Invention of MK-7845, a SARS-CoV-2 3CL Protease Inhibitor Employing a Novel Difluorinated Glutamine Mimic

As SARS-CoV-2 continues to circulate, antiviral treatments are needed to complement vaccines. The virus's main protease, 3CLPro, is an attractive drug target in part because it recognizes a unique cleavage site, which features a glutamine residue at the P1 position and is not utilized by human proteases. Herein, we report the invention of MK-7845, a novel reversible covalent 3CLPro inhibitor. While most covalent inhibitors of SARS-CoV-2 3CLPro reported to date contain an amide as a Gln mimic at P1, MK-7845 bears a difluorobutyl substituent at this position. SAR analysis and X-ray crystallographic studies indicate that this group interacts with His163, the same residue that forms a hydrogen bond with the amide substituents typically found at P1. In addition to promising in vivo efficacy and an acceptable projected human dose with unboosted pharmacokinetics, MK-7845 exhibits favorable properties for both solubility and absorption that may be attributable to the unusual difluorobutyl substituent.

Molnupiravir maintains antiviral activity against SARS-CoV-2 variants and exhibits a high barrier to the development of resistance

Molnupiravir, an oral prodrug of N-hydroxycytidine (NHC), previously demonstrated broad in vitro antiviral activity against multiple RNA viruses and has shown a high barrier to the development of resistance. Here, we present the antiviral activity of NHC against recent SARS-CoV-2 variants and the results of resistance selection studies to better understand the potential for viral resistance to NHC. NHC activity against SARS-CoV-2 variants omicron (BA.1, BA.1.1, BA.2, BA.4, BA.4.6, BA.5, BQ.1.1, XBB.1, and XBB.1.5), alpha (B.1.1.7), beta (B.1.351), gamma (P.1), delta (B.1.617.2), lambda (C.37), and mu (B.1.621) was evaluated in Vero E6 cells using cytopathic effect assays. Resistance selection studies were performed by passaging SARS-CoV-2 (WA1) in the presence of NHC or a 3C-like protease inhibitor (MRK-A) in Vero E6 cells. Supernatants from cultures exhibiting a cytopathic effect score of ≥2 were re-passaged, and IC50 values were estimated. Whole-genome deep sequencing was performed on viral RNA isolated at each passage. NHC demonstrated similar potency against all SARS-CoV-2 variants evaluated. No evidence of SARS-CoV-2 phenotypic or genotypic resistance to NHC was observed following 30 passages. A random pattern of nucleotide changes was observed in NHC cultures, consistent with the drug's mechanism of action. In contrast, resistance was readily selected in all three MRK-A control cultures with the selection of a T21I substitution in the 3C-like protease. In conclusion, molnupiravir maintains antiviral activity across all major SARS-CoV-2 variants. Furthermore, no evidence of viral resistance to NHC was observed, supporting previous reports that NHC has a high barrier to developing resistance.

The HIV-1 capsid core is an opportunistic nuclear import receptor

The movement of viruses and other large macromolecular cargo through nuclear pore complexes (NPCs) is poorly understood. The human immunodeficiency virus type 1 (HIV-1) provides an attractive model to interrogate this process. HIV-1 capsid (CA), the chief structural component of the viral core, is a critical determinant in nuclear transport of the virus. HIV-1 interactions with NPCs are dependent on CA, which makes direct contact with nucleoporins (Nups). Here we identify Nup35, Nup153, and POM121 to coordinately support HIV-1 nuclear entry. For Nup35 and POM121, this dependence was dependent cyclophilin A (CypA) interaction with CA. Mutation of CA or removal of soluble host factors changed the interaction with the NPC. Nup35 and POM121 make direct interactions with HIV-1 CA via regions containing phenylalanine glycine motifs (FG-motifs). Collectively, these findings provide additional evidence that the HIV-1 CA core functions as a macromolecular nuclear transport receptor (NTR) that exploits soluble host factors to modulate NPC requirements during nuclear invasion.

