A comprehensive review on the global efforts on vaccines and repurposed drugs for combating COVID-19

The recently discovered coronavirus, known as SARS-CoV-2, is a highly contagious and potentially lethal viral infection that was declared a pandemic by the World Health Organization on March 11, 2020. Since the beginning of the pandemic, an unprecedented number of COVID-19 vaccine candidates have been investigated for their potential to manage the pandemic. Herein, we reviewed vaccine development and the associated research effort, both traditional and forward-looking, to demonstrate the advantages and disadvantages of their technology, in addition to their efficacy limitations against mutant SARS-CoV-2. Moreover, we report repurposed drug discovery, which mainly focuses on virus-based and host-based targets, as well as their inhibitors. SARS-CoV-2 targets include the main protease (Mpro), and RNA-dependent RNA-polymerase (RdRp), which are the most well-studied and conserved across coronaviruses, enabling the development of broad-spectrum inhibitors of these enzymes.

Serinol-Based Versatile Disulfide-Reducing Reagent

Here, we report the synthesis of disulfide-reducing agents 2-(dibenzylamino) propane-1,3-dithiol (DPDT) and 2-(dibenzylamino)-2-methylpropane-1,3-dithiol (DMPDT) from serinol and methyl serinol, respectively. DPDT was found to show greater stability than DMPDT. Hence, the effectiveness of DPDT as a reducing agent was evaluated in both liquid and solid phases. The reducing capacity of this agent was comparable to that of DTT.

DBU mediated one-pot synthesis of triazolo triazines via Dimroth type rearrangement

Herein we report an efficient one-pot synthesis of [1,2,4]triazolo[1,5 a][1,3,5]triazines from commercially available substituted aryl/heteroaryl aldehydes and substituted 2-hydrazinyl-1,3,5-triazines via N-bromosuccinimide (NBS) mediated oxidative C–N bond formation. Isomerisation of [1,2,4]triazolo[4,3-a][1,3,5]triazines to [1,2,4]triazolo[1,5-a][1,3,5]triazines is driven by 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) affording both isomers with good to excellent yields (70–96%).

We demonstrate a simple yet efficient one-pot synthesis of two triazolotriazine isomers via DBU mediated Dimroth type rearrangement with excellent yields.

Novel thiomorpholine tethered isatin hydrazones as potential inhibitors of resistant Mycobacterium tuberculosis

Novel chemotherapeutic agents against multidrug resistant-tuberculosis (MDR-TB) are urgently needed at this juncture to save the life of TB-infected patients. In this work, we have synthesized and characterized novel isatin hydrazones 4(a-o) and their thiomorpholine tethered analogues 5(a-o). All the synthesized compounds were initially screened for their anti-mycobacterial activity against the H₃₇Rv strain of Mycobacterium tuberculosis (MTB) under level-I testing. Remarkably, five compounds 4f, 4h, 4n, 5f and 5m (IC₅₀ = 1.9 µM to 9.8 µM) were found to be most active, with 4f (IC₅₀ = 1.9 µM) indicating highest inhibition of H₃₇Rv. These compounds were further evaluated at level-II testing against the five drug-resistant strains such as isoniazid-resistant strains (INH-R1 and INH-R2), rifampicin-resistant strains (RIF-R1 and RIF-R2) and fluoroquinolone-resistant strain (FQ-R1) of MTB. Interestingly, 4f and 5f emerged as the most potent compounds with IC₅₀ of 3.6 µM and 1.9 µM against RIF-R1 MTB strain, followed by INH-R1 MTB strain with IC₅₀ of 3.5 µM and 3.4 µM, respectively. Against FQ-R1 MTB strain, the lead compounds 4f and 5f displayed excellent inhibition at IC₅₀ 5.9 µM and 4.9 µM, respectively indicating broad-spectrum of activity. Further, molecular docking, ADME pharmacokinetic and molecular dynamics simulations of the compounds were performed against the DNA gyrase B and obtained encouraging results.

Design and synthesis of pyrazolone-based compounds as potent blockers of SARS-CoV-2 viral entry into the host cells

