Lessons we learned during the past four challenging years in the COVID-19 era: pharmacotherapy, long COVID complications, and vaccine development

About four years have passed since the detection of the first cases of COVID-19 in China. During this lethal pandemic, millions of people have lost their lives around the world. Since the first waves of COVID-19 infection, various pharmacotherapeutic agents have been examined in the management of COVID-19. Despite all these efforts in pharmacotherapy, drug repurposing, and design and development of new drugs, multiple organ involvement and various complications occurred during COVID-19. Some of these complications became chronic and long-lasting which led to the "long COVID" syndrome appearance. Therefore, the best way to eradicate this pandemic is prophylaxis through mass vaccination. In this regard, various vaccine platforms including inactivated vaccines, nucleic acid-based vaccines (mRNA and DNA vaccines), adenovirus-vectored vaccines, and protein-based subunit vaccines have been designed and developed to prevent or reduce COVID-19 infection, hospitalization, and mortality rates. In this focused review, at first, the most commonly reported clinical presentations of COVID-19 during these four years have been summarized. In addition, different therapeutic regimens and their latest status in COVID-19 management have been listed. Furthermore, the "long COVID" and related signs, symptoms, and complications have been mentioned. At the end, the effectiveness of available COVID-19 vaccines with different platforms against early SARS-CoV-2 variants and currently circulating variants of interest (VOI) and the necessity of booster vaccine shots have been summarized and discussed in more detail.

Targeted drug delivery into glial scar using CAQK peptide in a mouse model of multiple sclerosis

In multiple sclerosis, lesions are formed in various areas of the CNS, which are characterized by reactive gliosis, immune cell infiltration, extracellular matrix changes and demyelination. CAQK peptide (peptide sequence: cysteine-alanine-glutamine-lysine) was previously introduced as a targeting peptide for the injured site of the brain. In the present study, we aimed to develop a multifunctional system using nanoparticles coated by CAQK peptide, to target the demyelinated lesions in animal model of multiple sclerosis. We investigated the binding of fluorescein amidite-labelled CAQK and fluorescein amidite-labelled CGGK (as control) on mouse brain sections. Then, the porous silicon nanoparticles were synthesized and coupled with fluorescein amidite-labelled CAQK. Five days after lysolecithin-induced demyelination, male mice were intravenously injected with methylprednisolone-loaded porous silicon nanoparticles conjugated to CAQK or the same amount of free methylprednisolone. Our results showed that fluorescein amidite-labelled CAQK recognizes demyelinated lesions in brain sections of animal brains injected with lysolecithin. In addition, intravenous application of methylprednisolone-loaded nanoparticle porous silicon conjugated to CAQK at a single dose of 0.24 mg reduced the levels of microglial activation and astrocyte reactivation in the lesions of mouse corpus callosum after 24 and 48 h. No significant effect was observed following the injection of the same dose of free methylprednisolone. CAQK seems a potential targeting peptide for delivering drugs or other biologically active chemicals/reagents to the CNS of patients with multiple sclerosis. Low-dose methylprednisolone in this targeted drug delivery system showed significant beneficial effect.

Fluorescence labeling of anchor-modified Mart-1 peptide for increasing its affinity for HLA-A*0201: Hit two targets with one arrow

One of the most successful strategies in designing peptide-based cancer vaccines is modifying natural epitope peptides to increase their binding strength to human leukocyte antigens (HLAs). Anchor-modified Mart-1 peptide (ELAGIGILTV) is among the artificial epitope peptides with the highest binding affinity for HLA-A*0201. In this study, by fluorescence labeling of its either C- or N-terminus with Nε -(5-carboxyfluorescein)-l-lysine, we not only made it traceable but also drastically increased its binding strength to HLA-A*0201. HLA streptamer, for the first time, is introduced for measuring the binding constants (Ka ) of the labeled peptides. The affinity of the labeled peptides for the HLA-A*201 of the MCF-7 cells was extraordinarily high and co-incubating them with the highest possible amount of the unlabeled peptide, as a competitor, did not significantly prohibit them from binding to the HLA. The reproducibility of the obtained results was confirmed by using the T2 cell line. The HLA-deficient K562 cell line was used as the negative control. With in silico simulations, we found two hydrophobic pockets on both sides of HLA-A*0201 for anchoring the C- or N-terminal 5-carboxyfluorescein probe, which can explain the extraordinary affinity of the labeled peptides for the HLA-A*0201.