Potent targeted activator of cell kill molecules eliminate cells expressing HIV-1

Antiretroviral therapy inhibits HIV-1 replication but is not curative due to establishment of a persistent reservoir after virus integration into the host genome. Reservoir reduction is therefore an important HIV-1 cure strategy. Some HIV-1 nonnucleoside reverse transcriptase inhibitors induce HIV-1 selective cytotoxicity in vitro but require concentrations far exceeding approved dosages. Focusing on this secondary activity, we found bifunctional compounds with HIV-1-infected cell kill potency at clinically achievable concentrations. These targeted activator of cell kill (TACK) molecules bind the reverse transcriptase-p66 domain of monomeric Gag-Pol and act as allosteric modulators to accelerate dimerization, resulting in HIV-1⁺ cell death through premature intracellular viral protease activation. TACK molecules retain potent antiviral activity and selectively eliminate infected CD4⁺ T cells isolated from people living with HIV-1, supporting an immune-independent clearance strategy.

A Phenotypic Screen Identifies Potent DPP9 Inhibitors Capable of Killing HIV-1 Infected Cells

Although current antiretroviral therapy can control HIV-1 replication and prevent disease progression, it is not curative. Identifying mechanisms that can lead to eradication of persistent viral reservoirs in people living with HIV-1 (PLWH) remains an outstanding challenge to achieving cure. Utilizing a phenotypic screen, we identified a novel chemical class capable of killing HIV-1 infected peripheral blood mononuclear cells. Tool compounds ICeD-1 and ICeD-2 ("inducer of cell death-1 and 2"), optimized for potency and selectivity from screening hits, were used to deconvolute the mechanism of action using a combination of chemoproteomic, biochemical, pharmacological, and genetic approaches. We determined that these compounds function by modulating dipeptidyl peptidase 9 (DPP9) and activating the caspase recruitment domain family member 8 (CARD8) inflammasome. Efficacy of ICeD-1 and ICeD-2 was dependent on HIV-1 protease activity and synergistic with efavirenz, which promotes premature activation of HIV-1 protease at high concentrations in infected cells. This in vitro synergy lowers the efficacious cell kill concentration of efavirenz to a clinically relevant dose at concentrations of ICeD-1 or ICeD-2 that do not result in complete DPP9 inhibition. These results suggest engagement of the pyroptotic pathway as a potential approach to eliminate HIV-1 infected cells.

Intact Human Immunodeficiency Virus (HIV) Reservoir Estimated by the Intact Proviral DNA Assay Correlates With Levels of Total and Integrated DNA in the Blood During Suppressive Antiretroviral Therapy

Accurate characterization of the human immunodeficiency virus (HIV) reservoir is imperative to develop an effective cure. HIV was measured in antiretroviral therapy-suppressed individuals using the intact proviral DNA assay (IPDA), along with assays for total or integrated HIV DNA, and inducible HIV RNA or p24. Intact provirus correlated with total and integrated HIV.

Gag p24 is a Marker of HIV Expression in Tissues and Correlates with Immune Response

We demonstrate that HIV gag p24 protein is more readily detected in gut and lymph node tissues than in blood CD4+ T-cells and correlates better with CD4 count during antiretroviral therapy (ART). Gut p24 levels also measurably decline with ART in natural controllers. During ART, gut p24 expression is more strongly associated both with HIV-specific CD8+ T-cell frequency and plasma sCD14 levels than gut HIV RNA expression. This study supports using gag p24 as a marker of HIV expression in HIV+ tissues to study effects of viral persistence and to monitor efficacy of treatment in HIV-based clearance studies.

