Identification and Design of Novel Potential Antimicrobial Peptides Targeting Mycobacterial Protein Kinase PknB.

Antimicrobial peptides have gradually gained advantages over small molecule inhibitors for their multifunctional effects, synthesising accessibility and target specificity. The current study aims to determine an antimicrobial peptide to inhibit PknB, a serine/threonine protein kinase (STPK), by binding efficiently at the helically oriented hinge region. A library of 5626 antimicrobial peptides from publicly available repositories has been prepared and categorised based on the length. Molecular docking using ADCP helped to find the multiple conformations of the subjected peptides. For each peptide served as input the tool outputs 100 poses of the subjected peptide. To maintain an efficient binding for relatively a longer duration, only those peptides were chosen which were seen to bind constantly to the active site of the receptor protein over all the poses observed. Each peptide had different number of constituent amino acid residues; the peptides were classified based on the length into five groups. In each group the peptide length incremented upto four residues from the initial length form. Five peptides were selected for Molecular Dynamic simulation in Gromacs based on higher binding affinity. Post-dynamic analysis and the frame comparison inferred that neither the shorter nor the longer peptide but an intermediate length of 15 mer peptide bound well to the receptor. Residual substitution to the selected peptides was performed to enhance the targeted interaction. The new complexes considered were further analysed using the Elastic Network Model (ENM) for the functional site's intrinsic dynamic movement to estimate the new peptide's role. The study sheds light on prospects that besides the length of peptides, the combination of constituent residues equally plays a pivotal role in peptide-based inhibitor generation. The study envisages the challenges of fine-tuned peptide recovery and the scope of Machine Learning (ML) and Deep Learning (DL) algorithm development. As the study was primarily meant for generation of therapeutics for Tuberculosis (TB), the peptide proposed by this study demands meticulous invitro analysis prior to clinical applications.

Machine learning assisted methods for the identification of low toxicity inhibitors of Enoyl-Acyl Carrier Protein Reductase (InhA).

Tuberculosis (TB) is one of the life-threatening infectious diseases with prehistoric origins and occurs in almost all habitable parts of the world. TB mainly affects the lungs, and its etiological agent is Mycobacterium tuberculosis (Mtb). In 2022, more than 10 million people were infected worldwide, and 1.3 million were children. The current study considered the in-silico and machine learning (ML) approaches to explore the potential anti-TB molecules from the SelleckChem database against Enoyl-Acyl Carrier Protein Reductase (InhA). Initially, the entire database of ∼ 119000 molecules was sorted out through drug-likeness. Further, the molecular docking study was conducted to reduce the chemical space. The standard TB drug molecule's binding energy was considered a threshold, and molecules found with lower affinity were removed for further analyses. Finally, the molecules were checked for the pharmacokinetic and toxicity studies, and compounds found to have acceptable pharmacokinetic parameters and were non-toxic were considered as final promising molecules for InhA. The above approach further evaluated five molecules for ML-based toxicity and synthetic accessibility assessment. Not a single molecule was found toxic and each of them was revealed as easy to synthesise. The complex between InhA and proposed and standard molecules was considered for molecular dynamics simulation. Several statistical parameters showed the stability between InhA and the proposed molecule. The high binding affinity was also found for each of the molecules towards InhA using the MM-GBSA approach. Hence, the above approaches and findings exposed the potentiality of the proposed molecules against InhA.

Synthesis and performance evaluation of plastic waste aerogel as sustainable and reusable oil absorbent.

Direct utilization of waste polyethylene terephthalate (PET) from the environment to form highly porous aerogel technology for oil absorption is an attractive approach from the view point of green chemistry. However, the oil absorption reaction is limited by low oil absorption capacity and less stability. For now, silica aerogel are used to solve these problem. Our goal is to substitute to these silica aerogel with PET aerogel technology. Herein, we have prepared an environmental waste PET based aerogel with 1.0:0.5 wt% PET, polyvinyl alcohol (PVA), and glutaraldehyde (GA) 0.2% v/v were dispersed in 10 mL DI water, followed by homogenization (30 min), sonication (10 min), and ageing (2 h) at 70 °C. To escape macroscopic cracking, cooling (8 h) at 4 °C was followed by freezing (6 h), freeze drying at -80 °C, and 5 mTorr for 18 h. The hybrid PET aerogel displays excellent performance towards oil absorption. Notably it showed high absorption capacity towards the different oils about 21-40 times its own weight, depending on the viscosity and density of the oil and solvents within 15-35 s, 25 °C, and 2 × 2 cm aerogel size. In addition, the aerogel shows there is no change in structure after several recycles due to high mechanical strength. Furthermore, because of the PET aerogel's high porosity (99.74%) and low density (0.0311 g/cm3), close bonding between PET-PVA occurs. Therefore, aerogel shows hydrophobic nature, good mechanical strength, high thermal stability, arrangement of the interconnected fibrillar pore network offers a high surface to volume ratio, low surface energy, high surface roughness, and more reusability. All these parameters are responsible for high oil absorption.

Competitive Metabolite Profiling of Natural Products Reveals Subunit Specific Inhibitors of the 20S Proteasome.

We have developed a syringolin-based chemical probe and explored its utility for the profiling of metabolite extracts as potent inhibitors of the 20S proteasome. Activity-guided fractionation by competitive labeling allowed us to isolate and identify glidobactin A and C as well as luminmycin A from a Burkholderiales strain. The natural products exhibited unique subunit specificities for the proteolytic subunits of human and mouse constitutive and immunoproteasome in the lower nanomolar range. In particular, glidobactin C displayed an unprecedented ß2/ß5 coinhibition profile with single-digit nanomolar potency in combination with sufficiently high cell permeability. These properties render glidobactin C a promising live cell proteasome inhibitor with potent activity against human breast cancer cell lines and comparably low immunotoxicity.