Molecular insights into the genetic diversity and population structure of Artemisia annua L. as revealed by insertional polymorphisms

The knowledge about the level of genetic diversity and population structure in natural populations of Artemisia annua L. is a primary step in breeding programs for development of new cultivars with higher artemisinin level and better quality of secondary metabolites composition. We used PCR-based "retrotransposon-microsatellite amplified polymorphisms" (REMAPs) to study insertional polymorphism in A. annua genome to assess genetic variability and population structure in a collection of 118 accessions collected from north and northwest of Iran. Twenty-five primer combinations of 10 retrotransposon and seven ISSR primers amplified a total of 693 clear and unambiguous fragments in the studied accessions. The average number of bands, polymorphic bands, polymorphism, effective number of alleles, Shannon's information index and expected heterozygosity were 27.72, 24.76, 88.14%, 1.47, 0.42 and 0.28, respectively. The analysis of molecular variance revealed high genetic variation present within sampled geographical regions. Distance-based cluster analysis assigned the studied accessions into four clusters according to their geographical origin, which were also confirmed by principal coordinate analysis. In model-based Bayesian clustering, the maximum value of Δk was obtained when the collection of 118 assayed A. annua accessions assigned into two subgroups (K = 2). The results showed the high genetic variation in the collection of Iranian sweet wormwood which revealed by REMAP markers indicating the reliability and efficiency of this marker system for analysis of genetic diversity and population structure of A. annua.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s40415-022-00860-x.

Effects of diesel-engine exhaust emissions on seed germination and seedling growth of Brassicaceae family using digital image analysis

This paper describes a multi-phase investigation into the direct effect of diesel exhaust emission on seed germination traits and biochemical changes responsible for observed effects in seeds belongs to the Brassica family. Diesel exhaust emissions were collected in germination boxes and seeds were exposed to diesel exhaust pollutants for durations of 30 to 120 min with 30 min intervals. Observed effects include seed germination inhibition, changes in seeds' antioxidants activity, and protein content. The lowest seed germination of canola (71 %) and arugula (84 %) was observed when seeds were exposed to 120 min of diesel exhaust pollution. Seed exposure to diesel exhaust emission for 60 min, caused a 23 % and 8 % decline of germination index of canola and arugula, respectively. The maximum seed soluble protein for canola (3.72 mg/g FW) was observed in seeds exposed to 120 min diesel exhaust pollution declined to 1.65 mg/g FW, and 0.60 mg/g FW after 60 and 30 min exposure to diesel exhaust, respectively. The maximum protein content of arugula seeds (0.95 mg/g FW) was observed in the control treatment and it was reduced to 0.72 mg/g FW and 0.53 mg/g FW after 60 and 90 min exposure to diesel exhaust pollution. Catalase activity was significantly reduced as canola seed exposure to diesel exhausted was increased while there were no statistically significant changes for catalase activity of arugula seeds. All evidence suggested that time of exposure was the key phytotoxic component of exhaust emissions, and highlights the potential for detrimental effects of vehicle emissions on agro-ecosystems.

Comparative phylogenetic analysis of SARS-CoV-2 spike protein-possibility effect on virus spillover

Coronavirus disease 2019 has developed into a dramatic pandemic with tremendous global impact. The receptor-binding motif (RBM) region of the causative virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), binds to host angiotensin-converting enzyme 2 (ACE2) receptors for infection. As ACE2 receptors are highly conserved within vertebrate species, SARS-CoV-2 can infect significant animal species as well as human populations. An analysis of SARS-CoV-2 genotypes isolated from human and significant animal species was conducted to compare and identify mutation and adaptation patterns across different animal species. The phylogenetic data revealed seven distinct phylogenetic clades with no significant relationship between the clades and geographical locations. A high rate of variation within SARS-CoV-2 mink isolates implies that mink populations were infected before human populations. Positions of most single-nucleotide polymorphisms (SNPs) within the spike (S) protein of SARS-CoV-2 genotypes from the different hosts are mostly accumulated in the RBM region and highlight the pronounced accumulation of variants with mutations in the RBM region in comparison with other variants. These SNPs play a crucial role in viral transmission and pathogenicity and are keys in identifying other animal species as potential intermediate hosts of SARS-CoV-2. The possible roles in the emergence of new viral strains and the possible implications of these changes, in compromising vaccine effectiveness, deserve urgent considerations.

