Increases in expression of carbohydrate sulfotransferases CHST11 and CHST15 and decline in N-acetylgalactosamine-4-sulfatase (Arylsulfatase B, ARSB) require phospho-p38-MAPK following exposure to SARS-CoV-2 spike protein receptor binding domain in human a

Objective: Immunohistochemistry of post-mortem lung tissue from Covid-19 patients with diffuse alveolar damage demonstrated marked increases in chondroitin sulfate and CHST15 and decline in N-acetylgalactosamine-4-sulfatase. Studies were undertaken to identify the mechanisms involved in these effects. Method(s): Human primary small airway epithelial cells (PCS 301-010;ATCC) were cultured and exposed to the SARSCoV- 2 spike protein receptor binding domain (SPRBD;AA: Lys310-Leu560;Amsbio). Expression of the spike protein receptor, angiotensin converting enzyme 2 (ACE2), was enhanced by treatment with Interferon-beta. Promoter activation, DNA-binding, RNA silencing, QPCR, Western blots, ELISAs, and specific enzyme inhibitors were used to elucidate the underlying molecular mechanisms. Result(s): Treatment of the cultured cells by the SPRBD led to increased CHST15 and CHST11 expression and decline in ARSB expression. Sulfotransferase activity, total chondroitin sulfate, and sulfated glycosaminoglycan (GAG) content were increased. Phospho-T180/T182-p38-MAPK and phospho- S423/S425-Smad3 were required for the activation of the CHST15 and CHST11 promoters. Inhibition by SB203580, a phospho-p38 MAPK inhibitor, and by SIS3, a Smad3 inhibitor, blocked the CHST15 and CHST11 promoter activation. SB203580 reversed the SPRBD-induced decline in ARSB expression, but SIS3 had no effect on ARSB expression or promoter activation. Phospho-p38 MAPK was shown to reduce retinoblastoma protein (RB) S807/S811 phosphorylation and increase RB S249/T252 phosphorylation. E2F-DNA binding declined following exposure to SPRBD, and SB203580 reversed this effect. This indicates a mechanism by which SPRBD, phospho-p38 MAPK, E2F, and RB can regulate ARSB expression and thereby impact on chondroitin 4-sulfate and dermatan sulfate and molecules that bind to these sulfated GAGs, including Interleukin-8, bone morphogenetic protein-4, galectin-3 and SHP-2 (Src homology region 2-containing protein tyrosine phosphatase 2). Conclusion(s): The enzyme ARSB is required for the degradation of chondroitin 4-sulfate and dermatan sulfate, and accumulation of these sulfated GAGs can contribute to lung pathophysiology, as evident in Covid-19. Some effects of the SPRBD may be attributable to unopposed Angiotensin II, when Ang1-7 counter effects are diminished due to binding of ACE2 with the SARS-CoV-2 spike protein and reduced production of Ang1-7. Aberrant cell signaling and activation of the phospho-p38 MAPK and Smad3 pathways increase CHST15 and CHST11 production, which can contribute to increased chondroitin sulfate in infected cells. Decline in ARSB may occur as a consequence of effects of phospho-p38 MAPK on RB phosphorylation and E2F1 availability. Decline in ARSB and the resulting impaired degradation of sulfated GAGs have profound consequences on cellular metabolic, signaling, and transcriptional events. Funding is VA Merit Award.Copyright © 2023 The American Society for Biochemistry and Molecular Biology, Inc.

Presence of rare potential pathogenic variants in subjects under 60 years old with very severe or fatal COVID-19

