ABSTRACT
Context: The coronavirus disease 2019 (COVID-19) pandemic is still a cause of worldwide health concern. Diabetes and its associated comorbidities are risk factors for mortality and morbidity in COVID-19. Selecting the right antidiabetic drug to achieve optimal glycemic control might mitigate some of the negative impacts of diabetes. Metformin continues to be the most widely administered antidiabetic agent. There is evidence of its beneficial outcome in COVID-19 independent of its glucose-lowering effect. Evidence Acquisition: A thorough literature search was conducted in PubMed, Google Scholar, Scopus, and Web of Science to identify studies investigating metformin in COVID-19. Result(s): Several overlapping mechanisms have been proposed to explain its antiviral properties. It could bring about conformational changes in the angiotensin-converting enzyme-2 receptor and decrease viral entry. The effects on the mammalian target of the rapamycin pathway and cellular pH have been proposed to reduce viral protein synthesis and replication. The immunomodulatory effects of metformin might counter the detrimental effects of hyperinflammation associated with COVID-19. Conclusion(s): These findings call for broader metformin usage to manage hyperglycemia in COVID-19.Copyright © 2023, International Journal of Endocrinology and Metabolism.
ABSTRACT
The SARS-CoV-2 replication and transcription complex (RTC) is made up of nine distinct non-structural viral proteins encoded by the ORF1ab gene. These proteins house seven enzymatic sites that synthesize new viral genomic and subgenomic RNA, proofread and correct errors in the synthesis, add a 5'-cap to the nascent RNA, and truncate the intermediate negative sense 5'-poly-U tail. While x-ray crystallography and cryo-EM have provided high resolution structures of each of the individual proteins of the RTC and have shed light on how subsets of the proteins associate, a full picture of the RTC has remained elusive. Using molecular modeling tools, including protein-protein docking, we have generated a model of the RTC centered around hexameric nsp15, which is capped on two faces by trimers of nsp14/nsp16/(nsp10)2. A conformational change of nsp14, necessary to facilitate binding to nsp15, then recruits six nsp12/nsp7/(nsp8)2 polymerase subunits. To this, six nsp13 subunits are distributed around the complex. The resulting superstructure is composed of 60 subunits total and positions the nsp14 exonuclease and nsp15 endonuclease sites in line with the dsRNA exiting the nsp12 polymerase site. Nsp10 acts to separate the RNA strands, directing the nascent strand to the nsp12 NiRAN site, where a transiently associated nsp9 facilitates the first step in mRNA capping. The RNA is then directed to the nsp14 N7-methyltransferase site and the nsp16 2'O-methyltransferase site to complete the capping. Additionally, template switching during transcription is proposed to be facilitated by positioning of the TRS-L RNA-bound N-protein above the polymerase active site, between two subunits of nsp13. The model, while constructed based on structural considerations, offers a unifying set of hypotheses to explain the diverse set of processes involved in coronavirus genome replication and transcription. All work presented was funded by Gilead Sciences.Copyright © 2023 The American Society for Biochemistry and Molecular Biology, Inc.
ABSTRACT
The genomic material of SARS-CoV-2 is a positive-sense single-stranded RNA. SARS-CoV-2 produces non-structural protein 1 (NSP1), which inhibits host cell translation by binding its' N-terminal to the host's 40S ribosomal subunit. Once NSP1 is bound its C-terminal domain folds and binds to the mRNA entry channel. Stem loop 1 (SL1) in the 5'-UTR of the viral mRNA binds to NSP1 to abrogate translation inhibition leading to the expression of viral proteins. SL1 contains a 1 x 2 internal loop that is not seen in other coronaviruses and may be involved in conformational changes that influence SL1-NSP1 interactions. The 1 x 2 internal loop of SL1 contains a putative A*C non-canonical base pair. The U6 snRNA also contains a 1 x 2 internal loop known to undergo conformation changes in response to pH and magnesium ion binding. Here we examine the thermodynamic properties and magnesium binding of the 1 x 2 internal loop of SL1 in varying helical contexts. Thermal denaturation experiments were performed on various DNA and RNA constructs in the presence of 1 M KCl or 10 mM magnesium chloride at a pH of 5.5 and 7. We show that formation of the A+*C base pair and the construct stability in the presence of magnesium ions is dependent on the helical context.Copyright © 2023 The American Society for Biochemistry and Molecular Biology, Inc.