Pseudo-Biomineralization: Complex Mineral Structures Shaped by Microbes.

Biomineralization is an active, biologically governed process of mineral formation, established early on in the history of life. The appearance of biomineralizing organisms heavily influenced the course of evolution, leading to the development of the large diversity of the extant taxa. Yet, we are still only beginning to grasp the intricate, genetically regulated mechanisms involved. Since prokaryotic organisms were the first to emerge from the primordial environments, we investigated bacteria-mineral interactions using titration and gas diffusion systems adapted to emulate conditions, which may have facilitated the development of biomineralization initially. By screening the minerals and bacteria from titration experiments with scanning electron microscopy, we discovered a broad spectrum of behavioral strategies employed by bacteria confronted with calcification, which fell into three main categories: (1) evasion of mineralization by the formation of the biofilm, (2) random embedding into the mineral, and (3) control over the mineral shape during its formation. The latter phenomenon we termed pseudo-biomineralization. Our experiments indicate that pseudo-biomineralization is an active process obligatorily reliant on the external calcifying conditions and allowing considerable degree of control over mineral shape, thus producing structures reminiscent of true biominerals. Here, we describe this notion for the first time, thus providing vital insight into the genesis of a transitional stage to calcium carbonate-based biomineralization systems.

Synthesis of cerium and nickel doped titanium nanofibers for hydrolysis of sodium borohydride.

A recyclable titanium nanofibers, doped with cerium and nickel doped was successfully synthesized by using sol-gel and electrospinning method for hydrogen generation from alkali free hydrolysis of NaBH4. The resultant nanocomposite was characterized to find out the structural and physical-chemical properties by a series of analytical techniques such as FT-IR (Fourier transform infrared spectroscopy), XRD (X-ray diffraction), SEM (scanning electron microscope), EDX (energy-dispersive X-ray spectroscopy),N2 adsorption-desorption and BET (Brunauer-Emmett-Teller), etc. The results revealed that cerium and nickel nanoparticles were homogeneously distributed on the surface of the TiO2 nanofibers due to having similar oxidation state and atomic radium of TiO2nanofibers with CeO2 and NiO for the effective immobilization of metal ions. The NiO doped catalyst showed superior catalytic performance towards the hydrolysis reaction of NaBH4 at room temperature. These catalysts have ability to produce 305 mL of H2 within the time of 160 min at room temperature. Additionally, reusability test revealed that the catalyst is active even after five runs of hydrolytic reaction, implying the as-prepared NiO doped TiO2 nanofibers could be considered as a potential candidate catalyst for portable hydrogen fuel system such as PEMFC (proton exchange membrane fuel cells).

In silico approach to ascertain the calcium dependent role of Plasmodium falciparum SERA5.

The P. falciparum serine repeat antigen (PfSERA5) is the most abundantly expressed protein in the parasitophorous vacuole during the asexual blood stage and serves as both drug and vaccine target. The processed central fragment (56 KDa) of PfSERA5 is implicated to play an important role in parasite exit (egress) during schizont rupture from erythrocytes. Structural characterization of its enzymatic domain supports protease-like function for this central domain. The understanding of exact functional role of PfSERA5 in parasite egress remains unconfirmed as recent studies also indicate an indispensable non-catalytic role for PfSERA5 putative enzyme domain in the blood stage. No structural insight into PfSERA5 prodomain is available. Structure prediction of PfSERA5 prodomain using in silico approach in our study, showed it to have structural similarity with calcium-binding proteins. An earlier observation of steep rise in intracellular calcium concentration as an important factor in egress makes the prodomain calcium-binding role significant. The implication of calcium on structure and activity of PfSERA5 putative enzyme domain is also unknown, and such information would aid to substantiating any calcium-dependent effects on PfSERA5. To understand this, we performed molecular dynamic (MD) simulation both in the presence and absence of calcium. MD results show secondary structure conformational differences in local regions of protein structure. Our results support calcium to be an important parameter for stability and function of PfSERA5. This computational assessment suggest a need to design future experiments like calcium-dependent inhibition studies to reveal exact functional role of PfSERA5 in parasite egress.

Genetic and structural characterization of PvSERA4: potential implication as therapeutic target for Plasmodium vivax malaria.

Plasmodium vivax malaria is geographically the most widely distributed and prevalent form of human malaria. The development of drug resistance by the parasite to existing drugs necessitates higher focus to explore and identify new drug targets. Plasmodial proteases have key roles in parasite biology and are involved in nutritional uptake, egress from infected reticulocytes, and invasion of the new target erythrocytes. Serine repeat antigens (SERA) of Plasmodium are parasite proteases that remain attractive drug targets and are important vaccine candidates due to their high expression profiles in the blood stages. SERA proteins have a unique putative papain-like cysteine protease motif that has either serine or cysteine in its active site. In P. vivax, PvSERA4 is the highest transcribed member of this multigene family. In this study, we have investigated the genetic polymorphism of PvSERA4 central protease domain and deduced its 3D model by homology modeling and also performed MD simulations to acquire refined protein structure. Sequence analysis of protease domain of PvSERA4 from Indian field isolates reveals that the central domain is highly conserved. The high sequence conservation of the PvSERA4 enzyme domain coupled with its high expression raises the possibility of it having a critical role in parasite biology and hence, being a reliable target for new selective inhibitor-based antimalarial chemotherapeutics. The 3D model showed the presence of an unusual antiparallel Beta hairpin motif between catalytic residues similar to hemoglobin binding motif of Plasmodial hemoglobinases. Our PvSERA4 model will aid in designing structure-based inhibitors against this enzyme.