Background/Objectives: Genetic variants affecting host defense against pathogens may help explain COVID-19 fatal outcomes. Our aim was to identify rare genetic variants related to COVID-19 severity in a selected group of patients under 60 years who required intubation or resulting in death. Method(s): Forty-four very severe COVID-19 patients were selected from the Spanish STOP-Coronavirus cohort, which comprises more than 3,500 COVID-19 patients. Genotype was performed by whole exome sequencing and variants were selected by using a gene panel of 867 candidate genes (immune response, primary immunodeficiencies or coagulation, among other). Variants were filtered, priorized and their potential pathogenicity was assessed following ACGM criteria. Result(s): We detected 44 different variants of interest, in 29 different patients (66%). Some of these variants were previously described as pathogenic (26%). Mostly, the candidate variants were located in genes related to immune response (38%), congenital disorders of glycosylation (14%) or damaged DNA binding genes (9%). A network analysis, showed three main components, consisting of 25 highly interconnected genes related to immune response and two additional networks enriched in carbohydrate metabolism and in DNA metabolism and repair processes. Conclusion(s): The variants identified affect different, but interrelated, functional pathways such as immune response and glycosylation. Further studies are needed for confirming the ultimate role of the new candidate genes described in the present study on COVID-19 severity.

Modeling DNA Oligonucleotide Binding to DNA-mimetic Stem-Loop 1 of the SARS-CoV-2 RNA

SARS-CoV-2 is a positive-sense RNA virus that contains open reading frame 1ab (ORF1ab) to produce 16 nonstructural proteins (nsps). Five stem-loops (SL) are found in the 5' UTR of the RNA that are involved in myriad viral functions and are labeled SL1 through SL5. SL1 is crucial to viral replication. Upon viral infection, nsp1 binds the ribosomal 40S subunit to inhibit all host mRNA translation. Upon SL1 binding to nsp1, viral mRNA can be processed by the ribosome, allowing viral proteins to be produced. In this study, we are examining small DNA oligonucleotides that bind to SL1-mimetic DNA in order to block SL1-nsp1 interactions. We designed a DNA analog of the SL1 hairpin and two small DNA oligonucleotides that are complementary to either the helical stem or the loop region of SL1. The binding of these oligonucleotides to the SL1 hairpin should allow the formation of either an alternate duplex or a triplex structure. Isothermal titration calorimetry (ITC) and circular dichroism (CD) techniques were performed in 1 MKCl and 10 mM MgCl2 at two different pH (5.5 and 7.0) to examine structural and thermodynamics of binding. ITC of the two oligonucleotides showed modest binding. Results from DNA binding experiments, thermal denaturation, and CD show the hairpin structure is thermodynamically more favored and mostly remains intact under the conditions examined.Copyright © 2023 The American Society for Biochemistry and Molecular Biology, Inc.

Towards New Antimicrobials - Targeting Bacterial Response Regulators

Purpose of Study: Antibiotic resistance remains one of the largest healthcare and public health challenges. Several studies have documented that the spread of antibiotic resistant bacteria in nosocomial settings has been exacerbated worldwide due to increased rates of hospitalization and intubation in the wake of the COVID-19 pandemic. One way to address antibiotic resistance is to identify novel compounds that inhibit essential microbial processes. Two-component regulatory systems are important mediators of signal transduction that allow bacteria to communicate with and respond to changes in their environment. The WalRK system is a two-component system that is conserved and essential for viability in many Gram-positive human pathogens. We hypothesize that a ligand that specifically binds with the DNA-interaction surface of the WalR protein can lead to cell death and can serve as a lead compound for future drug development efforts. Methods Used: We describe the development process of an assay to identify WalR binding compounds. In silico molecular dynamics docking approaches were utilized to identify potential WalR binding compounds from virtual compound libraries. To assess their WalR-binding capacity in vitro, overexpression strains for several WalR recombinant constructs were engineered and protein constructs were purified to homogenicity. Isothermal titration calorimetry (ITC) is a technique that measures heat release or absorption when two molecules interact. A MicroCal PEAQ ITC instrument was utilized to develop a WalR-binding assay. Summary of Results: WalR is a two-domain protein featuring a regulatory and a DNA-binding domain. Two constructs, a truncated DNA-binding domain and a full-length protein construct proved soluble, and pure quantities necessary to conduct ITC measurements could be successfully obtained (12 mg full-length protein and 23 mg truncated protein). These proteins were amenable to ITC experiments. We found that experiments were best run with at least a two-fold increase of ligand concentration to protein concentration supplied in identical buffer conditions over nineteen injections. We are currently assessing the binding affinities of our in silico hit compounds. Conclusion(s): Our results show that ITC enables the detailed, rapid, and reproducible characterization of the binding relationship between the DNA-binding domain of the WalR protein and any potential ligands. The protocol discussed herein will enable further drug discovery studies on the WalR response regulator protein to identify and characterize inhibitors, providing insight towards the development of novel antimicrobial compound.