ABSTRACT
BACKGROUND: Inflammatory bowel disease (IBD) flares are common and unpredictable. Disease monitoring relies on symptom reporting or single timepoint assessments of stool, blood, imaging, or endoscopy-these are inconvenient and invasive and do not always reflect the patient perspective. Advances in wearable technology allow for passive, continuous and non-invasive assessment of physiological metrics including heart rate variability (HRV), the measure of small time differences between each heartbeat, a marker of autonomic nervous system function. Our group has previously demonstrated that changes in autonomic function precedes an IBD flare, can predict psychological state transitions and even identify inflammatory events including SARS-CoV-2 infection. To develop algorithms that can predict IBD flares using wearable device signatures, we launched a national wearable device study called The IBD Forecast study. To assess data quality and feasibility, the first 125 Apple Watch users to enroll were evaluated. METHOD(S): The IBD Forecast study is a prospective cohort study enrolling anyone >=18 years of age in the United States (US) with IBD who is willing to (1) use a commercially available wearable device, (2) download our custom eHive app and (3) answer daily survey questions. HRV metrics (mean of the standard deviations of all the NN intervals [SDNN]) were analyzed using a mixed-effect cosigner model that incorporated body mass index, age, and sex. SDNN is a time domain HRV index that reflects both sympathetic and parasympathetic nervous system activity and is calculated from the variance of intervals between adjacent QRS complexes (the normal-to-normal [NN] intervals). Clinical flare was assessed with daily Patient Reported Outcome (PRO)-2 surveys (flare;PRO-2 Crohn's disease >7, PRO-2 ulcerative colitis >2). Inflammatory flare was assessed via patient reported C-reactive protein (CRP), with inflammatory flare defined as >5 mg/L. RESULT(S): The first 125 study participants were enrolled across 29 states in the US (Table 1). Circadian features of changes of HRV were modelled (Figure 1). The mesor, or midline of the circadian pattern of the SDNN was higher in those with clinical flare (mean 44.43;95% CI 41.25-47.75) compared to those in clinical remission (mean 43.03;95% CI 39.94-46.22) (p<0.004). The mesor of the circadian pattern of the SDNN was lower in those with an inflammatory flare (mean 38.16;95% CI 30.86-45.72) compared to those with normal inflammatory markers (mean 49.51;95% CI 43.12-56.26) (p<0.001). CONCLUSION(S): Longitudinally collected HRV metrics from a commonly worn commercial wearable device can identify symptomatic and inflammatory flares. This preliminary analysis of a small proportion of the IBD Forecast Study cohort demonstrates the feasibility of using wearable devices to identify, and may potentially predict, IBD flares. [Formula presented] [Formula presented]Copyright © 2023
ABSTRACT
BACKGROUND: Inflammatory bowel disease (IBD) flares are common and unpredictable. Disease monitoring relies on symptom reporting or single timepoint assessments of stool, blood, imaging, or endoscopy-these are inconvenient and invasive and do not always reflect the patient perspective. Advances in wearable technology allow for passive, continuous and non-invasive assessment of physiological metrics including heart rate variability (HRV), the measure of small time differences between each heartbeat, a marker of autonomic nervous system function. Our group has previously demonstrated that changes in autonomic function precedes an IBD flare, can predict psychological state transitions and even identify inflammatory events including SARS-CoV-2 infection. To develop algorithms that can predict IBD flares using wearable device signatures, we launched a national wearable device study called The IBD Forecast study. To assess data quality and feasibility, the first 125 Apple Watch users to enroll were evaluated. METHOD(S): The IBD Forecast study is a prospective cohort study enrolling anyone >=18 years of age in the United States (US) with IBD who is willing to (1) use a commercially available wearable device, (2) download our custom eHive app and (3) answer daily survey questions. HRV metrics (mean of the standard deviations of all the NN intervals [SDNN]) were analyzed using a mixed-effect cosigner model that incorporated body mass index, age, and sex. SDNN is a time domain HRV index that reflects both sympathetic and parasympathetic nervous system activity and is calculated from the variance of intervals between adjacent QRS complexes (the normal-to-normal [NN] intervals). Clinical flare was assessed with daily Patient Reported Outcome (PRO)-2 surveys (flare;PRO-2 Crohn's disease >7, PRO-2 ulcerative colitis >2). Inflammatory flare was assessed via patient reported C-reactive protein (CRP), with inflammatory flare defined as >5 mg/L. RESULT(S): The first 125 study participants were enrolled across 29 states in the US (Table 1). Circadian features of changes of HRV were modelled (Figure 1). The mesor, or midline of the circadian pattern of the SDNN was higher in those with clinical flare (mean 44.43;95% CI 41.25-47.75) compared to those in clinical remission (mean 43.03;95% CI 39.94-46.22) (p<0.004). The mesor of the circadian pattern of the SDNN was lower in those with an inflammatory flare (mean 38.16;95% CI 30.86-45.72) compared to those with normal inflammatory markers (mean 49.51;95% CI 43.12-56.26) (p<0.001). CONCLUSION(S): Longitudinally collected HRV metrics from a commonly worn commercial wearable device can identify symptomatic and inflammatory flares. This preliminary analysis of a small proportion of the IBD Forecast Study cohort demonstrates the feasibility of using wearable devices to identify, and may potentially predict, IBD flares. (Table Presented).
