Polymers of Intrinsic Microporosity Based on Dibenzodioxin Linkage: Design, Synthesis, Properties, and Applications.

The development of polymers of intrinsic microporosity (PIMs) over the last two decades has established them as a distinct class of microporous materials, which combine the attributes of microporous solid materials and the soluble nature of glassy polymers. Due to their solubility in common organic solvents, PIMs are easily processable materials that potentially find application in membrane-based separation, catalysis, ion separation in electrochemical energy storage devices, sensing, etc. Dibenzodioxin linkage, Tröger's base, and imide bond-forming reactions have widely been utilized for synthesis of a large number of PIMs. Among these linkages, however, most of the studies have been based on dibenzodioxin-based PIMs. Therefore, this review focuses precisely on dibenzodioxin linkage chemistry. Herein, the design principles of different rigid and contorted monomer scaffolds are discussed, as well as synthetic strategies of the polymers through dibenzodioxin-forming reactions including copolymerization and postsynthetic modifications, their characteristic properties and potential applications studied so far. Towards the end, the prospects of these materials are examined with respect to their utility in industrial purposes. Further, the structure-property correlation of dibenzodioxin PIMs is analyzed, which is essential for tailored synthesis and tunable properties of these PIMs and their molecular level engineering for enhanced performances making these materials suitable for commercial usage.

Heterogeneous iron catalyst for C(1)-H functionalization of 2-naphthols with primary aromatic alcohols.

An iron oxide nanocatalyst supported on a potassium exchanged zeolite-Y (Fe2O3-KY) is an efficient and reusable catalyst that promotes the selective α-H functionalization of 2-naphthols with various aromatic primary alcohols. The reaction occurs at 110 °C in dichloroethane and requires 6 h for completion. The product yields were found to vary with respect to the nature of the substituents. Benzyl alcohols with electron-donating groups gave the highest yields of up to 90%.

Response of vaccination on community transmission of COVID-19: a dynamical approach.

Due to the severity of COVID-19, vaccination campaigns have been or are underway in most parts of the world. In the current circumstances, it is obligatory to examine the response of vaccination on transmission of the SARS-CoV-2 virus when there are many vaccines available. Considering the importance of vaccination, a dynamic model has been proposed to provide an insight in the same direction. A mathematical model has been developed where six population compartments viz. susceptible, infected, vaccinated, home-isolated, hospitalized and recovered population are considered. Moreover, two novel parameters are included in the model to ascertain the effectiveness and speed of the vaccination campaign. Reproduction number and local stability of both the disease-free and endemic equilibrium points are studied to examine the nature of population dynamics. Graphical results for the community stage of COVID-19 infection are simulated and compared with real data to ascertain the validity of our model. The data is then studied to understand the impact of vaccination. These numerical results evidently demonstrate that home isolation and hospitalization should continue for the infected people until the transmission of the virus from person to person reduces sufficiently after completely vaccinating every nation. This model also recommends that all type of prevention measures should still be taken to avoid any type of critical situation due to infection and also reduce the death rate.

Designing of peptide aptamer targeting the receptor-binding domain of spike protein of SARS-CoV-2: an in silico study.

Short synthetic peptide molecules which bind to a specific target protein with a high affinity to exert its function are known as peptide aptamers. The high specificity of aptamers with small-molecule targets (metal ions, dyes and theophylline; ATP) is within 1 pM and 1 µM range, whereas with the proteins (thrombin, CD4 and antibodies) it is in the nanomolar range (which is equivalent to monoclonal antibodies). The recently identified coronavirus (SARS-CoV-2) genome encodes for various proteins, such as envelope, membrane, nucleocapsid, and spike protein. Among these, the protein necessary for the virus to enter inside the host cell is spike protein. The work focuses on designing peptide aptamer targeting the spike receptor-binding domain of SARS-CoV-2. The peptide aptamer has been designed by using bacterial Thioredoxin A as the scaffold protein and an 18-residue-long peptide. The tertiary structure of the peptide aptamer is modeled and docked to spike receptor-binding domain of SARS CoV2. Molecular dynamic simulation has been done to check the stability of the aptamer and receptor-binding domain complex. It was observed that the aptamer binds to spike receptor-binding domain of SARS-CoV-2 in a similar pattern as that of ACE2. The aptamer-receptor-binding domain complex was found to be stable in a 100 ns molecular dynamic simulation. The aptamer is also predicted to be non-antigenic, non-allergenic, non-hemolytic, non-inflammatory, water-soluble with high affinity toward ACE2 than serum albumin. Thus, peptide aptamer can be a novel approach for the therapeutic treatment for SARS-CoV-2.