Post-COVID anosmia and the expression of pathological proteins in nasal mucosa nerves endings

Introduction: Anosmia and ageusia were observed as frequent neurological complications of SARS-CoV-2 infections. the aim of the study was to elaborate methods for detection of pathological proteins in nerve endings and to evaluate the frequency and intensity of pathological proteins expression in patients with persistent anosmia. Material(s) and Method(s): the study included 249 patients (181 females and 68 males) aged 47 +/-14 years from NeuroCOViD Polyclinic in Poznan observed from April 2021 untill now. the mucosal biopsy was performed using endoscopy from anterior ethmoid cells. the expression of alpha-synuclein was evaluated using immunofuorescence, and amyloid, tau and tDP43 proteins-using immunohistochemistry. Result(s): Anosmia was observed in 42% of patients and cacosmia-in 6%. Ageusia/dysgeusia was observed in 31% cases. in patients with mild clinical course of COViD19-not hospitalized anosmia (45%) and dys-geusia were more frequent (33%), and cacosmia was observed only in this group. in hospitalized patients anosmia was found in 22% of cases, dysgeusia in 13%, and cacosmia was not observed at all. the expression of alpha-synuclein, amyloid, tau and tDP43 proteins was found in nerve bundles, epithelial cells and in surrounding (nerve endings) of gland cells. Conclusion(s): SARS-CoV-2 infection may induce the expression of pathological proteins in olfactory mucosa of post-COViD patients with anosmia.

Pyrrole-Imidazole Polyamides - A Frontrunner in Nucleic Acid-Based Small Molecule Drugs

The remarkable success of messenger RNA vaccines against the ongoing coronavirus-2019 (COVID-19) pandemic renews attention toward nucleic acid therapeutics. While nucleic acid therapy using unmodified DNA or RNA is the primary focus in disease treatment, there is growing need to develop nucleic acid-based small molecules owing to their potential clinical benefits as drugs in terms of cost and scalability. While small molecules targeting protein-protein interactions are known to alter the transcriptional status of a cell, they can result in a transient effect and variation of bio-efficacy among patients. Small molecules targeting DNA and/or RNA are in demand in the precision medicine approach as they have consistent bioactivity among patients. This review details the progress of sequence-specific DNA-binding pyrrole-imidazole polyamides (PIPs) in modulating the transcriptional status of target gene(s) without altering the underlying DNA sequence. Here, the different versions of PIPs are listed, and also, how conjugating them with DNA alkylating agents, epigenetic modulators, and other drugs can improve their clinical utility as targeted transcription therapeutics. Owing to their specificity, functional diversity, and limited toxicity, PIP technology holds enormous promise as frontrunner in small-molecule-based nucleic acid drugs to precisely regulate therapeutically important genes on demand and treat intractable diseases.Copyright © 2023 Wiley-VCH GmbH.

Co(II), Ni(II), Cu(II) and Zn(II) complexes of Schiff base ligands: synthesis, characterization, DFT, in vitro antimicrobial activity and molecular docking studies