ABSTRACT
Selenium nanoparticles (SeNPs) are among the emerging selenium supplements because of their high bioactivity and low toxicity. However, bare SeNPs are prone to activity loss caused by aggregation and sedimentation. This study aims to stabilize SeNPs with curdlan (CUR), a polysaccharide, to maintain or even enhance their biological activity. Herein, the stable SeNPs were constructed via the unique conformational transition of CUR induced by alkali-neutralization (AN) pretreatment. The physicochemical properties and structures of the prepared SeNPs were characterized by dynamic light scattering (DLS), UV-visible spectroscopy, Fourier-transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), transmission electron microscopy (TEM), and free-radical-scavenging activity assays. The results show that most SeNPs are stabilized within the triple helix of CUR that has been pretreated with high-intensity AN treatment. These amorphous, small-sized (average size was 53.6 ± 17.7 nm), and stabilized SeNPs have significantly enhanced free-radical-scavenging ability compared to the control and can be well-stabilized for at least 240 days at 4 °C. This work indicates that CUR, as a food additive, can be used to well-stabilize SeNPs by AN pretreatment and provides a facile method to prepare and enhance the stability and bioactivity of SeNPs via triple-helix conformational transition.
ABSTRACT
Introduction. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), is a single-strand ribonucleic acid virus that was first identified in January 2020 in patients with viral pneumonia in Wuhan, China. The virus has since spread rapidly around the world, leading the World Health Organization to declare it a pandemic on 11 March 2020. In Brazil there have been 21.8 million cases of SARS-CoV-2 infection and 608,500 deaths. The objective of this study was to evaluate the cost utility of the Oxford, CoronaVac, and Janssen vaccines from the perspective of the Brazilian public health system. Methods. Three microsimulation models were constructed using individual data. The simulations contained seven transition states related to the natural history of COVID-19. The model with a daily cycle had a time horizon of one year and used data from 289 days of the pandemic. The analysis considered direct medical costs from the Brazilian health system perspective. Outpatient, hospital, and mortality databases were used for the model inputs and patient data were stratified by age. Effective vaccines reduced the likelihood of patients becoming ill. Information on the quality of life of patients receiving treatment in the outpatient or hospital setting and disease sequelae were extracted from the published literature. The main outcome of the analysis was quality-adjusted life-years (QALYs). Results. The vaccines had incremental cost-utility ratios ranging from USD 4,121 (Oxford) to USD 3,160 per QALY (CoronaVac). The older the population, the lower the incremental cost-utility ratio. Given a willingness-to-pay threshold of BRL 3,129 per QALY, all the vaccines were considered cost effective in the probabilistic sensitivity analysis. The incremental cost-effectiveness ratio stratified by age ranged from USD 6,327 per QALY in patients older than 75 years (Janssen) to USD 20,993 per QALY in patients younger than 59 years (CoronaVac). Conclusions. The results of this analysis, stratified by patient age, can help in the preparation of a vaccination prioritization plan.