Immunoinformatics mapping of potential epitopes in SARS-CoV-2 structural proteins.

All approved coronavirus disease 2019 (COVID-19) vaccines in current use are safe, effective, and reduce the risk of severe illness. Although data on the immunological presentation of patients with COVID-19 is limited, increasing experimental evidence supports the significant contribution of B and T cells towards the resolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Despite the availability of several COVID-19 vaccines with high efficacy, more effective vaccines are still needed to protect against the new variants of SARS-CoV-2. Employing a comprehensive immunoinformatic prediction algorithm and leveraging the genetic closeness with SARS-CoV, we have predicted potential immune epitopes in the structural proteins of SARS-CoV-2. The S and N proteins of SARS-CoV-2 and SARS-CoVs are main targets of antibody detection and have motivated us to design four multi-epitope vaccines which were based on our predicted B- and T-cell epitopes of SARS-CoV-2 structural proteins. The cardinal epitopes selected for the vaccine constructs are predicted to possess antigenic, non-allergenic, and cytokine-inducing properties. Additionally, some of the predicted epitopes have been experimentally validated in published papers. Furthermore, we used the C-ImmSim server to predict effective immune responses induced by the epitope-based vaccines. Taken together, the immune epitopes predicted in this study provide a platform for future experimental validations which may facilitate the development of effective vaccine candidates and epitope-based serological diagnostic assays.

Neutralization of Daboxin P activities by rationally designed aptamers.

Inefficacy and associated risks of current antivenom has raised the need for alternative approaches of snakebite management. Aptamers are one such alternative which is being pursued for therapeutic interventions as well as for design of diagnostic kits due to its high specificity. Present study focussed on designing and validating nucleic acid aptamers against snake venom PLA2, a hydrolytic enzyme present in all venomous snakes. The aptamers were designed by adding nucleic acid chain on the surface of Daboxin P, a major PLA2 enzyme of Daboia russelii venom. Binding characteristics of the aptamers were confirmed by docking to Daboxin P as well as acidic and basic PLA2s from different snake species using in silico docking. The aptamers folded into different tertiary structures and bound to the active and Ca2+ binding site of PLA2 enzymes. Molecular dynamics simulation analysis of Daboxin P-aptamer complexes showed that the complexes were stable in an aqueous environment. The electrophoretic mobility shift assay further confirmed the binding of the synthetic aptamers to Daboxin P and other snake venom PLA2 enzymes. The aptamers inhibited the sPLA2 activity with an IC50 value ranging between 0.52 µM and 0.77 µM as well as the anticoagulant activity of Daboxin P. The aptamers could also inhibit the PLA2 activity of Echis carinatus crude venom and anti-coagulant activity of Bungarus caeruleus crude venom, members of big four snakes. However, the aptamers didn't inhibit fibrinogenolytic or proteolytic activity of big four venom as well as the coagulation and hemolytic activities. Thus, aptamers can be rationally designed to inhibit the biochemical and biological activities of snake venom proteins.

Molecular mechanisms of action of Trehalose in cancer: A comprehensive review.

Cellular homeostasis maintained by several cellular processes such as autophagy, apoptosis, inflammation, oxidative stress, aging, and neurodegeneration, contribute to cell growth and development. Cancer cells undergo aberrant changes from a normal cell that show abnormal behaviour such as reduced apoptosis and autophagy, increased oxidative stress and inflammation. Various pharmacological and genetic inhibitors have been reported as drug candidates to control cancer cells, but the use of natural molecules as anti-cancer agents are limited. There is an emerging need for the development of alternative natural therapeutic agents that maintain cellular homeostasis without affecting cell viability and physiology. This review highlights the multifunctional roles of Trehalose, a natural disaccharide that can target various cellular processes in the cancer. Trehalose possessing an antioxidant activity also has effect on cancer, which is explained through targeting cell progression, angiogenesis and metastasis pathways at molecular level targeting EGFR, PI3K, Akt, VEGF and MMP 9 proteins inside the cell.