Three Schiff base ligands [H2L1-H2L3] containing nitrogen/oxygen donor atoms and their Co(II), Ni(II), Cu(II) and Zn(II) complexes were synthesized by stirring metal acetates with Schiff base ligands obtained from condensation reaction of 2-amino-6-chloro-4-nitrophenol with 5-chloro salicylaldehyde/3,5-dibromo salicylaldehyde/3-methoxy-5-nitro salicylaldehyde. The structural traits of the synthesized compounds were done by using elemental analysis, spectroscopic techniques (UV-Vis, H-1 and C-13 NMR, FT-IR), mass spectrometry and some physical studies (XRD, TGA). According to spectral data, ligands behave as a tridentate (ONO) and formed complexes with octahedral geometry. The thermogravimetric analysis revealed that metal complexes decay in multi-steps leaving metal oxide as an end product. Powder XRD study suggested crystalline nature of the compounds. The energy gap (HOMO-LUMO) and molecular electrostatic potential calculation were computed by using DFT/B3LYP/6-31G** basis set. Derived ligands and complexes were explored for in vitro antimicrobial potential toward two gram-positive bacteria, two gram-negative bacteria, i.e., S. aureus, B. subtilis, P. aeruginosa, E. coli, and two fungal strains, i.e., A. niger, C. albicans, through serial dilution method taking ciprofloxacin and fluconazole as standard. The investigated results showed that complexes are more potent than free Schiff base ligands. The Cu(L-2)(H2O)(3) (0.0115 mu mol/mL) and Zn(L-2)(H2O)(3) (0.0115 mu mol/mL) complexes were found to be more active among all the investigated compounds. Additionally, molecular docking studies were also performed for some compounds in the active site of DNA Gyrase enzyme (PDB code: 1AJ6), suggesting good hydrophobic interactions of compounds with the enzyme.

Corrigendum: TDP-43 and NEAT long non-coding RNA: Roles in neurodegenerative disease.

[This corrects the article DOI: 10.3389/fncel.2022.954912.].

Synthesis, Characterization, Biological Activity, Molecular Docking and Thermal Analysis of Binuclear Complexes

Because of their potential medical applications as antimicrobial medicines, metal-ligand complexes have sparked a lot of attention. Synthesis and characterization of various metal-diamine complexes were the goals of the research detailed in this paper. As a result, synthesis of new binuclear ligand;N,N'-bis(3-carboxysalcylidene)-4-chloro-1,2-phenylenediamine (H(4)fsacph) which is derivative from the condensation of 3-formyl-2-hydroxybenzoic acid and 4-chlorobenzene-1,2-diamine has been performed. The new synthesized ligand has formed a mononuclear complex with Cu(II). The mononuclear Cu(II) complex was used to form binary nuclear complexes with some metal ions, like Cr(III), Mn(II), Fe(III), Ru(III), Pd(II) and La(III) ions. Elemental analysis, IR, UV-Visible, and thermal analyzes have been used to characterize the complexes. The interaction of a ligand with the receptors of Candida albicans and SARS-CoV-2 was predicted using molecular docking. Toward bacteria and fungi showing predominant activity against all fungi verified antibacterial activity of the synthesized complexes, while they have almost no activity against all bacteria. All compounds have shown antibacterial and antifungal activities, but the metal complexes showed better activities as compared to the original ligands, especially all zinc(II) complexes. The above results suggest that both ligands and their metal complexes have the potential to be explored as active pharmaceutical agents.

Synthesis and characterization of violurate-based Mn(II) and Cu(II) complexes nano-crystallites as DNA-binders and therapeutics agents against SARS-CoV-2 virus

Synthesis and structural characterization of nano crystallites of bis-violurate-based manganese(II) and copper(II) chelates is the subject of the present study. Analytical data and mass spectra as well as thermal analysis determined the molecular formulas of the present metal chelates. Spectroscopic and magnetic measurements assigned the structural formula of the present violurate metal complexes. The spectroscopic and magnetic investigations along with structural analysis results indicated the square planar geometry of both the Mn(II) and Cu(II) complexes. The structural analysis of the synthesized metal complexes was achieved by processing the PXRD data using specialized software Expo 2014. Spectrophotometeric and viscosity measurements showed that violuric acid and its Mn(II) and Cu(II) complexes successfully bind to DNA with intrinsic binding constants Kb from 38.2 x 105 to 26.4 x 106 M-1. The antiviral activity study displayed that the inhibitory concentrations (IC50) of SARS-CoV-2 by violuric acid and its Mn(II) and Cu(II) complexes are 84.01, 39.58 and 44.86 lM respectively. Molecular docking calculations were performed on the SARS-CoV-2 virus protein and the computed binding energy values are -0.8, -3.860 -5.187 and -4.790, kcal/mol for the native ligand, violuric acid and its Mn(II) and Cu(II) complexes respectively. Insights into the relationship between structures of the current compounds and their degree of reactivity are discussed.(c) 2022 The Author(s). Published by Elsevier B.V. on behalf of King Saud University. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

HKAM-MKM: A hybrid kernel alignment maximization-based multiple kernel model for identifying DNA-binding proteins.