ABSTRACT
It is commonly considered that protein-protein interactions are extremely difficult to target using small molecules. Our group uses a chemical biology approach to study the allosteric, regulatory, mechanisms of protein kinases involved in growth factor signaling downstream of PI3-kinase. Over the years we have described small molecules that target a regulatory site in AGC kinases called "PIF-Pocket", and allosterically affect the active site, ATP-binding site. We also have shown that molecules that bind to the active site of protein kinases can stimulate or inhibit protein-protein interactions at the PIF-pocket regulatory site, by a mechanism that we have termed "reverse allostery". The reverse allosteric effects are widely produced by protein kinases inhibitors that target the ATP-binding site, although the phenomenon has been almost completely unperceived by pharmaceutical industries. The presence of a reverse allosteric effect is also the cause of the paradoxical effects on the protein kinases signal transduction detected for certain inhibitors. Thus, using the knowledge of the molecular mechanism involved in the bidirectional allostery, it becomes possible to exploit it to break protein-protein interactions between protein kinases in their protein complexes (Trends Biochem Sci 45(1):27-41, 2020). We will summarize our detailed research on the protein kinase PDK1 as a model of allosteric protein and will analyze the results in the context of the modern models of allostery, "conformational selection" and "population shift". We suggest that the principles of allostery should be used to rationalize new approaches to push forward the discovery of novel drugs that break proteinprotein interactions. In line with the allosteric mechanism to disrupt protein kinase interactions, we also hypothesized that such a mechanism could also be used to break the interactions between other proteins, for example, between the angiotensin converting enzyme II (ACE2) and SARS-CoV-2 spike protein, which could be used as treatment against coronavirus infection (ChemMedChem. 15(18):1682-1690, 2020). Current studies confirm that compounds with allosteric mechanism can indeed disrupt the interaction between ACE2 and Spike. Enzymology.
ABSTRACT
Aims: The burden of the COVID-19 pandemic resulted in an unintended reduction of available healthcare capacity for regular care. To guide prioritization of semi-elective surgery in times of scarcity, we previously developed a decision model to quantify the expected health loss due to delay of surgery, in an academic setting. The aim of this study is to validate our decision model in a non-academic setting and include additional surgical procedures. Method(s): In this study, we used the previously published three-state cohort state-transition model, to evaluate the health effects of surgery postponement for 28 surgical procedures commonly performed in non-academic hospitals. Scientific literature and national registries yielded nearly all input parameters, except for the quality of life estimates which were obtained from experts using the Delphi method. Two expert panels, one from a single non-academic hospital and one from different nonacademic hospitals in the Netherlands, were invited to estimate quality of life weights. We compared estimated model results (disability adjusted life years (DALY)/month of surgical delay) based on the QoL estimates from the two panels by calculating the mean difference and the correlation between the ranks of the different surgical procedures. The eventual model was based on the combined QoL estimates from both panels. Result(s): Pacemaker implantation was associated with the most DALY due to surgical delay (0.05 DALY/month, 95% CI 0.03-0.10) and hemithyreoidectomy with the least DALY/month (0.01 DALY/month, 95% CI 0.00-0.01). The overall mean difference between the two panels was 0.00 (95% CI -0.01 to 0.00). The correlation between ranks was 0.98 (p<0.001). Conclusion(s): Our study provides an accurate overview of incurred health loss due to surgical delay for frequently performed non-academic surgeries. The quality of life estimates used in our model are robust and validate towards a different group of experts. These results enrich our earlier published results on academic surgeries and contribute to prioritizing a more complete set of surgeries.
ABSTRACT
The coronavirus disease 2019 (COVID-19) is caused by the recently discovered coronavirus and affects several countries worldwide. Some medications may alleviate or minimize some of the disease symptoms, but no drug have been proven to prevent or cure it. However, this study was aimed at investigating the role of some medicinal plants as potent inhibitors of COVID-19 main protease (MPro). More than 250 plant extracts with antiviral activity were exploited for their potential SARS-CoV2 medication using molecular docking. The conformational stability of the compounds extracted from the plants with MPro interactions was evaluated using molecular dynamics simulations. Then, the plant extracts with the highest binding energies were used for treatments by administering them to 50 COVID-19 patients, while the other 50 cases received only the drug without the plant extracts. The results of the theoretical analysis revealed high binding energies for seven compounds. Alliin stabilized COVID-19’s MPro while retaining critical connections and remained stable throughout the simulations. Marrubin and thymoquinone are also capable of protein stabilization over the simulated time. The test plants were observed to be effective against the virus in the COVID-19 patients, with a disease symptom improvement response rate of 78-86 and 60-72% for the first and second groups, respectively. Also, the percentage of oxygen increased from the second day after taking the extracts. Ground-glass opacity disappeared from the second group that received the plant extracts. The findings of this study suggest that these compounds have a great potential for therapeutic activity if isolated and administered alone.