In silico designing of multi-epitope vaccine construct against human coronavirus infections.

Single stranded RNA viruses were known to cause variety of diseases since many years and are gaining much importance due to pandemic after the identification of a novel corona virus (severe acute respiratory syndrome-coronavirus (SARS-CoV-2)). Seven coronaviruses (CoVs) are known to infect humans and they are OC43 CoV, NL63 CoV, HKU1 CoV, Middle East respiratory syndrome, SARS CoV, and SARS CoV-2. Virus replication weakens the immune system of host thereby altering T-cell count and much of interferon response. Although no vaccine or therapeutic treatment has been approved till now for CoV infection, trials of vaccine against SARS CoV-2 are in progress. One of the epitopes used for vaccine production is of the spike protein on the surface of virus. The work focuses on designing of multi-epitope vaccine construct for treatment of seven human CoV infections using the epitopes present on the spike protein of human CoVs. To address this, immuno-informatics techniques have been employed to design multi-epitope vaccine construct. B- and T-cell epitopes of the spike proteins have been predicted and designed into a multi-epitope vaccine construct. The tertiary structure of the vaccine construct along with the adjuvant has been modelled and the physiochemical properties have been predicted. The multi-epitope vaccine construct has antigenic and non-allergenic property. After validation, refinement and disulphide engineering of the vaccine construct, molecular docking with toll-like receptors (TLRs) have been performed. Molecular dynamics simulation in aqueous environment predicted that the vaccine-TLRs complexes were stable. The vaccine construct is predicted to be able to trigger primary immune response in silico. Communicated by Ramaswamy H. Sarma.

In silico and in vitro neutralization of PLA2 activity of Daboxin P by butein, mimosine and bakuchiol.

Medicinal plants have always been used for snakebite treatment by traditional healers but they lack scientific evidence of action. However secondary metabolites of such plants have been explored and found to inhibit the toxic effect of venom proteins. Literature survey from 2003 to 2019 resulted in identification of 251 secondary metabolites with such properties. In silico docking studies of these metabolites with modelled structure of Daboxin P, a PLA2 from Indian Daboia russelii revealed that butein, mimosine and bakuchiol bind to Daboxin P with high affinity. Butein interacted with the catalytic triad but mimosine and bakuchiol interacted with the Ca2+ binding residues of Daboxin P. In vitro validation showed that the molecules inhibited the sPLA2 activity of Daboxin P. Interestingly, mimosine and bakuchiol could also neutralize the anti-coagulatory activity of Daboxin P. Further, it was observed that butein and mimosine could neutralize the PLA2 activity of Indian big four venoms dose dependently. On the other hand, mimosine and bakuchiol could also neutralize the pro/anti-coagulatory effect of big four crude venom. Thus, in this study, three molecules have been identified which can neutralize the PLA2 activity and pro/anti-coagulatory effect of Daboxin P as well as crude venom of big four.

Targeting SARS CoV2 (Indian isolate) genome with miRNA: An in silico study.

The newly identified SARS CoV2 has become a global pandemic since December 2019. Various researchers are trying to design a vaccine candidate against the virus. On the other hand, another group is focussing on repurposing approved or clinically tested drugs for treatment. However, there is always a search for alternative therapies. Thus, we propose an alternative approach apart from chemotherapy that is the usage of miRNA as novel antisense therapy to cure SARS CoV2 infected patients. To address the objective, miRNAs have been designed by targeting the genome of SARS CoV2 (Indian isolate). First, the open reading frames in the viral genome have been identified, and the proteins encoded by those open reading frames have been predicted. Using computational biology, several miRNAs have been designed and their probability to bind to a viral gene has been predicted. In addition, miRNA target mining in the host cell has been done to rule out the possibility of non-specific binding of the miRNAs. The miRNAs having the highest chances to bind to the viral genome have been converted into pre-miRNAs, and their interaction with dicer endoribonuclease has been studied by molecular docking. Results revealed that the pre-miRNAs interact with the RNAse III 2 domain of dicer. Thus, it is predicted that the pre-miRNAs after delivery to the infected host cell will be processed by dicer to generate mature miRNAs that will target the SARS CoV2 viral genome. Therefore, miRNA therapy can be an alternative approach for the treatment of SARS CoV2 infection.