SARS-CoV-2 are enveloped positive-stranded RNA viruses that replicate in the cytoplasm. It relies on the fusion of their envelope with the host cell membrane to deliver their nucleocapsid into the host cell. The spike glycoprotein (S) mediates virus entry into cells via the human Angiotensin-converting enzyme 2 (hACE2) protein located on many cell types and tissues' outer surface. This study, therefore, aimed to design and synthesize novel pyrazolone-based compounds as potential inhibitors that would interrupt the interaction between the viral spike protein and the host cell receptor to prevent SARS-CoV 2 entrance into the cell. A series of pyrazolone compounds as potential SARS-CoV-2 inhibitors were designed and synthesized. Employing computational techniques, the inhibitory potentials of the designed compounds against both spike protein and hACE2 were evaluated. Results of the binding free energy from the in-silico analysis, showed that three compounds (7i, 7k and 8f) and six compounds (7b, 7h, 7k, 8d, 8g, and 8h) showed higher and better binding high affinity to SARS-CoV-2 Sgp and hACE-2, respectively compared to the standard drugs cefoperazone (CFZ) and MLN-4760. Furthermore, the outcome of the structural analysis of the two proteins upon binding of the inhibitors showed that the two proteins (SARS-CoV-2 Sgp and hACE-2) were stable, and the structural integrity of the proteins was not compromised. This study suggests pyrazolone-based compounds might be potent blockers of the viral entry into the host cells.

One-Pot, Multicomponent, Diastereoselective, Green Synthesis of 3,4-Dihydro-2H-benzo[b][1,4]oxazine Analogues

A novel green and efficient catalyst-free, mild one-pot, multicomponent synthetic strategy has been developed to construct substituted 3,4-dihydro-2H-benzo[b][1,4]oxazine. This reaction proceeds via in situ formation of Schiff-base followed by base mediated alkylation with phenacyl bromide/substituted phenacyl bromide, finally leading to intramolecular cyclization to give a mixture of diastereomers with excellent diastereoselectivity (up to dr = 99:1), which were isolated as a single diastereomer in moderate to excellent yields (41-92%). Besides, this new versatile methodology provides a wide scope for the synthesis of different functionally substituted benzoxazine scaffolds and can be further exploited as building blocks for the synthesis of multifaceted molecular structures, especially for pharmaceutical applications.

Authentication of five Barilius species from Indian waters using DNA barcoding

Authentic identification of fish species is essential for conserving them as a valuable genetic resource in our environment. DNA barcoding of living beings has become an important and ultimate tool for establishing their molecular identity. Among cyprinids, Barilius is an important genus having nearly 23 species in Indian region whose morphological identification is often difficult due to minute differences in their features. Five species collected from Indian waters and primarily identified as Opsarius bakeri (syn. Barilius bakeri), B. gatensis, B. vagra, B. bendelisis and B. ngawa were authenticated by their DNA barcoding based on mitochondrial COI gene sequences. Five individuals of each species were taken for barcode preparation by COI gene sequencing which yielded one barcode for B. ngawa, two barcodes each for O. bakeri, B. gatensis, B. bendelisis and three barcodes for B. vagra. The order of inter and intra-specific variation was estimated to know a preliminary status of variation prevailing in these cold stream fish species significant for evolution and conservation of these valued species of our ichthyofauna. Average variation within genera was found to be 13.6% with intra-specific variation ranging from 0.0% (B. ngawa) to 0.6% (B. gatensis). These distance data are in the same order found by various researchers globally using COI barcode sequences in different fish species. Phylogenetic relatedness among Barilius species and some other cyprinids validate their status of individual species as established by conventional taxonomy.

Low-depth shotgun sequencing resolves complete mitochondrial genome sequence of Labeo rohita

Labeo rohita, popularly known as rohu, is a widely cultured species in whole Indian subcontinent. In the present study, we used in-silico approach to resolve complete mitochondrial genome of rohu. Low-depth shotgun sequencing using Roche 454 GS FLX (Branford, Connecticut, USA) followed by de novo assembly in CLC Genomics Workbench version 7.0.4 (Aarhus, Denmark) revealed the complete mitogenome of L. rohita to be 16 606 bp long (accession No. KR185963). It comprised of 13 protein-coding genes, 22 tRNAs, 2 rRNAs and 1 putative control region. The gene order and organization are similar to most vertebrates. The mitogenome in the present investigation has 99% similarity with that of previously reported mitogenomes of rohu and this is also evident from the phylogenetic study using maximum-likelihood (ML) tree method. This study was done to determine the feasibility, accuracy and reliability of low-depth sequence data obtained from NGS platform as compared to the Sanger sequencing. Thus, NGS technology has proven to be competent and a rapid in-silico alternative to resolve the complete mitochondrial genome sequence, thereby reducing labors and time.

