Calcium-induced structural transitions are central to the folding, function, and processing of serratiopeptidase zymogen into mature form.

Serratia marcescens is an emerging health-threatening, gram-negative opportunistic pathogen associated with a wide variety of localized and life-threatening systemic infections. One of the most crucial virulence factors produced by S. marcescens is serratiopeptidase, a 50.2-kDa repeats-in-toxin (RTX) family broad-specificity zinc metalloprotease. RTX family proteins are functionally diverse exoproteins of gram-negative bacteria that exhibit calcium-dependent structural dynamicity and are secreted through a common type-1 secretion system (T1SS) machinery. To evaluate the impact of various divalent ligands on the folding and maturation of serratiopeptidase zymogen, the protein was purified and a series of structural and functional investigations were undertaken. The results indicate that calcium binding to the C-terminal RTX domain acts as a folding switch, triggering a disordered-to-ordered transition in the enzyme's conformation. Further, the auto-processing of the 16-amino acid N-terminal pro-peptide results in the maturation of the enzyme. The binding of calcium ions to serratiopeptidase causes a highly cooperative conformational transition in its structure, which is essential for the enzyme's activation and maturation. This conformational change is accompanied by an increase in solubility and enzymatic activity. For efficient secretion and to minimize intracellular toxicity, the enzyme needs to be in an unfolded extended form. The calcium-rich extracellular environment favors the folding and processing of zymogen into mature serratiopeptidase, i.e., the holo-form required by S. marcescens to establish infections and survive in different environmental niches.

Anticancer mechanisms of ß-carbolines.

ß-Carboline nucleus is therapeutically valuable in medicinal chemistry for the treatment of varied number of diseases, most importantly cancer. The potent and wide-ranging activity of ß-carboline has established them as imperative pharmacological scaffolds especially in the cancer treatment. Numerous derivatives such as Tetrahydro ß-carbolines, metal complexed ß-carbolines, mono, di and tri substituted ß-carbolines have been reported to possess dynamic anticancer activity. These different substituted ß-carboline derivatives had shown different mechanism of action and plays important role in anticancer drug discovery and development. The review is an update of the chemistry of ß-carbolines, both synthetic and natural origin acting through various targets against cancerous cells. In addition to this, studies of multitarget molecules designed by coupling ß-carbolines along with other mechanisms for treatment of neoplasm are also summarized.

Molecular Docking Improved with Human Spatial Perception Using Virtual Reality.

Adaptive steered molecular dynamics (ASMD) is a computational biophysics method in which an external force is applied to a selected set of atoms or a specific reaction coordinate to induce a particular molecular motion. Virtual reality (VR) based methods for protein-ligand docking are beneficial for visualizing on-the-fly interactive molecular dynamics and performing promising docking trajectories. In this paper, we propose a novel method to guide ASMD with optimal trajectories collected from human experiences using interactive molecular dynamics in virtual reality (iMD-VR). We also explain the benefits of using VR as a tool for expediting the process of ligand binding, outlining an experimental protocol that enables iMD-VR users to guide Amprenavir into and out of the binding pockets of HIV-1 protease and recreate their respective crystallographic binding poses within 5 minutes. Later, we discuss our analysis of the results from iMD-VR-assisted ASMD simulation and assess its performance compared to a standard ASMD simulation. From the accuracy point of view, our proposed method calculates higher Potential Mean Force (PMF) values consistently relative to a standard ASMD simulation with an almost twofold increase in all the experiments. Finally, we describe the novelty of the research and discuss results showcasing a faster and more effective convergence of the ligand to the protein's binding site as compared to a standard molecular dynamics simulation, proving the effectiveness of VR in the field of drug discovery. Future work includes the development of an artificial intelligence algorithm capable of predicting optimal binding trajectories for many protein-ligand pairs, as well as the required force needed to steer the ligand to follow the said trajectory.

Carbon-based biosensors: Next-generation diagnostic tool for target-specific detection of SARS-CoV-2 (COVID-19).

Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) was declared a global pandemic in 2020. Having rapidly spread around the globe, with the emergence of new variants, there is a crucial need to develop diagnostic kits for its rapid detection. Since it validated accuracy and reliability, the reverse transcription polymerase chain reaction (RT-PCR) test has been declared the gold standard for disease detection. However, despite its reliability, the requirement of specialized facilities, reagents, and duration of a PCR run limits its usage for rapid detection. There is thus a continuous increase in the design and development of rapid, point-of-care (PoC), and cost-effective diagnostic kits. In this review, we discuss the potential of carbon-based biosensors for target-specific detection of coronavirus disease 19 (COVID-19) and present an overview of investigation within the timeframe of the last four years (2019-2022), which have developed novel platforms using carbon nanomaterial-based approaches for viral detection. The approaches discussed offer rapid, accurate, and cost-effective strategies for COVID-19 detection for healthcare personnel and research workers.

Potential of Desert Medicinal Plants for Combating Resistant Biofilms in Urinary Tract Infections.

Urinary tract infections (UTIs) are among the most prevalent bacterial infections worldwide, with 11% of the global population getting infected every year. These infections are largely attributed to quorum sensing (QS)-dependent ability of pathogens to form biofilms in the urinary tract. Antimicrobial resistance is increasing, and the use of antimicrobial medicines in the future is yet uncertain. The desert medicinal plants have great potential to treat several diseases as per the available ethnobotanical database. Some of these plants have been used in folklore medicines to treat urinary tract infections also. There are many bioactive compounds derived from these desert medicinal plants that have been documented to possess antimicrobial as well as antibiofilm activity against uropathogens. The minimum biofilm inhibitory concentration (MBIC) of these plant extracts have been reported in the range of 31.5-250 µg/mL. The rising prevalence of drug-resistant diseases necessitates standardised modern analytical technologies to detect and isolate novel bioactive compounds from medicinal plants. This review seeks to combine the studies of desert plants with antimicrobial and anti-quorum sensing properties, supporting their sustainable use in treatment of urinary tract infections.

Security provisions in smart edge computing devices using blockchain and machine learning algorithms: a novel approach.

It is difficult to manage massive amounts of data in an overlying environment with a single server. Therefore, it is necessary to comprehend the security provisions for erratic data in a dynamic environment. The authors are concerned about the security risk of vulnerable data in a Mobile Edge based distributive environment. As a result, edge computing appears to be an excellent perspective in which training can be done in an Edge-based environment. The combination of Edge computing and consensus approach of Blockchain in conjunction with machine learning techniques can further improve data security, mitigate the possibility of exposed data, and it reduces the risk of a data breach. As a result, the concept of federated learning provides a path for training the shared data. A dataset was collected that contained several vulnerable, exposed, recovered, and secured data and data security was precepted under the surveillance of two-factor authentication. This paper discusses the evolution of data and security flaws and their corresponding solutions in smart edge computing devices. The proposed model incorporates data security using consensus approach of Blockchain and machine learning techniques that include several classifiers and optimization techniques. Further, the authors applied the proposed algorithms in an edge computing environment by distributing several batches of data to different clients. As a result, the client privacy was maintained by using Blockchain servers. Furthermore, the authors segregated the client data into batches that were trained using the federated learning technique. The results obtained in this paper demonstrate the implementation of a Blockchain-based training model in an edge-based computing environment.

Effect of radiation-reaction on charged particle dynamics in a focused electromagnetic wave.

The effect of radiation-reaction force on the dynamics of a charged particle in an intense focused light wave is investigated using the physically appealing Hartemann-Luhmann equation of motion. It is found that, irrespective of the choice of initial conditions, radiation reaction force causes the charged particle to cross the focal region, provided the particle is driven into regions where the radiation reaction force dominates over the Lorentz force, thus enhancing the forward energy gained by the particle from the intense light wave. This result is in sharp contrast to the well known result, derived in the absence of radiation reaction forces, where for certain initial conditions the particle reflects from the high intensity region of the focused light wave, thereby losing forward energy. From the perspective of energy gain, our studies clearly show that the parameter space for forward energy gain which is reduced by ponderomotive effects is compensated by radiation reaction effects. These results, which are of relevance to the present day direct laser acceleration schemes of charged particle, also agrees with that obtained using the well known Landau-Lifshitz equation of motion.

Cytokine database of stress and metabolic disorders (CdoSM): a connecting link between stress and cardiovascular disease, hypertension, diabetes and obesity.