The identification of DNA-binding proteins (DBPs) has always been a hot issue in the field of sequence classification. However, considering that the experimental identification method is very resource-intensive, the construction of a computational prediction model is worthwhile. This study developed and evaluated a hybrid kernel alignment maximization-based multiple kernel model (HKAM-MKM) for predicting DBPs. First, we collected two datasets and performed feature extraction on the sequences to obtain six feature groups, and then constructed the corresponding kernels. To ensure the effective utilisation of the base kernel and avoid ignoring the difference between the sample and its neighbours, we proposed local kernel alignment to calculate the kernel between the sample and its neighbours, with each sample as the centre. We combined the global and local kernel alignments to develop a hybrid kernel alignment model, and balance the relationship between the two through parameters. By maximising the hybrid kernel alignment value, we obtained the weight of each kernel and then linearly combined the kernels in the form of weights. Finally, the fused kernel was input into a support vector machine for training and prediction. Finally, in the independent test sets PDB186 and PDB2272, we obtained the highest Matthew's correlation coefficient (MCC) (0.768 and 0.5962, respectively) and the highest accuracy (87.1% and 78.43%, respectively), which were superior to the other predictors. Therefore, HKAM-MKM is an efficient prediction tool for DBPs.

DIFFERENTIAL TRANSCRIPTOMIC CHANGES IN THE CENTRAL NERVOUS SYSTEM AND NEUROGENIC BLADDERS OF MICE INFECTED WITH A CORONAVIRUS

INTRODUCTION AND OBJECTIVE: Neurodegenerative diseases, such as multiple sclerosis (MS), often lead to the development of neurogenic lower urinary tract symptoms (LUTS). We previously characterized neurogenic bladder dysfunction in a mouse model of MS induced by a coronavirus, mouse hepatitis virus (MHV). The objective of this study was to identify genes and pathways linking neuroinflammation in the central nervous system with urinary bladder dysfunction to enhance our understanding of the mechanisms underlying LUTS in demyelinating diseases. METHODS: Adult C57BL/6 male mice (N=12) received either an intracranial injection of MHV (6,000 PFU) or sterile saline (control). The lumbosacral (L6-S2) spinal cord (SC) segments and urinary bladders were collected during acute infection stage (week 1) and at the first peak of demyelination (week 4) after inoculation with the virus. Total RNA was isolated and analyzed using Nanostring nCounter Neuroinflammation panel. The expression levels of 770 genes associated with neuroinflammation were assessed and compared between the specimens. RESULTS: Transcriptome analysis of SC specimens confirmed a significantly increased expression of 132 genes in MHV mice (tens to hundreds fold change) involved in the regulation of astrocyte, microglia and oligodendrocyte functions, neuroinflammation and immune responses. Out of 132 genes up-regulated in the SC, only 2 genes (siglec1, 46-fold in the SC, 2.6-fold at 1 week and 1.8-fold at 4 weeks in the bladder;and zbp1, 568-fold in the SC, 2.8-fold at 1 week and 2.2-fold at 4 weeks in the bladder) were up-regulated in the urinary bladders of MHV-infected mice. Additionally, two genes were significantly up-regulated (ttr, 2.2-fold at 1week and 1.7-fold at 4 weeks;and ms4a4a, 2.3-fold at 1week and 1.6-fold at 4 weeks), and two were down-regulated (asb2, -1.8-fold at 1 week and -1.6-fold at 4 weeks, and myct1, -1.7-fold at 1week and -1.6-fold at 4 weeks) exclusively in the urinary bladders of MHV mice. CONCLUSIONS: Two genes, siglec1 (encodes type 1 transmembrane protein, expressed in microglia and macrophages, promotes neuroinflammation) and zbp1 (encodes a Z-DNA binding protein, plays role in the innate immune response) link the development of neuroinflammation in the central nervous system with neurogenic changes in the urinary bladders of MHV-infected mice. Further research is needed to establish a functional relationship between expression of these genes and neurogenic LUTS.