Assessment of tissue-specific effect of cadmium on antioxidant defense system and lipid peroxidation in freshwater murrel, Channa punctatus

The effects of different concentrations of cadmium chloride on the extent of lipid peroxidation (LPO) and alterations in the antioxidant enzyme activities were studied in liver, kidney and gill tissues of freshwater murrel, Channa punctatus. The fish specimens were exposed to 6.7, 13.4 and 20.1 mg l(-1) sublethal concentrations of cadmium chloride and the oxidative stress was assessed after 24, 48, 72 and 96 h post-exposure. The biomarkers selected for the study were thiobarbituric acid reactive substances for assessing the extent of lipid peroxidation and antioxidant defense system such as reduced glutathione (GSH), glutathione reductase (GR), glutathione peroxidase (GP(X)), glutathione-S-transferase (GST), catalase (CAT) and superoxide dismutase (SOD) activities. In general, the cadmium exposure elevated the LPO in subject tissues of treated group and modulated the activities of GPx, GST, SOD, CAT, GR and level of GSH after given exposure as compared to the control. All enzymes activities, except CAT (in kidney and gills), and amount of LPO elevated significantly (P < 0.05) in treated group with respect to control in all tissues, while significant difference was not observed between the exposed concentrations and within exposure duration. The results indicated that increase in LPO level and the fluctuation in antioxidant defense system in fish could be due to cadmium-induced increase in the production of reactive oxygen species (ROS). The potential role of these parameters as biomarkers of heavy metal pollution in aquatic system is discussed.

Nucleotide variation and physical mapping of ribosomal genes using FISH in genus Tor (Pisces, Cyprinidae)

Molecular cytogenetic studies were carried out for localization of 18S and 5S ribosomal DNAs on chromosomes of three cyprinid fish species viz., T. khudree, T. mussullah and T. mosal mahanadicus using two color fluorescence in situ hybridization (FISH). All the species typically possessed 100 diploid chromosomes with minor variation in karyo-morphology. The 18S rDNA signals were observed on two pair of chromosomes in T. khudree and T. mussullah, and three pairs in T. mosal mahanadicus. The location of 18S signals also showed affinity to silver nitrate and chromomycin A3 staining. Similarly, variation in localization of 5S rDNA among the three species has been detected with the presence of FISH signals on one pair of chromosome in T. khudree and T. mussullah, and on two pairs in T. mosal mahanadicus. These molecular markers could be used as species specific markers for taxonomic identification and can further add in understanding the dynamics of genome organization and karyotypic evolution of these species. The 18S rDNA region was sequenced that generated 1811, 1810 and 1776 bp long 18S sequence in T. khudree, T. mussullah and T. mosal mahanadicus, respectively. The 18S rDNA sequence showed 95-98% identity among the subject species. Similarly, 5S sequencing generated 203 bp long fragments in these species with 100% identity in coding and 9.63% variability in non-transcribed spacer regions. The nucleotide sequence variations could be used for understanding the genetic diversity and will add new informative characters in comparative genomics. These results, in general, would enhance the value and interpretation of ecological assessment data for conservation of Tor species.

Extensive NOR site polymorphism in geographically isolated populations of Golden mahseer, Tor putitora

Analyses of nucleolar organizer region (NOR) site polymorphism using silver staining were carried out in 72 individuals of 5 geographically isolated populations of Tor putitora from India. All Ag-NORs analyzed were constituted by rDNA that was confirmed by the presence of positive fluorescence in situ hybridization (FISH) signals. Analyses of the extra NORs among the populations confirmed the hypothesis that multi-chromosomal NOR site polymorphism is not an exception but a rule. We found a negative correlation between the mean number of extra NORs and geographical distance from the Alaknanda River population, and a significant positive correlation between the genetic distances obtained by NOR data and geographical distances among the isolated populations. These findings suggest a single geographical origin of this NOR polymorphism, from which it might have radiated to neighboring populations before their isolation. The distribution of NOR site variation was compared with the sequence variation of the ITS1 region of major rDNA (45S) and the two were found to be positively related. Different mechanisms such as transposable elements adjacent to ribosomal genes, repetitive elements which could serve as a point for chromosome exchange, amplification of minor rDNA loci, and reinsertion of extrachromosomal rDNA amplified during oogenesis have been proposed to explain the apparent NOR site polymorphism. The high dispersion of NOR site variants within and among the populations suggests that whatever transposition phenomenon is responsible for repetitive DNA or NOR jumping, it could still be active in T. putitora.

Karyotypic diversity and evolution of seven mahseer species (Cyprinidae) from India

