Current advancements in nanotechnology and nanoscience have resulted in new nanomaterials, which may pose health and environmental risks. Furthermore, several researchers are working to optimize ecologically friendly procedures for creating metal and metal oxide nanoparticles. The primary goal is to decrease the adverse effects of synthetic processes, their accompanying chemicals, and the resulting complexes. Utilizing various biomaterials for nanoparticle preparation is a beneficial approach in green nanotechnology. Furthermore, using the biological qualities of nature through a variety of activities is an excellent way to achieve this goal. Algae, plants, bacteria, and fungus have been employed to make energy-efficient, low-cost, and nontoxic metallic nanoparticles in the last few decades. Despite the environmental advantages of using green chemistry-based biological synthesis over traditional methods as discussed in this article, there are some unresolved issues such as particle size and shape consistency, reproducibility of the synthesis process, and understanding of the mechanisms involved in producing metallic nanoparticles via biological entities. Consequently, there is a need for further research to analyze and comprehend the real biological synthesis-dependent processes. This is currently an untapped hot research topic that required more investment to properly leverage the green manufacturing of metallic nanoparticles through living entities. The review covers such green methods of synthesizing nanoparticles and their utilization in the scientific world.

Background: ATP-binding cassette super family G2 protein is an active ATP-binding cassette transporter with potential to combat cancer stem cells. Objective: Due to the lack of potential ATP-binding cassette super family G2 inhibitors we screened natural inhibitors, which could be safe source to control multidrug resistance by blocking the regulation of ATP-binding cassette super family G2 protein. Method: Three-dimensional structure of ATP-binding cassette super family G2 protein downloaded from the protein databank and chemical structures of selected 166 compounds of the training dataset retrieved from PubChem. Drug-likeness and docking analysis shortlisted the dataset for pharmacophore generation. LigandScout 4.1.5 used for pharmacophore-based screening of Zbc library of ZINC database and Autodock Vina utilized for molecular docking against the predicted active pocket of the target protein to evaluate potential association of protein and ligands. Physiochemical properties of novel compounds calculated by admetSAR respectively. Results: Through pharmacophore-based screening, ZINC4098704 (Rhein) was identified as a lead compound which demonstrates least binding energy (-8.5) and highest binding affinity with the target protein and showed optimal physiochemical profile. This compound is highly recommended for laboratory test to confirm its activity as ATP-binding cassette super family G2 inhibitors. Conclusion: Our computer-based study systematically selected natural lead compound, which could be effective in inhibiting ATP-binding cassette super family G2 and may be helpful in reversing the effect of multidrug resistance in order to increase the effectiveness of chemotherapy in cancer treatment.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). Reports of new variants that potentially increase virulence and viral transmission, as well as reduce the efficacy of available vaccines, have recently emerged. In this study, we computationally analyzed the N439K, S477 N, and T478K variants for their ability to bind Angiotensin-converting enzyme 2 (ACE2). We used the protein-protein docking approach to explore whether the three variants displayed a higher binding affinity to the ACE2 receptor than the wild type. We found that these variants alter the hydrogen bonding network and the cluster of interactions. Additional salt bridges, hydrogen bonds, and a high number of non-bonded contacts (i.e., non-bonded interactions between atoms in the same molecule and those in other molecules) were observed only in the mutant complexes, allowing efficient binding to the ACE2 receptor. Furthermore, we used a 2.0-μs all-atoms simulation approach to detect differences in the structural dynamic features of the resulting protein complexes. Our findings revealed that the mutant complexes possessed stable dynamics, consistent with the global trend of mutations yielding variants with improved stability and enhanced affinity. Binding energy calculations based on molecular mechanics/generalized Born surface area (MM/GBSA) further revealed that electrostatic interactions principally increased net binding energies. The stability and binding energies of N439K, S477 N, and T478K variants were enhanced compared to the wild-type-ACE2 complex. The net binding energy of the systems was −31.86 kcal/mol for the wild-type-ACE2 complex, −67.85 kcal/mol for N439K, −69.82 kcal/mol for S477 N, and −69.64 kcal/mol for T478K. The current study provides a basis for exploring the enhanced binding abilities and structural features of SARS-CoV-2 variants to design novel therapeutics against the virus.