Alterations in respiratory epithelial gene SPDEF segregate with severe disease in a family with variable response to COVID19 infection

Background: The clinical spectrum of coronavirus disease 2019 (COVID19) is wide. While some individuals have severe disease, themajority of individuals are either asymptomatic or have mildsymptoms with minimal hypoxia. There is emerging evidence thatrare genetic variation can contribute to risk for more severe COVID19infection. The goal of this study was to investigate if rare geneticvariation was contributing to severe disease presentation in a familywith varying clinical responses to COVID19 infection.Methods: This case series describes clinical, laboratory and radiographicfeatures in a three generation family of seven individualswithout previous known immunodeficiency that were all directlyexposed to COVID19. Four individuals developed COVID19 infection:three individuals had critical disease, and one had mild symptoms.Three exposed family members were asymptomatic and did not haveclinical evidence of COVID19 infection. All family members werepreviously healthy and did not have a history ofmajor chronic diseaseincluding respiratory disease, known immunodeficiency, or any othergenetic disorder. Exome sequencing analysis was completed toinvestigate monogenic risk factors segregating with severe diseasein this family.Results: Seven family members spanning three generations wereincluded in final analysis. Individuals with severe COVID19 diseasewere male, had a mean age of 71 years old (range 61–87), and a meanbody mass index (BMI) of 27 (range 28–32). All three severely affectedmales were intubated and died within 33 days of presentation (mean25 days, range 16–33 days). One female family member with COVID19infection and a milder clinical coursewas 68 years old on presentationand had a BMI of 34. She did not require intubation but was mildlyhypoxic on room air requiring nasal cannula for oxygenation. All fourfamily members with symptomatic COVID19 infection receivedRemdesivir antiviral therapy and systemic steroids as part of thetreatment course. Unaffected family members (n = 3) had a mean ageof 35 years old (range 30–58). All were exposed to affected familymembers and all remained clinically asymptomatic. Whole exomesequencing and segregation analysis of this family identified amissense alteration of SPDEF that segregated with family memberswith severe COVID19 infection and was not detected in the mildlyaffected and unaffected family members. SPDEF is a transcriptionfactor that is highly intolerant to loss of function (pLI 0.97). Thealteration detected in this family (c.830G>A;p.Gly277Asp) is withinthe functional DNA binding domain of the protein product, and ispredicted to be damaging by in-silico models.Conclusions: Here we report exome findings from a family withvariable clinical response to COVID19 infection and describe a raremissense alteration in SPDEF segregating with severe COVID19infection. SPDEF is essential for goblet cell differentiation andmucociliary clearance within respiratory epithelial cells and has arole in mediating innate immune response. This report demonstratesthat studying large families with variable clinical outcomes can be auseful approach for identifying rare genetic variation associated withincreased risk for severe COVID19 infection. Moreover, our findingsprovide insight into the putative link between the altered inflammatoryresponse and respiratory comprise observed in some individualswith severe COVID19 infection

Metal-organic frameworks encapsulated with an anticancer compound as drug delivery system: Synthesis, characterization, antioxidant, anticancer, antibacterial, and molecular docking investigation