Titanium dioxide nanomaterials cause endothelial cell leakiness by disrupting the homophilic interaction of VE-cadherin

The use of nanomaterials has raised safety concerns, as their small size facilitates accumulation in and interaction with biological tissues. Here we show that exposure of endothelial cells to TiO₂ nanomaterials causes endothelial cell leakiness. This effect is caused by the physical interaction between TiO₂ nanomaterials and endothelial cells' adherens junction protein VE-cadherin. As a result, VE-cadherin is phosphorylated at intracellular residues (Y658 and Y731), and the interaction between VE-cadherin and p120 as well as β-catenin is lost. The resulting signalling cascade promotes actin remodelling, as well as internalization and degradation of VE-cadherin. We show that injections of TiO₂ nanomaterials cause leakiness of subcutaneous blood vessels in mice and, in a melanoma-lung metastasis mouse model, increase the number of pulmonary metastases. Our findings uncover a novel non-receptor-mediated mechanism by which nanomaterials trigger intracellular signalling cascades via specific interaction with VE-cadherin, resulting in nanomaterial-induced endothelial cell leakiness.

Hybrid and nonhybrid lipids exert common effects on membrane raft size and morphology

Nanometer-scale domains in cholesterol-rich model membranes emulate lipid rafts in cell plasma membranes (PMs). The physicochemical mechanisms that maintain a finite, small domain size are, however, not well understood. A special role has been postulated for chain-asymmetric or hybrid lipids having a saturated sn-1 chain and an unsaturated sn-2 chain. Hybrid lipids generate nanodomains in some model membranes and are also abundant in the PM. It was proposed that they align in a preferred orientation at the boundary of ordered and disordered phases, lowering the interfacial energy and thus reducing domain size. We used small-angle neutron scattering and fluorescence techniques to detect nanoscopic and modulated liquid phase domains in a mixture composed entirely of nonhybrid lipids and cholesterol. Our results are indistinguishable from those obtained previously for mixtures containing hybrid lipids, conclusively showing that hybrid lipids are not required for the formation of nanoscopic liquid domains and strongly implying a common mechanism for the overall control of raft size and morphology. We discuss implications of these findings for theoretical descriptions of nanodomains.

Competition between line tension and curvature stabilizes modulated phase patterns on the surface of giant unilamellar vesicles: a simulation study

When prepared in the liquid-liquid coexistence region, the four-component lipid system distearoyl-phospha-tidylcholine-dioleoyl-phosphatidylcholine-palmitoyl,oleoyl-phosphatidylcholine-cholesterol (DSPC-DOPC-POPC-Cholesterol), with certain ratios of DOPC and POPC, shows striking modulated phase patterns on the surface of giant unilamellar vesicles (GUVs). In this simulation study, we show that the morphology of these patterns can be explained by the competition of line tension (which tends to favor large round domains) and curvature, as specified by the Helfrich energy functional. In this study we use a Monte-Carlo simulation on the surface of a GUV to determine the equilibrium shape and phase morphology. We find that the patterns arising from these competing interactions very closely approximate those observed, that the patterned morphologies represent thermodynamically stable configurations, and that the geometric nature of these patterns is closely tied to the relative and absolute values of the model parameters.

Badminton injuries in youth competitive players

AIM

The aim of the study was to examine sports injury pattern and establish cost of injuries in relation to training of 58 competitive badminton players in a Malaysian National Sports School.

METHODS

This one-year prospective observational study recruited all the 13-16 year old students after obtaining informed consent from their appointed guardian. All participants were requested to report any injuries, which were pain or disabilities that occur within the study period (September 1, 2008 to August 31, 2009) either during training or competition. Injured students were to seek treatment from the researcher(s) who made weekly visits and they were then followed up accordingly until they return to full training. Details and progress of the injuries were documented during each visit.

RESULTS

Sixty-three injuries were recorded. Soft tissue sprains/strains were the commonest injury (64%). About one third of the injuries occurred in the lower limb especially the knees and was followed by back injuries; 38% of the injuries did not require training modification, half of these injuries resumed training within one week. Upon full training, half of them were still symptomatic. Injury risk was 57%; injury rate was 0.9 injuries/ player/1000 training hours.

CONCLUSION

Badminton injuries mostly involved the lower limb and almost all overuse injuries occurred in the lower limb. However, badminton injuries as a whole were predominantly sprains and strains, and not overuse in nature as widely believed.