The risk of metabolic diseases is greatly increased by both chronic and acute stress. Irrespective of the cause, chronic or acute stress has the capacity to alter an individual's cytokine profile. For instance, it has been observed that stress significantly increased concentrations of IL 1 beta, IL 6 and TNF alpha. Alteration in cytokine profiles increase the likelihood of dysregulated metabolism, which subsequently acts as a driving force in the development of disorders, such as cardiovascular disease (CVD), hypertension, diabetes and obesity. Considering the dynamic and versatile role of cytokines in health and disease, an in-depth computational analysis (qualitative and quantitative) was performed to study the role of cytokines as an immuno-molecular link between rising stress levels and an increase in CVD, hypertension, diabetes and obesity. Upon a qualitative comparative analysis of cytokine profiles, a total of 14 cytokines (IL-6, TNF-alpha, IFN-gamma, IL-10, etc.) were observed to be commonly involved in stress and aforementioned four metabolic disorders. Further analysis of quantitative studies has revealed that the cytokine profile for coronary artery disease (CAD) showed remarkable increase in a couple of cytokines. IL 9 registered an increase of 67 percent to reach a concentration of 75 pg/mL. IL 3, on the other hand, was absent in control candidates but reached 56 ± 14 pg/mL in CAD patients. In case of diabetes, IFN-gamma showed an increase of 290 pg/mL. For obesity it was observed that both MCP-1 and IL-1 beta fell by 12.2 pg/mL to reach 44.4 pg/mL in obese patients. A fall of approximately 50 pg/mL was observed in the concentration of VEGF in obese patients. Similarly, hypertension was marked by reduction in concentration of several cytokines - MCP-1 and VEGF being a couple of them. Apart from performing an analysis of cytokine profiles, an innovative database [Cytokine database of Stress and Metabolic disorders (CdoSM)-https://www.akbi-nsut.co.in/] has also been created comprising cytokines involved in stress and the aforementioned metabolic disorders. Upon accessing the database, a user can find the list cytokines associated with a particular condition along with information on cytokine receptor/s; related research articles; cytokine concentration in control v/s diseased candidates for some specific cytokines and the Uniprot ID for the respective cytokine. Database can be accessed by the link-https://www.akbi-nsut.co.in/. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-022-03375-0.

Design, Synthesis and Evaluation of Benzimidazole Hybrids to Inhibit Acetylcholinesterase and COX for Treatment of Alzheimer's Disease.

BACKGROUND: A simultaneous administration of an acetylcholinesterase (AChE) inhibitor and a NSAID as a drug cocktail has been documented to exhibit significantly protective effects in AD patients. But it suffers from poor patent compliance, pharmacodynamics and pharmacokinetic issues. OBJECTIVE: The present study is aimed to design and synthesize a hybrid molecule capable of exhibiting both AChE inhibition and anti-inflammatory activities for de-accelerating the progression of AD. The synthesized molecules will be evaluated for in vitro and in vivo models. METHODS: The present study involves the coupling of ibuprofen or naproxen to varied disubstituted amines (AChE inhibitor pharmacophore) through benzimidazole to develop two series of compounds i.e. IB01-IB05 and NP01-NP05. The synthesized compounds were characterized using FTIR, 1H-NMR, 13C-NMR and MS. All compounds were evaluated for in vitro AChE inhibitory and COX inhibitory activities. The most active compound was taken for in vivo evaluation. RESULTS: Compounds of series IB01-IB05 are found more potent as compared to NP01-NP05. The maximally potent compound IB04 in in vitro evaluation is selected for in vivo evaluation of memory restoration activity using scopolamine-induced amnesia model in mice. It significantly reverses the scopolamine-induced changes (i.e., escape latency time, mean time spent in target quadrant, brain AChE activity and oxidative stress) in a dose-dependent manner. IB04 at 8 mg/kg is significantly effective in lowering AD manifestation in comparison to donepezil. CONCLUSION: The findings indicate that Benzimidazole hybrids utilizing ibuprofen and pyrrolidine moiety may prove a useful template for the development of new chemical moieties against AD with multiple potencies.

Local ferroelectric polarization switching driven by nanoscale distortions in thermoelectric [Formula: see text].