Tunneling-induced Talbot effect

We investigate the reforming of a plane wave into a periodic waveform in its propagation through a structural asymmetry four-level quantum dot molecule (QDM) system that is induced by an inter-dot tunneling process and present the resulting tunneling-induced Talbot effect. The tunneling process between two neighborhood dots is provided with the aid of a gate voltage. Using a periodic coupling field the response of the medium to the propagating plane probe beam becomes periodic. The needed periodic coupling field is generated with the interference of two coherent plane waves having a small angle and propagating almost parallel to the probe beam direction. In the presence of the tunneling effect of an electron between two adjacent QDs, for the probe beam propagating through the QDM system, the medium becomes transparent where the coupling fields interfere constructively. As a result, the spatial periodicity of the coupling field modulates the passing plane probe beam. We determine the minimum length of the QDM system to generate a periodic intensity profile with a visibility value equal to 1 for the probe field at the exit plane of the medium. It is also shown that by increasing the propagation length of the probe beam through the QDM medium, the profile of the maximum intensity areas becomes sharper. This feature is quantified by considering a sharpness factor for the intensity profile of the probe beam at the transverse plane. Finally, we investigate free space propagation of the induced periodic field and present the Talbot images of the tunneling-induced periodic patterns at different propagation distances for different values of the QDM medium lengths. The presented dynamically designing method of the periodic coherent intensity patterns might find applications in science and technology. For instance, in optical lithography, the need to use micro/nanofabricated physical transmission diffraction gratings, in which preparation of them is expensive and time-consuming, can be eliminated.

Synthesis of biological based hennotannic acid-based salts over porous bismuth coordination polymer with phosphorous acid tags

In this paper, a novel porous polymer capable of coordinating to bismuth (PCPs-Bi) was synthesized. The Bi-PCPs was then reacted with phosphorous acid to produce a novel polymer PCPs(Bi)N(CH2PO3H2)2 which is shown to act as an efficient and recyclable catalyst. The mentioned catalyst was applied for the efficient synthesis of new mono and bis naphthoquinone-based salts of piperidine and/or piperazine via the reaction of hennotannic acid with various aldehydes, piperidine and/or piperazine, respectively. The structure of the resulting mono and bis substituted piperazine or piperidine-based naphthoquinone salts was thoroughly characterized spectroscopically. The electrochemical behavior of the products was also investigated. The presented protocol has the advantages of excellent yields (82-95%), short reaction times (4-30 min) and simple work-up.

Viral metagenomic analysis of fecal samples reveals an enteric virome signature in irritable bowel syndrome

BACKGROUND

Changes in the enteric microbiota have been suggested to contribute to gastrointestinal diseases, including irritable bowel syndrome. Most of the published work is on bacterial dysbiosis with meager data on the role of the virome in irritable bowel syndrome and other gastrointestinal diseases. In the current study, we therefore aimed to investigate the viral community composition of the gut and test for potential dysbiosis linked to irritable bowel syndrome.

RESULTS

A metagenomics analysis on fecal samples of 50 individuals - 30 of whom met the Rome IV criteria for IBS and 20 healthy controls- was conducted. There was a noticeable alteration in viral taxa observed in association with irritable bowel syndrome when compared to healthy individuals - where some eukaryotic viral taxa noticeably prevail over others. We observed a significant decrease in the diversity and abundance of enteric virome particularly in eukaryotic viruses of Megavirales in patients with irritable bowel syndrome.

CONCLUSIONS

These findings shed light on a new hypothesis that the alteration of the viral taxa contributes to the pathogenesis of irritable bowel syndrome and related symptoms, and therefore, pave the way for developing a new diagnostic biomarker or anti-viral drugs for the treatment of irritable bowel syndrome.