Naja kaouthia venom protein, Nk-CRISP, upregulates inflammatory gene expression in human macrophages.

Cysteine-Rich Secretory Proteins (CRISP) are widespread in snake venoms and known to target ion channels. More recently, CRISPs have been shown to mediate inflammatory responses. Involvement of potential receptor in CRISP-induced inflammatory reactions, however, remains unknown. A CRISP protein named as Nk-CRISP, was isolated from the venom of Naja kaouthia. The molecular mass of the purified protein was found to be ~25 kDa and the primary sequence was determined by MALDI TOF-TOF. The involvement of this protein in proinflammatory effects were evaluated in THP-1 macrophage-like cells. Nk-CRISP treated cells induced up-regulation of several inflammatory marker genes in dose dependent manner. Toll like receptor 4 (TLR4)-myeloid differentiation factor 2 (MD2) complex are known to play crucial role in recognition of damage/pathogen-associated molecular patterns and activation of innate immune response. Therefore, we hypothesized that snake venom CRISP could also modulate the innate immune response via TLR4-MD2 complex. In-silico molecular docking study of cobra CRISP with TLR4-MD2 receptor complex reveals CRISP engages its cysteine-rich domain (CRD) to interact with complex. Inhibition of TLR4 signalling pathway using CLI-095 confirmed the role of TLR4 in Nk-CRISP induced inflammatory responses. Collectively, these findings imply that TLR4 initiates proinflammatory signalling following recognition of cobra CRISP and alteration of TLR4 receptor might improve or control CRISP induced inflammation.

Exploring rotavirus proteome to identify potential B- and T-cell epitope using computational immunoinformatics.

Rotavirus is the most common cause of acute gastroenteritis in infants and children worldwide. The functional correlation of B- and T-cells to long-lasting immunity against rotavirus infection in the literature is limited. In this work, a series of computational immuno-informatics approaches were applied and identified 28 linear B-cells, 26 conformational B-cell, 44 TC cell and 40 TH cell binding epitopes for structural and non-structural proteins of rotavirus. Further selection of putative B and T cell epitopes in the multi-epitope vaccine construct was carried out based on immunogenicity, conservancy, allergenicity and the helical content of predicted epitopes. An in-silico vaccine constructs was developed using an N-terminal adjuvant (RGD motif) followed by TC and TH cell epitopes and B-cell epitope with an appropriate linker. Multi-threading models of multi-epitope vaccine construct with B- and T-cell epitopes were generated and molecular dynamics simulation was performed to determine the stability of designed vaccine. Codon optimized multi-epitope vaccine antigens was expressed and affinity purified using the E. coli expression system. Further the T cell epitope presentation assay using the recombinant multi-epitope constructs and the T cell epitope predicted and identified in this study have not been investigated. Multi-epitope vaccine construct encompassing predicted B- and T-cell epitopes may help to generate long-term immune responses against rotavirus. The computational findings reported in this study may provide information in developing epitope-based vaccine and diagnostic assay for rotavirus-led diarrhea in children's.

In silico Designing of Novel Inhibitors for Triple Inhibition of Aldose Reductase, Aldose Reductase Like Protein 1, and Aldehyde Reductase.