Mahseer is a group of fish species that are well known as food and game fishes. The taxonomy of the mahseer species is confusing owing to the morphological variations and habitat adaptation. Detailed karyomorphological investigations have been carried out in seven species of mahseer, using karyotyping, Ag-NOR and fluorescent staining techniques. The basic diploid chromosome number (2n), in all mahseer species, was observed to be 100; however, the karyotype formula varied among the species, which were recorded as: 20m + 14sm + 22st + 44t (fundamental arm number, FN = 134) in Tor khudree; 22m + 24sm + 24st + 30t (FN = 146) in Tor mussullah; 12m + 22sm + 14st + 52t (FN = 134) in Tor putitora; 20m + 24sm + 24st + 32t (FN = 144) in Tor tor; 20m + 30sm + 24st + 26t (FN = 150) in Tor chelynoides; 20m + 20sm + 20st + 40t (FN = 140) in Tor progeneius; and 20m + 18sm + 14st + 48t (FN = 138) in Neolissochilus hexagonolepis. Silver staining of the chromosomes revealed the presence of multiple nucleolar organizer regions (NOR) in these mahseer species. The highest number of NORs was observed in T. tor (four pairs of chromosomes), whereas the other six species possessed Ag-NOR signals on only two pairs of chromosomes. Although chromomycin A(3) (CMA(3)) staining induced bright fluorescence signals on same Ag-NORs sites, with CMA(3), one additional signal was observed on the p arm of subtelocentric chromosomes in T. tor, T. chelynoides, T. progeneius and N. hexagonolepis, which may indicate the presence of inactive NOR in these species. The information on cytogenetic profile of these mahseer species is discussed in the light of cytotaxonomic implications and understanding the karyoevolution of these fish species.

Physical mapping of rRNA gene in endangered fish Osteobrama belangeri (Valenciennes, 1844) (family: Cyprinidae)

Physical mapping of the 18S ribosomal RNA gene (rDNA) was carried out by fluorescent in situ hybridization (FISH) in the endangered freshwater fish O. belangeri. The specimens were collected from Imphal valley, Manipur, India and metaphase chromosome preparation was made using standard hypotonic treatment, methanol-acetic acid fixation and flame-drying technique followed by Giemsa, silver, CMA3 staining for complete cytogenetic characterization of the species. The diploid chromosome number was found to be 50 and the karyotype composed of 6m+16sm+12st+16t (FN=72). One active rDNA site, located on short arm of 3rd submetacentric chromosome, was mapped by FISH and confirmed by silver and CMA3 staining. The karyomorphology, chromosomal location of rDNA loci in this species and the utility of these cytogenetic markers have been discussed in the paper.

Genotoxicity assessment of acute exposure of chlorpyrifos to freshwater fish Channa punctatus (Bloch) using micronucleus assay and alkaline single-cell gel electrophoresis

Chlorpyrifos (O,O-diethyl O-3,5,6-trichloro-2-pyridylphosphorothioate) is one of the organophosphate pesticides widely used in agricultural practices throughout world and irreversible inhibitor of cholinesterase in all animal species. Limited efforts have been made to study acute genotoxic effects of chlorpyrifos (CPF) in different tissues of fish using genotoxic biomarkers. Therefore, the present investigation was aimed to study the induction of DNA damage by CPF in freshwater teleost fish Channapunctatus using micronucleus assay (MN assay) and alkaline single-cell gel electrophoresis (comet assay). The value of LC(50) - 96 h of CPF was determined as 811.98 microgl(-1) for C. punctatus, in a semi-static system and on the basis of LC(50) value three acute concentrations viz., 203, 406 and 609 microgl(-1) were determined. The fishes were exposed to the different concentrations of CPF for 96 h and samplings were done at regular intervals for assessment of the MN frequencies and DNA damage. In general, significant effects (P<0.01) from both concentrations and time of exposure were observed in exposed fishes. It was found that the micronucleus induction was highest on 96 h at all concentrations in the peripheral blood. Similar trend was observed for the DNA damage measured in terms of the percentage of tail DNA in the lymphocyte and gill cells. This study explored the combined use of micronucleus assay and comet assay for in vivo laboratory studies using fresh water fish for screening the genotoxic potential of xenobiotics.

Ovarian development in Labeo dyocheilus (McClelland) during active reproductive phase under captive and wild conditions

Ovarian development in Labeo dyocheilus was assessed during active reproductive phase under ambient environmental conditions in captivity and wild. Increasing day length and water temperature seemed favourable for ovarian development in female L. dyocheilus under both conditions. Gonadosomatic index (GSI) was lower in May and higher in July in captivity (6.168 and 13.366) and wild (5.798 and 16.166) respectively Ovarian development started little bit in advance in captivity with late yolk vesicle stage oocyte in May when yolk globule stage oocytes were prominent in wild. Fully grown oocytes with germinal vesicle migration (GVM) and germinal vesicle breakdown (GVBD) stages were observed in July in both conditions. Degree of transformation of developing oogonials into advance stage oocytes was observed to be better in wild fish compared to captivity reared ones. The histophysiological changes in liver corresponded well to the progression of ovarian development. Successive granulation and vacuolization of hepatocyte cytoplasm were indicative of augmented synthetic activity and probably mobilization of energy content for oocyte growth. These observations indicated that normal ovarian development of L. dyocheilus under captivity in Tarai region of Uttarakhand would be useful for success of its seed production in captivity for stock augmentation in wild or species diversification in aquaculture.