition.

In silico comparisons between natural inhibitors of ABCB1/P-glycoprotein to overcome doxorubicin-resistance in the NCI/ADR-RES cell line.

To investigate compound-protein binding mode and molecular dynamic simulation of P-glycoprotein (P-gp), in silico studies were performed to compare 12 naturally occurring compounds using two softwares. The net results showed that piperine (PIP) had the best binding affinity. In vitro studies on doxorubicin (DOX)-resistant NCI/ADR-RES cells, known to express P-gp, showed that, dose-dependently, PIP significantly increased intracellular accumulation of rhodamine-123 and had cytotoxic effects accessed by MTT assay. In addition, PIP at 25 and 50µM significantly potentiated DOX-induced cytotoxicity on the same cell line. P-gp ATPase assay showed that both DOX and PIP had dose-dependent inhibition of orthovandate-sensitive ATPase activity, indicating they are both P-gp inhibitors, with IC50 of 84±1 and 37±2µM, respectively. PIP did not show any activation of ATPase activity, while DOX did, indicating that P-gp does not accept PIP as a substrate. Using DOX at concentration 33.33µM together with PIP (100µM), DOX-mediated P-gp ATPase activity was decreased to levels 4-folds lower than DOX alone. In conclusion, both in silico and in vitro studies confirm that PIP is an inhibitor of P-gp mediated DOX efflux, suggesting PIP as a promising adjuvant to DOX cancer chemotherapy.

Protective mechanisms of resveratrol against methotrexate-induced renal damage may involve BCRP/ABCG2.

Resveratrol (RES) is a well-known polyphenol antioxidant. We have previously shown that testicular protective effect of RES against the anticancer drug methotrexate (MTX)-induced toxicity involves transporter-mediated mechanisms. Here, we investigated the effect of RES on MTX-induced nephrotoxicity. Rats were administered RES (10 mg/kg/day) for 8 days, with or without a single MTX dose (20 mg/kg i.p.) at day 4 of the experiment. MTX induced nephrotoxicity, as evidenced by a significant increase in serum blood urea nitrogen and creatinine compared to the control, as well as distortion of kidney microscopic structure. MTX also significantly increased renal nitric oxide level along with inducible nitric oxide synthase, fas ligand, and caspase 3 expressions. Administering RES prior to MTX significantly improved kidney function and microscopic picture and also significantly decreased nitrosative and apoptotic markers compared to MTX alone. RES, but not MTX, caused a significant increase in expression of breast cancer resistance protein (BCRP), an apical efflux renal transporter that participates in urinary elimination of both MTX and RES. Interestingly, concomitant MTX and RES caused further upregulation of renal BCRP compared to RES alone. Using Human BCRP ATPase assay, both RES and MTX exhibited a dose-dependent increase in ATPase activity, with Km values of 0.52 ± 0.03 and 30.9 ± 4.2 µm, respectively. Furthermore, combined RES and MTX caused ATPase activity which was significantly less than maximum ATPase activity attained by the positive control, sulfasalazine (12.5 µm). In conclusion, RES exerted nephroprotection against MTX-induced toxicity through antinitrosative and anti-apoptotic effects, as well as via upregulation of renal BCRP.

Multi-drug resistance protein (Mrp) 3 may be involved in resveratrol protection against methotrexate-induced testicular damage.

AIMS: To investigate the effect of resveratrol (RES) on methotrexate (MTX)-induced testicular damage. MAIN METHODS: RES (10mg/kg/day) was given for 8 days orally and MTX (20mg/kg i.p.) was given at day 4 of the experiment, with or without RES in rat. KEY FINDINGS: MTX decreased serum testosterone, induced histopathological testicular damage, and increased testicular tumor necrosis factor-α level and expression of nuclear factor-κB and cyclooxygenase-2. In MTX/RES group, significant reversal of these parameters was noticed, compared to MTX group. Testicular expression of multidrug resistance protein (Mrp) 3 was three- and five-folds higher in RES- and MTX/RES-treated groups, respectively. In vitro, using prostate cancer cells, each of MTX and RES alone induced cytotoxicity with IC50 0.18 ± 0.08 and 20.5 ± 3.6 µM, respectively. RES also significantly enhanced cytotoxicity of MTX. SIGNIFICANCE: Thus, RES has dual beneficial effects, as it promotes MTX tumor cytotoxicity, while protecting the testes, probably via up-regulation of testicular Mrp3 as a novel mechanism.