ABSTRACT
The SARS-CoV-2 pandemic, waning now after over two years, generated a global response from the structural biology community. The first experiments at the 4th generation Synchrotron source SIRIUS, in Brazil, were focused on the structural studies of the viral proteases, including those encoded by SARS-CoV-2, their transition states and potential ligands. In this talk, we will present some of the findings concerning SARS-CoV-2 proteases and the status of MANACA beamline, as well as the latest developments in phasing (native SAD), multi-crystal, serial and room-temperature data collection. The MX beamline, MANACA, (MAcromolecular micro and Nano Serial CrystAllography), was commissioned during 2020, and the initial results helped to assess not only important features of the proteins and ligands, but also the quality and potential of the new beamline. Natural products and fragment libraries have been used by our users and collaborators [1], in academic and industrial settings. MANACA is optimised for high flux, micro-beam size and small beam divergence (0.44 mrad). Setups for serial crystallography data collection and analyses, as well as automation procedures, are being prepared [2]. The great beam characteristics provided by Sirius [3] and the high stability and precision of the optics and experimental station allows the diffraction of challenging samples such as viruses (and other crystals with large unit cells), membrane proteins and complexes, which commonly yield small crystals. The experiment control uses a userfriendly graphical interface (MXCuBE) [4], and automatic data processing (from data reduction to initial modelling) is available. The MANACA beamline is also prepared for remote access and has already performed remote experiments with foreign scientists.
ABSTRACT
The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has killed over 5 million people and is causing a devastating social and economic impact all over the world. The rise of new variants represents a difficult challenge due to the loss of vaccine and natural immunity, and increased transmissibility. These variants contain mutations in the spike glycoprotein, which mediates fusion between the viral and host cell membranes, via its receptor binding domain (RBD) that binds to angiotensin-converting enzyme 2 (ACE2). To understand the effect of RBD mutations, a lot of attention has been given to the RBD-ACE2 interaction. However, this type of analysis is limited since it ignores the conformational dynamics of the RBD itself. Observing that some variants mutations occur in residues that are not in direct contact with ACE2, we hypothesized that they could affect RBD conformational dynamics. To test this, we performed long atomistic molecular dynamics simulations to investigate the structural dynamics of wt RBD, and that of three variants (alpha, beta and delta). Our results show that in solution, wt RBD presents two distinct conformations: an 'open' conformation where it is free to bind ACE2;and a 'closed' conformation, where the RBM ridge blocks the binding surface. The alpha and beta variants significantly impact the open/closed equilibrium, shifting it towards the open conformation by roughly 20%. This shift likely increases ACE2 binding affinity. In the delta variant RBD simulations, the closed conformation was never observed. Instead, the system alternated between the before mentioned open conformation and an alternative 'reversed' one, with a significantly changed orientation of the RBMridge flanking the RBD. These results support the hypothesis that variants impact RBD conformational dynamics in a direction that simultaneously promotes efficient binding to ACE2 and antibody escape.
ABSTRACT
SARS-CoV-2 is the causative agent of COVID-19. The dimeric form of the viral Mpro is responsible for the cleavage of the viral polyprotein in 11 sites, including its own N- and C-terminus. The lack of structural information for intermediary forms of Mpro is a setback for the understanding its self-maturation process. Herein, we used X-ray crystallography combined with biochemical data to characterize multiple forms of SARS-CoV-2 Mpro. For the immature form, we show that extra N-terminal residues caused conformational changes in the positioning of domainthree over the active site, hampering the dimerization and diminishing its activity. We propose that this form preludes the cis and trans-cleavage of N-terminal residues. Using fragment screening, we probe new cavities in this form which can be used to guide therapeutic development. Furthermore, we characterized a serine site-directed mutant of the Mpro bound to its endogenous Nand C-terminal residues during dimeric association stage of the maturation process. We suggest this form is a transitional state during the C-terminal trans-cleavage. This data sheds light in the structural modifications of the SARS-CoV-2 main protease during its self-maturation process.