A remarkable decrease in the lattice thermal conductivity and enhancement of thermoelectric figure of merit were recently observed in rock-salt cubic SnTe, when doped with germanium (Ge). Primarily, based on theoretical analysis, the decrease in lattice thermal conductivity was attributed to local ferroelectric fluctuations induced softening of the optical phonons which may strongly scatter the heat carrying acoustic phonons. Although the previous structural analysis indicated that the local ferroelectric transition temperature would be near room temperature in [Formula: see text], a direct evidence of local ferroelectricity remained elusive. Here we report a direct evidence of local nanoscale ferroelectric domains and their switching in [Formula: see text] using piezoeresponse force microscopy(PFM) and switching spectroscopy over a range of temperatures near the room temperature. From temperature dependent (250-300 K) synchrotron X-ray pair distribution function (PDF) analysis, we show the presence of local off-centering distortion of Ge along the rhombohedral direction in global cubic [Formula: see text]. The length scale of the [Formula: see text] off-centering is 0.25-0.10 Å near the room temperatures (250-300 K). This local emphatic behaviour of cation is the cause for the observed local ferroelectric instability, thereby low lattice thermal conductivity in [Formula: see text].

Enhanced production of recombinant serratiopeptidase in Escherichia coli and its characterization as a potential biosimilar to native biotherapeutic counterpart.

BACKGROUND: Serratia marcescens, a Gram-negative nosocomial pathogen secretes a 50 kDa multi-domain zinc metalloprotease called serratiopeptidase. Broad substrate specificity of serratiopeptidase makes it suitable for detergent and food processing industries The protein shows potent anti-inflammatory, anti-edemic, analgesic, antibiofilm activity and sold as an individual or fixed-dose enteric-coated tablets combined with other drugs. Although controversial, serratiopeptidase as drug is used in the treatment of chronic sinusitis, carpal tunnel syndrome, sprains, torn ligaments, and postoperative inflammation. Since the native producer of serratiopeptidase is a pathogenic microorganism, the current production methods need to be replaced by alternative approaches. Heterologous expression of serratiopeptidase in E. coli was tried before but not found suitable due to the limited yield, and other expression related issues due to its inherent proteolytic activity such as cytotoxicity, cell death, no expression, minimal expression, or inactive protein accumulation. RESULTS: Recombinant expression of mature form serratiopeptidase in E. coli seems toxic and resulted in the failure of transformation and other expression related issues. Although E. coli C43(DE3) cells, express protein correctly, the yield was compromised severely. Optimization of protein expression process parameters such as nutrient composition, induction point, inducer concentration, post-induction duration, etc., caused significant enhancement in serratiopeptidase production (57.9 ± 0.73% of total cellular protein). Expressed protein formed insoluble, enzymatically inactive inclusion bodies, and gave 40-45 mg/l homogenous (> 98% purity) biologically active and conformationally similar serratiopeptidase to the commercial counterpart upon refolding and purification. CONCLUSION: Expression of mature serratiopeptidase in E. coli C43(DE3) cells eliminated the protein expression associated with toxicity issues. Further optimization of process parameters significantly enhanced the overexpression of protein resulting in the higher yield of pure and functionally active recombinant serratiopeptidase. The biological activity and conformational features of recombinant serratiopeptidase were very similar to the commercially available counterpart suggesting it-a potential biosimilar of therapeutic and industrial relevance.

The chromatin-binding protein HMGN3 stimulates histone acetylation and transcription across the Glyt1 gene.

HMGNs are nucleosome-binding proteins that alter the pattern of histone modifications and modulate the binding of linker histones to chromatin. The HMGN3 family member exists as two splice forms, HMGN3a which is full-length and HMGN3b which lacks the C-terminal RD (regulatory domain). In the present study, we have used the Glyt1 (glycine transporter 1) gene as a model system to investigate where HMGN proteins are bound across the locus in vivo, and to study how the two HMGN3 splice variants affect histone modifications and gene expression. We demonstrate that HMGN1, HMGN2, HMGN3a and HMGN3b are bound across the Glyt1 gene locus and surrounding regions, and are not enriched more highly at the promoter or putative enhancer. We conclude that the peaks of H3K4me3 (trimethylated Lys(4) of histone H3) and H3K9ac (acetylated Lys(9) of histone H3) at the active Glyt1a promoter do not play a major role in recruiting HMGN proteins. HMGN3a/b binding leads to increased H3K14 (Lys(14) of histone H3) acetylation and stimulates Glyt1a expression, but does not alter the levels of H3K4me3 or H3K9ac enrichment. Acetylation assays show that HMGN3a stimulates the ability of PCAF [p300/CREB (cAMP-response-element-binding protein)-binding protein-associated factor] to acetylate nucleosomal H3 in vitro, whereas HMGN3b does not. We propose a model where HMGN3a/b-stimulated H3K14 acetylation across the bodies of large genes such as Glyt1 can lead to more efficient transcription elongation and increased mRNA production.