No abstract

Clonal propagation is a process of asexually reproducing plants by multiplication of one copy to produce several copies that are genetically identical. One of the best methods of clonal propagation is using the cuttings. There are many plants that can be propagated through cuttings and one of them is guava. Guava is popular in Pakistan. To ensure that a guava tree will produce fruits that belong to its original cultivar, this study was conducted. Softwood cuttings of guava were treated with IBA (1600 ppm and 2000 ppm), NAA (7000 ppm and 10,000 ppm) and IBA+NAA (1600+7000 ppm and 2000+10,000 ppm). There were five media used (Soil, Peatmoss+Soil, Sand+Soil, Baggasse+Soil and Soil+Peatmoss+Sand+Bagasse. The experiment was laid out using Completely Randomized Block Design (CRBD) with two-factor factorial arrangement. A total of 105 cuttings were used, each with 12 cm length and with 2-4 nodes. Media samples were collected and physio-chemically analyzed at the Soil and Water Testing Laboratory in Layyah, Pakistan to assess the properties and fertility status. Guava cuttings with 1600 ppm IBA showed the best results in terms of the number of roots, root length and days to sprout, followed by 7000 ppm NAA in Peat moss+soil and soil+peat mass+sand+bagasse. For the combination of growth regulators, the best results were observed in IBA 1600 ppm + NAA 7000 ppm. Poorest result in all parameters (days to sprout, number of roots, and root length) was recorded in control. The 1600 ppm IBA with 10 second dipping time for softwood cuttings of guava yielded best results in peatmoss+soil media for all the parameters tested. Hence, this study concluded that treatment with auxin (such as IBA) can yield best results and can help to solve the problem in propagating guava using cuttings.

Klebsiella oxytoca is a gram-negative bacterium. It is opportunistic in nature and causes hospital acquired infections. Subtractive proteomics and reverse vaccinology approaches were employed to screen out the best proteins for vaccine designing. Whole proteome of K. oxytoca strain ATCC 8724, consisting of 5483 proteins, was used for designing the vaccine. Total 1670 cytotoxic T lymphocyte (CTL) epitope were predicted through NetCTL while 1270 helper T lymphocyte (HTL) epitopes were predicted through IEDB server. The epitopes were screened for non-toxicity, allergenicity, antigenicity and water solubility. After epitope screening 300 CTL and 250 HTL epitopes were submitted to IFN-γ epitope server to predict their Interferon-γ induction response. The selected IFN-γ positive epitopes were tested for their binding affinity with MHCI-DRB1 by MHCPred. The 15 CTL and 13 HTL epitopes were joined by linkers AAY and GPGPG respectively in vaccine construct. Chain C of Pam3CSK4 (PDB ID; 2Z7X) was linked to the vaccine construct as an adjuvant. A 450aa long vaccine construct was submitted to I-TASSER server for 3D structure prediction. Thirteen Linear B cells were predicted by ABCPred server and 10 sets of discontinues epitopes for 3D vaccine structure were predicted by DiscoTope server. The modeled 3D vaccine construct was docked with human Toll-like receptor 2 (PDB ID: 6NIG) by PatchDock. The docked complexes were refined by FireDock. The selected docked complex showed five hydrogen bonds and one salt bridge. The vaccine sequence was reverse transcribed to get nucleotide sequence for In silico cloning. The reverse transcribed sequence strand was cloned in pET28a(+) expression vector. A clone containing 6586 bp was constructed including the 450 bp of query gene sequence.

Glucose-regulated protein 78 (GRP78) might be a receptor for SARS-CoV-2 to bind and enter the host cell. Recently reported mutations in the spike glycoprotein unique to the receptor-binding domain (RBD) of different variants might increase the binding and pathogenesis. However, it is still not known how these mutations affect the binding of RBD to GRP78. The current study provides a structural basis for the binding of GRP78 to the different variants, i.e., B.1.1.7, B.1.351, B.1.617, and P.1 (spike RBD), of SARS-CoV-2 using a biomolecular simulation approach. Docking results showed that the new variants bound stronger than the wild-type, which was further confirmed through the free energy calculation results. All-atom simulation confirmed structural stability, which was consistent with previous results by following the global stability trend. We concluded that the increased binding affinity of the B.1.1.7, B.1.351, and P.1 variants was due to a variation in the bonding network that helped the virus induce a higher infectivity and disease severity. Consequently, we reported that the aforementioned new variants use GRP78 as an alternate receptor to enhance their seriousness.

Lepidoptera is the second most diverse insect order outnumbered only by the Coeleptera. Acetylcholinesterase (AChE) is the major target site for insecticides. Extensive use of insecticides, to inhibit the function of this enzyme, have resulted in the development of insecticide resistance. Complete knowledge of the target proteins is very important to know the cause of resistance. Computational annotation of insect acetylcholinesterase can be helpful for the characterization of this important protein. Acetylcholinesterase of fourteen lepidopteran insect pest species was annotated by using different bioinformatics tools. AChE in all the species was hydrophilic and thermostable. All the species showed lower values for instability index except L. orbonalis, S. exigua and T. absoluta . Highest percentage of Arg, Asp, Asn, Gln and Cys were recorded in P. rapae . High percentage of Cys and Gln might be reason for insecticide resistance development in P. rapae. Phylogenetic analysis revealed the AChE in T. absoluta , L. orbonalis and S. exigua are closely related and emerged from same primary branch. Three functional motifs were predicted in eleven species while only two were found in L. orbonalis, S. exigua and T. absoluta. AChE in eleven species followed secretory pathway and have signal peptides. No signal peptides were predicted for S. exigua , L. orbonalis and T. absoluta and follow non secretory pathway. Arginine methylation and cysteine palmotylation was found in all species except S. exigua , L. orbonalis and T. absoluta . Glycosylphosphatidylinositol (GPI) anchor was predicted in only nine species.