ABSTRACT
Molecular simulations have been instrumental in identifying the structure-function relationships of biomolecules in the atomic level as well as providing a means for structure-based drug discovery, thereby explaining and guiding experimental findings. The increase in computational power, the new physics and machine-learning-based algorithms is significantly driving the boost in the field and gives access to addressing biomolecular phenomena of increasing length and timescales. In this talk I will discuss examples where using state-of-the-art integrative structural biology methods that inject Cryo-EM experimental data into the simulation, we can reveal accurate protein-functional dynamics of the SARS-CoV-2 spike protein in an atomistic level. In this way we can a) reveal virus vulnerabilities by identifying cryptic binding sites exposed during the S protein conformational transition related to the recognition to the host cell and b) provide with the molecular motion and energetics of protein-antibody complexes which enables to suggest mutations that increase the spike-antibody affinity. These predictions are validated in further CryoEM experiments.
ABSTRACT
While the new coronavirus has turned our lives upside down causing millions of deaths, the historically known tuberculosis (TB) disease caused by Mycobacterium tuberculosis (MTB) was responsible for the loss of approximately 1.5 million lives alone in 2021. New anti- TB drugs are in an urgent need. A promising target is dUTPase, an enzyme preventing uracil incorporation into DNA. It is present in all multicellular species and in most microbes. Abolition of its activity potentially leads to DNA double strand breaks and cell death. Therefore, species-specific inhibition of MTB dUTPase may be a successful way of TB disease treatment. Currently no species-specific dUTPase inhibitor exists, but an interaction partner, protein Stl shows significantly different ability to inhibit dUTPase homologues from various species. We use Stl as a model to understand how species- specific differences in dUTPase structure may be harnessed in future inhibitor development. A remarkable species-specific characteristic of MTB dUTPase is a small surface sequence loop playing no direct role in enzyme activity but being essential for mycobacterial survival in a yet unknown way. What is the exact structural background of MTB dUTPase-Stl interaction? For this reason, we have crystallized a complex of MTB dUTPase and a truncated Stl protein mutant. And how the loop sequence may affect the MTB dUTPase protein structure on its own? For this answer, we obtained another X-ray diffraction dataset of a loop-lacking mutant of MTB dUTPase with 1.3 Å resolution. Surprisingly, electron density of the flexible C-terminal “arm” segment of the mutant dUTPase was missing from our dataset, contrary to the already crystallized wildtypeMTB dUTPase structures. We postulate that the loop sequence may restrict conformational flexibility of the dUTPase “arm”, making it more inhibitable by Stl compared to the loop-lacking mutant, as we know from our comparative steady-state enzyme activity inhibition measurements.
ABSTRACT
We have explored the inhibitory capability of Thymus vulgaris compounds against ACE2 protein -the host receptor for SARS-CoV-2, papain-like and main protease of the SARS-CoV-2 through molecular simulations. The docking results showed that the compounds had a greater capability to inhibit ACE2 and papain-like protease in comparison to the main protease. The majority of compounds (61.7%) bind to the S2 active pocket of ACE2. The most powerful anticoronavirus activity is expressed in the order: Terpinolene > Thymol > Bicyclogermacrene. Pi interactions play key roles in the binding of three compounds to the active sites of ACE2 enzyme. 34 out of these 60 compounds were fitted in the PLpro active site. α-humulene followed by (+)-Spathulenol, and (-)-β-Bourbonene showed strong capacity to inhibit PLpro binding site. Except for (+)-Spathulenol which also formed H-bond with Asp165 and Tyr274 amino acids, α-humulene and (-)-β-Bourbonene conjugate with PLpro were stabilized mainly through alkyl and pi interactions. According to the Mpro docking results, 58.3% of thyme compounds could block the active site. The binding energy order was (-)-Spathulenol at highest, then Bicyclogermacrene, (+)-δ-cadinene, (+)-Spathulenol, and Viridiflorol, followed by (-)-β-Caryophyllene oxide. Cys145, His41, Met49, and Met165 are key residues in the interaction of these ligands with the enzyme binding site. The weakest interaction with all three enzymes was observed for (R)-(-)-1-Octen-3-ol and (3S)-Oct-1-en-3-ol. Based on the molecular dynamics simulation lowest conformational change was detected for ACE2 in the present of Terpinolene. (-)-Spathulenol and α-Humulene had the least and most displacement compared to its initial positions, respectively.