BACKGROUND: Cancer is a well-known and well-studied disease. There are environmental as well as genetic factors that trigger cancer. All forms of cancer are associated with the deregulation of genes and proteins. Aldose reductase, Aldose Reductase like protein 1 and Aldehyde Reductase are homologous proteins that are overexpressed in different types of cancer. They are NADPHdependent oxidoreductases. The active site is conserved, thus there is very less substrate specificity among those proteins. In this study, novel molecules targeting the three proteins are designed. METHODS: LigBuilder V2 software is used to design novel molecules. Molecular docking is performed to study the binding affinity of each ligand towards the targets. Molecular Dynamics Simulation was done to check the stability of protein-ligand complexes in an aqueous environment. RESULTS: Six novel molecules have been designed. The six molecules studied are found to have better in silico affinity than tolrestat (known inhibitor). The designed molecules are predicted to be orally active. Finally, Molecular Dynamics Simulation showed that the protein-ligand complexes are stable in an aqueous environment. CONCLUSION: New molecules targeting Aldose reductase, Aldose Reductase like protein 1 and Aldehyde Reductase have been designed.

Expression and characterization of Flavikunin: A Kunitz-type serine protease inhibitor identified in the venom gland cDNA library of Bungarus flaviceps.

Trancriptomic analysis of the venom gland cDNA library of Bungarus flaviceps revealed Kunitz-type serine protease inhibitor as one of the major venom protein families with three groups A, B, C. One of the group B isoforms named Flavikunin, which lacked an extra cysteine residue involved in disulfide bond formation in ß-bungarotoxin, was synthesized, cloned, and overexpressed in Escherichia coli. To decipher the structure-function relationship, the P1 residue of Flavikunin, histidine, was mutated to alanine and arginine. Purified wild-type and mutant Flavikunins were screened against serine proteases-thrombin, factor Xa, trypsin, chymotrypsin, plasmin, and elastase. The wild-type and mutant Flavikunin (H∆R) inhibited plasmin with an IC 50 of 0.48 and 0.35 µM, respectively. The in-silico study showed that P1 residue of wild-type and mutant (H∆R) Flavikunin interacted with S1' and S1 site of plasmin, respectively. Thus, histidine at the P1 position was found to be involved in plasmin inhibition with mild anticoagulant activity.

Molecular docking and molecular dynamics studies reveal structural basis of inhibition and selectivity of inhibitors EGCG and OSU-03012 toward glucose regulated protein-78 (GRP78) overexpressed in glioblastoma.

Glioblastoma (GBM), a malignant form of brain tumor, has a high mortality rate. GRP78, one of the HSP70 protein family members, is overexpressed in GBM. GRP78 is the key chaperone protein involved in the unfolded protein response. Upregulated GRP78 expression in cancer cells inhibits apoptosis and promotes chemoresistance. GRP78 has an ATPase domain, a substrate-binding domain, and a linker region. ATP-competitive inhibitors such as EGCG and OSU-03012 inhibit GRP78 activity and reduce its expression in GBM. However, there is a lack of structural data on the binding modes of these inhibitors to GRP78 ATPase domain. Further, the mode of selectivity of these inhibitors toward GRP78 also is unknown. Toward this end, molecular docking was performed with AutoDock Vina and confirmation obtained by docking using ROSIE. The stability and MM-PBSA binding energy of GRP78-inhibitor complexes as well as energetic contribution of individual residues was analyzed by 50 ns molecular dynamics run with GROMACS. MSA by ClustalW2 identified unique amino acid residues in the ATPase domain of GRP78 which were different from the residues present in other HSP70 proteins. Important and unique amino acid residues of GRP78 such as Ile61, Glu293, Arg297, and Arg367 played a major role in the intermolecular interactions with these inhibitors. The interactions with unique residues of GRP78 as compared with those of HSP70-1A provided the basis for selectivity. It was found that the binding affinity and specificity/selectivity of EGCG toward GRP78 was higher than that toward HSP70-1A, and selectivity was even better than OSU-03012. OSU-03012 was predicted to bind to GRP78. Analyses from MD runs showed tight binding and stability of complexes, and the highest number of hydrogen bonds during the trajectory runs were comparable to those found in the docking studies. Energetic contribution of individual inhibitor-interacting residues showed that energy values of Ile61 and Glu293 were among the most negative. These studies are, to the best of our knowledge, the first studies characterizing EGCG and OSU-03012 interactions with GRP78 on a structural basis and provide a significant insight into their binding modes, selectivity, and structural stability.