Versatile membrane deformation potential of activated pacsin

Endocytosis is a fundamental process in signaling and membrane trafficking. The formation of vesicles at the plasma membrane is mediated by the G protein dynamin that catalyzes the final fission step, the actin cytoskeleton, and proteins that sense or induce membrane curvature. One such protein, the F-BAR domain-containing protein pacsin, contributes to this process and has been shown to induce a spectrum of membrane morphologies, including tubules and tube constrictions in vitro. Full-length pacsin isoform 1 (pacsin-1) has reduced activity compared to its isolated F-BAR domain, implicating an inhibitory role for its C-terminal Src homology 3 (SH3) domain. Here we show that the autoinhibitory, intramolecular interactions in pacsin-1 can be released upon binding to the entire proline-rich domain (PRD) of dynamin-1, resulting in potent membrane deformation activity that is distinct from the isolated F-BAR domain. Most strikingly, we observe the generation of small, homogenous vesicles with the activated protein complex under certain experimental conditions. In addition, liposomes prepared with different methods yield distinct membrane deformation morphologies of BAR domain proteins and apparent activation barriers to pacsin-1's activity. Theoretical free energy calculations suggest bimodality of the protein-membrane system as a possible source for the different outcomes, which could account for the coexistence of energetically equivalent membrane structures induced by BAR domain-containing proteins in vitro. Taken together, our results suggest a versatile role for pacsin-1 in sculpting cellular membranes that is likely dependent both on protein structure and membrane properties.

Control of a nanoscopic-to-macroscopic transition: modulated phases in four-component DSPC/DOPC/POPC/Chol giant unilamellar vesicles

We have found modulated phase morphology in a particular region of composition within the liquid-ordered + liquid-disordered coexistence region in the four-component lipid bilayer mixture DSPC/DOPC/POPC/Chol. By controlling lipid composition, we could see distinct types of modulated liquid-liquid phase morphologies, including linear, irregular, and angular features in giant unilamellar vesicles. We used a combination of confocal, two-photon, wide-field fluorescence, and differential interference contrast microscopies, and used stringent controls to minimize light-induced artifacts. These studies establish that both the size and morphology of membrane rafts can be controlled by the concentration and the type of low-melting lipid in mixtures with cholesterol and a high-melting lipid.

Comparison of three ternary lipid bilayer mixtures: FRET and ESR reveal nanodomains

Phase diagrams of ternary lipid mixtures containing cholesterol have provided valuable insight into cell membrane behaviors, especially by describing regions of coexisting liquid-disordered (Ld) and liquid-ordered (Lo) phases. Fluorescence microscopy imaging of giant unilamellar vesicles has greatly assisted the determination of phase behavior in these systems. However, the requirement for optically resolved Ld + Lo domains can lead to the incorrect inference that in lipid-only mixtures, Ld + Lo domain coexistence generally shows macroscopic domains. Here we show this inference is incorrect for the low melting temperature phosphatidylcholines abundant in mammalian plasma membranes. By use of high compositional resolution Förster resonance energy transfer measurements, together with electron spin resonance data and spectral simulation, we find that ternary mixtures of DSPC and cholesterol together with either POPC or SOPC, do indeed have regions of Ld + Lo coexistence. However, phase domains are much smaller than the optical resolution limit, likely on the order of the Förster distance for energy transfer (R(0), ∼2-8 nm).

Serum leptin levels in older patients with hip fracture--impact on peri-operative myocardial injury

To evaluate whether there is a relationship between admission serum leptin concentrations and peri-operative myocardial injury, 238 consecutive older patients (mean age 81.9+/-7.9 years; 172 women) with low-trauma hip fracture were assessed. Myocardial injury as defined by elevated serum cardiac troponin I was associated with lower leptin levels analyzed as continuous or categorical variables. Patients with serum leptin concentrations <12ng/ml (medium value) had a two-fold greater increased risk for such complications compared with those with higher leptin levels (odd ratio 2.13, 95% confidence interval 1.06-4.28; p=0.033). This association remained significant after adjustments for age, gender, clinical (history of coronary artery disease [CAD], stroke, hypertension, diabetes, dementia), hematological (red, white, and lymphocyte count, hemoglobin, hematocrit), metabolic (parathyroid hormone [PTH], albumin), renal(creatinine, urea, glomerular filtration rate [GFR]), and inflammatory (C-reactive protein [CRP], ferritin) factors. The predictive value of lower leptin levels increased significantly when used in combination with traditional risk factors for myocardial injury.