ABSTRACT
Corona virus disease 2019 is an acute infectious disease caused by SARS-CoV-2 infection and has entered the state of global pandemic. Spike protein ( S protein) , a key protein that mediates SARS-CoV-2 to infect host cells, has the characteristics of specific receptor binding and membrane fusion, playing an important role in host tropism and virulence. The spontaneous closed and open conformation of S protein trimer is crucial for receptor binding and initiation of conformational changes in membrane fusion, and its unique furin recognition site may be a crucial factor leading to high infectivity. Therefore, to study the structure and function of SARS-CoV-2 S protein and its receptor has important implications for invasion mechanisms of SARS- CoV-2 and the development of relevant targeted drugs.
ABSTRACT
The structural transition of the health care system in Germany is accelerated by the COVID-19 pandemic. Simultaneously, therapeutical concepts of the broad spectrum of abdominal diseases are permanently changing. Our common patients benefit from the close collaboration between gastroenterologists and visceral surgeons. The present article gives an overview of relevant, innovative, and interesting developments in 2021 and beyond from the surgical perspective.
ABSTRACT
During the ongoing Covid-19 pandemic, collection and donation of human cadaveric corneas are cumbersome. Decellularized corneas (DC) have gained intense popularity as a possible scaffold for corneal remodeling and as an alternative tissue source for corneal replacement. However, DC elicits immune response inspite of elimination of the cellular contents/antigens due to distortion of the collagen fibrils that exposes certain antigenic sites, which often lead to graft rejection. Therefore, here, we tested the hypothesis that cross-linking DC with chondroitin sulfate (CS) may help in restoring distorted conformational changes of the fibrous matrix and would reduce graft rejection. An in vitro immune response study confirmed that the cross-linked DC elicited the least immune response than DC. We implanted three sets of corneal scaffolds obtained from goat, i.e., native, decellularized, and DC conjugated with CS into rabbit stroma. Histology analysis, three months post-implantation confirmed seamless graft integration, cell migration, and no sign of inflammation in the crosslinked cornea. However, so far we have checked the immunogenic potential of decellularized and crosslinked cornea among cross-species(goat to rabbit). Now, before moving to a human clinical trial (patients with infectious keratitis), we are validating the decellularization of the human stromal layer using discarded human corneas not suitable for implantation, for the regeneration of the corneal endothelial layer. The decellularized, chemically decorated cornea will be tectonically strong, offer less immunogenicity, can be sterilized, and will have a longer shelf life. Through this novel study, we can meet the demand for alternative bioengineered human cornea for keratitis patients.
ABSTRACT
Human vitamin K epoxide reductase (hVKORC1) enzymatic activity requires an initial activation by a specific redox protein, a less studied step in the hVKORC1 vital cycle. Significant steric conditions must be met by enzymes, being that to adapt their configurations is mandatory for hVKORC1 activation. We studied, by molecular dynamics (MD) simulations, the folding and conformational plasticity of hVKORC1 in its inactive (fully oxidised) state using available structures, crystallographic and from de novo modelling. According to the obtained results, hVKORC1 is a modular protein composed of the stable transmembrane domain (TMD) and intrinsically disordered luminal (L) loop, possessing the great plasticity/adaptability required to perform various steps of the activation process. The docking (HADDOCK) of Protein Disulfide Isomerase (PDI) onto different hVKORC1 conformations clearly indicated that the most interpretable solutions were found on the target closed L-loop form, a prevalent conformation of hVKORC1's oxidised state. We also suggest that the cleaved L-loop is an appropriate entity to study hVKORC1 recognition/activation by its redox protein. Additionally, the application of hVKORC1 (membrane protein) in aqueous solution is likely to prove to be very useful in practice in either in silico studies or in vitro experiments.