Metal organic framework (MOF) hybrid materials could be one of the answers in this investigation. We describe a simple and effective encapsulation of doxorubicin (DOX), an anticancer drug, inside Zr-MOF, which have been little studied as drug delivery organizations. We investigated the measured release of the drug from Zr-MOF in response to external incentives such as pH changes and interaction with biomimetic schemes. Zr-MOF with encapsulated doxorubicin (DOX@Zr-MOF) can be manufactured in one pot by addition the anticancer medication DOX to the reaction combination. They demonstrated pH-responsive medication release and cancer cell killing capability. MOFs can be designed as multifunctional distribution vehicles for a diversity of loads, including medicinal and imaging agents, using our simple one-pot approach. Fourier transform infrared (FTIR), X-ray diffraction, scanning electron microscopy, and N-2 sorption isotherm were used to analyze MOF and the developed drug delivery (DOX@Zr-MOF) scheme. It investigated the effects of MOF and a bespoke drug delivery system on the feasibility of patient breast as well as liver tumor cell lines. At pH 5, the trapped drug can be released more quickly than at pH 7.4. Zr-MOF nanoparticles had modest cytotoxicity;however, DOX@Zr-MOF has higher cytotoxicity in MCF-7 and HepG-2 cells than DOX at concentrations greater than 31.25 mu g ml(-1). These results were discovered that DOX@Zr-MOF could be a promising technique for delivering medicines to cancer cells. Furthermore, using the agar well dispersion technique, Zr-MOF, DOX, and captured DOX@Zr-MOF samples were assessed for their potential antibacterial activity against pathogenic bacteria in comparison to traditional antibiotics. In compared to the reference medication Gentamycin, the DOX@Zr-MOF exhibits a large inhibitory zone against Gram negative organisms (Escherichia coli). The docking active place interactions were assessed to see if DOX might bind to the breast cancer 3hb5-oxidoreductase receptor, prostate cancer protein 2q7k, and SARS-CoV-2 protease 6YB7 for anticancer and anticovid-19 activities.

PAMAM-calix-dendrimers: Synthesis and Thiacalixarene Conformation Effect on DNA Binding.

A convenient method for the synthesis of the first generation PAMAM dendrimers based on the thiacalix[4]arene has been developed for the first time. Three new PAMAM-calix-dendrimers with the macrocyclic core in cone, partial cone, and 1,3-alternate conformations were obtained with high yields. The interaction of the obtained compounds with salmon sperm DNA resulted in the formation of the associates of the size up to 200 nm, as shown by the UV-Vis spectroscopy, DLS, and TEM. It was demonstrated by the CD method that the structure of the DNA did not undergo significant changes upon binding. The PAMAM-calix-dendrimer based on the macrocycle in cone conformation stabilized DNA and prevented its degradation.

RNA binding to human METTL3-METTL14 restricts N6-deoxyadenosine methylation of DNA in vitro.

Methyltransferase like-3 (METTL3) and METTL14 complex transfers a methyl group from S-adenosyl-L-methionine to N6 amino group of adenosine bases in RNA (m6A) and DNA (m6dA). Emerging evidence highlights a role of METTL3-METTL14 in the chromatin context, especially in processes where DNA and RNA are held in close proximity. However, a mechanistic framework about specificity for substrate RNA/DNA and their interrelationship remain unclear. By systematically studying methylation activity and binding affinity to a number of DNA and RNA oligos with different propensities to form inter- or intra-molecular duplexes or single-stranded molecules in vitro, we uncover an inverse relationship for substrate binding and methylation and show that METTL3-METTL14 preferentially catalyzes the formation of m6dA in single-stranded DNA (ssDNA), despite weaker binding affinity to DNA. In contrast, it binds structured RNAs with high affinity, but methylates the target adenosine in RNA (m6A) much less efficiently than it does in ssDNA. We also show that METTL3-METTL14-mediated methylation of DNA is largely restricted by structured RNA elements prevalent in long noncoding and other cellular RNAs.