Structure and plasticity of Endophilin and Sorting Nexin 9

Endophilin and Sorting Nexin 9 (Snx9) play key roles in endocytosis by membrane curvature sensing and remodeling via their Bin/Amphiphysin/Rvs (BAR) domains. BAR and the related F-BAR domains form dimeric, crescent-shaped units that occur N- or C-terminally to other lipid-binding, adaptor, or catalytic modules. In crystal structures, the PX-BAR unit of Snx9 (Snx9(PX-BAR)) adopts an overall compact, moderately curved conformation. SAXS-based solution studies revealed an alternative, more curved state of Snx9(PX-BAR) in which the PX domains are flexibly connected to the BAR domains, providing a model for how Snx9 exhibits lipid-dependent curvature preferences. In contrast, Endophilin appears to be rigid in solution, and the SH3 domains are located at the distal tips of a BAR domain dimer with fixed curvature. We also observed tip-to-tip interactions between the BAR domains in a trigonal crystal form of Snx9(PX-BAR) reminiscent of functionally important interactions described for F-BAR domains.

Elevated serum cardiac troponin I in older patients with hip fracture: incidence and prognostic significance

INTRODUCTION

Cardiovascular complications are the main causes of morbidity and mortality in patients with osteoporotic hip fracture (HF). The aim of this prospective study was to evaluate the incidence and prognostic significance of elevated cardiac troponin I (cTnI) in the early peri-operative period in older patients with HF.

MATERIALS AND METHODS

A blind evaluation of myocardial injury as detected by cTnI elevation in 238 consecutive older patients with low-trauma HF (mean age 81.9 +/- 7.8 (SD) years; 72% females). Data on demographic and clinical characteristics, in-hospital mortality, hospital length of stay and discharge destination were collected prospectively. Serum cTnI level was analysed from blood collected routinely in the first 72 h of hospital admission.

RESULTS

Sixty-nine (29%) patients had elevated cTnI (>0.06 microg/l) but myocardial injury was clinically recognised in only 23 (33%) and only 24 (34.8%) had a history of coronary artery disease (CAD). Patients with elevated cTnI were significantly older, more often had American Society of Anaesthesiologist status score >or=3, a history of CAD or stroke and more often were current smokers than the patients without cTnI elevation. In multivariate regression analysis only age was an independent predictor of cTnI elevation. Patients with cTnI release were twice as likely to have a length of stay >or=20 days (P = 0.047) and 2.7 times more likely to be discharged to a long-term residential care facility (RCF) (P = 0.013). cTnI level >or=1 microg/l was a strong independent predictor of all-cause mortality with 98.3% specificity and 89.1% negative predictive value.

CONCLUSION

Peri-operative myocardial injury is common in older HF patients but is frequently unrecognised clinically. Elevated blood cTnI level is an independent predictor of prolonged length of hospital stay (>or=20 days), need for long-term RCF and mortality (if cTnI >or=1 microg/l).

Recurrent neural tube defects

We report a case of recurrent neural tube defects in a 30-year-old multigravida with no medical or family history of note. She presented with a significant history of having three (out of four) previous pregnancies affected by neural tube defects diagnosed at the 20-week foetal anomaly ultrasonographical scans, and which resulted in mid-trimester pregnancy terminations. Previous investigations for the foetuses did not yield any obvious cause. We discuss the possible differential diagnoses and aetiological factors. Rare causes of neural tube defects need to be excluded in recurrent cases with no obvious aetiology.