Copper (triazole-5-yl)methanamine complexes onto MCM-41: the synthesis of pyridine-containing pseudopeptides through the 6-endo-dig cyclization of 1,5-enynes

An efficient approach for the synthesis of immobilized copper (triazole-5-yl)methanamine complexes onto MCM-41 (Cu@TZMA@MCM-41), as a novel recyclable nanocatalyst, is described. This nanocatalyst was used for the synthesis of pyridine-containing pseudopeptides through a sequential Ugi/nucleophilic addition/1,5-enyne cyclization reaction and elicited good-to-excellent yields. The nanocatalyst was fully characterized by SEM, EDS, TEM, BET, ICP-OES, TGA, and XRD techniques. Furthermore, the catalyst was recovered by simple filtration and could be used for at least 5 cycles without significant loss of activity.

Anti-leishmanial activity of Brevinin 2R and its Lauric acid conjugate type against L. major: In vitro mechanism of actions and in vivo treatment potentials

Leishmaniasis, as a major health problem in tropical and sub-tropical areas in the world, needs novel, safe, nontoxic and plausible therapeutic solutions for its control. As a part of innate immune system, natural antimicrobial peptides have a potential to be used as new generation of antibiotics especially after persistent resistance of conventional antimicrobial agents. Brevinin 2R, a member of Defensin families of host defense peptides, showed promising effects against bacterial and fungal infections as well as cancerous cell lines. In the current research, the anti-leishmanial effect of Brevinin 2R and its lauric acid conjugate was investigated against Leishmania major (L. major) parasite. The data revealed that, conjugation of fatty acid to Brevinin 2R, strengthen its effect on L. major promastigotes as well as toxicity and hemolytic effect. These peptides showed anitleishmanial activity through cell membrane disruption and changes in the electrical and mitochondrial membrane potential. No signs of apoptosis induction or caspase activation were detected. Despite its hemolytic and cytotoxic effect in in vitro conditions, lauric acid- Brevinin 2R (L- Brevinin 2R) did not show site specific adverse reactions in animal model. Treatment course with L- Brevinin 2R in the L. major infected mice exhibited decreased parasite load in the lymph nodes adjacent to the infected site despite cytokine production profile and footpad swelling data.

Seeking novel drugs against leishmaniasis is a necessity due to inefficiency of current medications. Brevinin 2R, as a non-hemolytic natural antimicrobial peptide, was effective against vast majority of bacterial and fungal infections as well as cancerous cell lines. In this regard in the current study, the efficacy of Brevinin 2R and its lauric acid conjugate version were studied against L. major parasite growth inhibition at in vitro and in animal model. The results exhibited that, conjugation of fatty acid to Brevinin 2R exacerbated anti-leishmanial effect. L- Brevinin 2R resolved the promastigotes through membrane disruption and changes in the membrane and mitochondrial potential. Also, L- Brevinin 2R was able to limit successfully the parasite load in the lymph nodes of L. major infected animals.

Nanosized (Ni1-x Zn x )Fe2O4 for water oxidation

Performing water splitting for H₂ production is an interesting method to store different energies. For water splitting, an efficient and stable water-oxidizing catalyst is important. Ni-Fe (hydr)oxides are among the best catalysts for water oxidation in alkaline electrolytes. An Fe amount higher than 50% in Ni-Fe (hydr)oxides increases the overpotential for water oxidation. Thus, Ni-Fe (hydr)oxides with a high ratio of Fe to Ni have rarely been focused on for water oxidation. Herein, we report water oxidation using nanosized (Ni_1-x Zn _x )Fe₂O₄. The catalyst was characterized via some methods and tested at pH values of 3, 7 and 11 in phosphate buffer. Nanosized (Ni_1-x Zn _x )Fe₂O₄ is a good catalyst for water oxidation only under alkaline conditions. In the next step, amperometry studies showed current densities of 3.50 mA cm^-2 and 11.50 mA cm^-2 at 1.25 V in 0.10 M and 1.0 M KOH solution, respectively. The amperometric measurements indicated high catalyst stability in both 0.10 M and 1.0 M KOH. Tafel plots were obtained in KOH solution at concentrations of both 0.10 M and 1.0 M. At pH = 13 in KOH solution (0.10 M), linearity of lg(j) vs. potential was shown, with two slopes relating to both relatively low (170.9 mV per decade) and high overpotentials (484.2 mV per decade). In 1.0 M KOH solution, the Tafel plot showed linearity of lg(j) vs. potential, with two slopes relating to both relatively low (192.5 mV per decade) and high overpotentials (545.7 mV per decade). After water oxidation, no significant change was observed in the catalyst.