Longitudinal changes of neurospecific serum proteins in COVID-19 patients

INTRODUCTION/HYPOTHESIS: COVID-19 has been associated with distinct types of neuronal damage. We hypothesize that the progression of neurological damage will be related to an imbalance between neurodegeneration, neuroinflammatory, and neuroprotective markers, therefore suggesting a potential mechanism for the emergence of adverse, chronic outcomes. METHODS: 105 patients admitted to an urban, academic hospital with a diagnosis of COVID-19 were enrolled. Serum neuroprotective (clusterin, fetuin), neurodegenerative (τ, phosphorylated τ, amyloids, TDP43, NRGN, NCAM-1, and KLK6), and neuroinflammatory (CCL23, YKL40, MIF) markers were collected. These were analyzed longitudinally in conjunction with immune system activators (RAGE, IL-34) using the multiplex platform. Electronic medical records were used to collect demographic and clinical data. RESULTS: Of the 105 patients, 5 were diagnosed with stroke within 28 days of admission, followed by an additional 6 strokes occurring by 6 months, or a 9.5% occurrence of stroke overall. Serum levels of Amyloid β42 declined significantly for the general population 7 days after admission when compared to initial collections (p< 0.001), while Amyloid β40, KLK6, and MIF declined and recovered within the same 7 days (p< 0.001, p< 0.001, p=0.003). The neuroprotective markers fetuin and clusterin were particularly dynamic with fetuin decreasing and restoring in less than 7 days (p=0.02) and clusterin remaining low after admission (p< 0.001). Most patients had persistently elevated CCL23 levels, with the stroke patient cohort having the highest values (p=0.018). The IL-6 levels of stroke patients were significantly higher compared to their non-stroke counterparts one week after admission (p=0.001), while IL-8 levels fluctuated before declining (p< 0.001). CONCLUSIONS: Our data reveals elevations in neuronal damage in the 7 days following hospital admission for COVID-19 patients. The down-regulation of fetuin and clusterin is particularly compelling as their declines may be linked to the elevated neuronal injury seen with increased neuroinflammatory markers, specifically CCL23 and IL-6. Serum levels of neurodegeneration markers proved complex, therefore possibly suggesting a more dynamic relationship to the neural abnormalities seen in COVID-19 patients.

Optimization of reaction condition of recombinase polymerase amplification to detect SARS-CoV-2 DNA and RNA using a statistical method.

Recombinase polymerase amplification (RPA) is an isothermal reaction that amplifies a target DNA sequence with a recombinase, a single-stranded DNA-binding protein (SSB), and a strand-displacing DNA polymerase. In this study, we optimized the reaction conditions of RPA to detect SARS-CoV-2 DNA and RNA using a statistical method to enhance the sensitivity. In vitro synthesized SARS-CoV-2 DNA and RNA were used as targets. After evaluating the concentration of each component, the uvsY, gp32, and ATP concentrations appeared to be rate-determining factors. In particular, the balance between the binding and dissociation of uvsX and DNA primer was precisely adjusted. Under the optimized condition, 60 copies of the target DNA were specifically detected. Detection of 60 copies of RNA was also achieved. Our results prove the fabrication flexibility of RPA reagents, leading to an expansion of the use of RPA in various fields.

Recent development of nucleic acid nanosensors to detect sequence-specific binding interactions: From metal ions, small molecules to proteins and pathogens.

DNA carries important genetic instructions and plays vital roles in regulating biological activities in living cells. Proteins such as transcription factors binds to DNA to regulate the biological functions of DNA, and similarly many drug molecules also bind to DNA to modulate its functions. Due to the importance of protein-DNA and drug-DNA binding, there has been intense effort in developing novel nanosensors in the same length scale as DNA, to effectively study these binding interactions in details. In addition, aptamers can be artificially selected to detect metal ions and pathogens such as bacteria and viruses, making nucleic acid nanosensors more versatile in detecting a large variety of analytes. In this minireview, we first explained the different types and binding modes of protein-DNA and drug-DNA interactions in the biological systems, as well as aptamer-target binding. This was followed by the review of five types of nucleic acid nanosensors based on optical or electrochemical detection. The five types of nucleic acid nanosensors utilizing colorimetric, dynamic light scattering (DLS), surface-enhanced Raman spectroscopy (SERS), fluorescence and electrochemical detections have been recently developed to tackle some of the challenges in high-throughput screening technology for large scale analysis, which is especially useful for drug development and mass screening for pandemic outbreak such as SARS or COVID-19.