Cysteine protease falcipain 1 in Plasmodium falciparum is biochemically distinct from its isozymes

Falcipains form a class of papain-like cysteine proteases found in Plasmodium falciparum. This group of proteases has been suggested to be promising targets for anti-malarial chemotherapy. Despite being the first falcipain to be identified, the physiological role(s) of falcipain 1 (fp1) remains a mystery. Its suggested functions include haemoglobin degradation, erythrocytic invasion and oocyst production. In this study, the procurement of the gene coding for fp1 and its soluble expression in a heterologous host, Escherichia coli, have enabled further enzyme characterization. The recombinant fp1 protease was found to be unlike falcipain 2 (fp2A) in being more active at neutral pH than at acidic pH against the Z-LR-AMC fluorogenic substrate, suggesting a probable localization in the cytosol and not in the food vacuole. Interestingly, a common cysteine specific inhibitor, E64, did not inhibit fp1 activity, indicating dissimilar biochemical characteristics of fp1 from the other falcipains. This may be explained by computational analysis of the primary structures of the falcipain isozymes, as well as that of papain. The analysis revealed that Tyr61 (papain numbering), which is correspondingly absent in fp1, might be an important residue involved in E64 substrate binding.

Acetylcholinesterase and synapses in the nervous system of Phocanema decipiens (Nematoda): a histochemical and ultrastructural study

The nervous system of Phocanema decipiens was examined histochemically for acetylcholinesterases (EC 3.1.1.7) using the acetylthiocholine method with specific inhibitors (eserine and diisopropylfluorophosphate) and different substrates (butyrylthiocholine and acetylthiocholine). The enzymes, which are localized mainly as small discrete granules, are found in the nerve ring, the six longitudinal nerve cords, and the three pharyngeal nerves. With the electron microscope, these neurons are found to contain presumptive cholinergic synaptic contacts with aggregations of small lucent vesicles in the presynaptic axons. In the nerve ring, such synapses are observed in axoaxonal, neuromuscular and axoglial cell contacts. The longitudinal nerve cords have neuromuscular junctions similar to those observed in other nematodes. In the four sublateral nerve cords, the alternating regions with and without synaptic contacts correspond to the discontinuous histochemical pattern of enzymatic activity. The pharyngeal nerves have axoaxonal and axooesophageal musculature synapses. In most of the synapses, some large dense or dense-core vesicles are found intermingled with the small lucent vesicles. This coexistence of different vesicles is discussed in the light of the cholinergic link hypothesis, whereby acetylcholine is initially released to facilitate the release of other neurotransmitters.

Selective uptake of noradrenaline, dopa, and 5-hydroxytryptamine by the nervous system of Phocanema decipiens (Nematoda): a light autoradiographic and ultrastructural study

As determined by light microscopic autoradiography, parts of the nervous system of Phocanema decipiens have selective and high affinity mechanisms for the uptake of tritiated noradrenaline, dihydroxyphenylalanine (dopa) and 5-hydroxytryptamine. In the nervous system, noradrenaline is accumulated only by the four papillary nerves and two fibers in the nerve ring. The precursor dopa is also taken up by these neurons and, in addition, by the lateral nerves. 5-Hydroxytryptamime is accumulated by the three pharyngeal nerves, two cells in each lateral ganglion, and two other fibers in the nerve ring. With adjacent ultrathin sections, the labelled papillary nerve and lateral ganglion were examined ultrastructurally and found to contain various dense core vesicles which are similar to those in other aminergic neurons. The adjoining unlabelled cells of the same neurons are found, on the other hand, to contain dense agranular vesicles. With these results, the noradrenaline accumulating neurons are suggested to be noradrenergic and to contain the amine synthesizing enzymes. The lateral nerves are regarded, for the present, as dopaminergic neurons. These suggestions are in agreement with the previous demonstration of catecholaminergic neurons in this nematode. The 5-hydroxytryptamine accumulating neurons are tentatively identified as tryptaminergic.