Targeting the Main Protease (Mpro, nsp5) by Growth of Fragment Scaffolds Exploiting Structure-Based Methodologies.

The main protease Mpro, nsp5, of SARS-CoV-2 (SCoV2) is one of its most attractive drug targets. Here, we report primary screening data using nuclear magnetic resonance spectroscopy (NMR) of four different libraries and detailed follow-up synthesis on the promising uracil-containing fragment Z604 derived from these libraries. Z604 shows time-dependent binding. Its inhibitory effect is sensitive to reducing conditions. Starting with Z604, we synthesized and characterized 13 compounds designed by fragment growth strategies. Each compound was characterized by NMR and/or activity assays to investigate their interaction with Mpro. These investigations resulted in the four-armed compound 35b that binds directly to Mpro. 35b could be cocrystallized with Mpro revealing its noncovalent binding mode, which fills all four active site subpockets. Herein, we describe the NMR-derived fragment-to-hit pipeline and its application for the development of promising starting points for inhibitors of the main protease of SCoV2.

Validation of X-ray Crystal Structure Ensemble Representations of SARS-CoV-2 Main Protease by Solution NMR Residual Dipolar Couplings.

Considerable debate has focused on whether sampling of molecular dynamics trajectories restrained by crystallographic data can be used to develop realistic ensemble models for proteins in their natural, solution state. For the SARS-CoV-2 main protease, Mpro, we evaluated agreement between solution residual dipolar couplings (RDCs) and various recently reported multi-conformer and dynamic-ensemble crystallographic models. Although Phenix-derived ensemble models showed only small improvements in crystallographic Rfree, substantially improved RDC agreement over fits to a conventionally refined 1.2-Å X-ray structure was observed, in particular for residues with above average disorder in the ensemble. For a set of six lower resolution (1.55-2.19 Å) Mpro X-ray ensembles, obtained at temperatures ranging from 100 to 310 K, no significant improvement over conventional two-conformer representations was found. At the residue level, large differences in motions were observed among these ensembles, suggesting high uncertainties in the X-ray derived dynamics. Indeed, combining the six ensembles from the temperature series with the two 1.2-Å X-ray ensembles into a single 381-member "super ensemble" averaged these uncertainties and substantially improved agreement with RDCs. However, all ensembles showed excursions that were too large for the most dynamic fraction of residues. Our results suggest that further improvements to X-ray ensemble refinement are feasible, and that RDCs provide a sensitive benchmark in such endeavors. Remarkably, a weighted ensemble of 350 PDB Mpro X-ray structures provided slightly better cross-validated agreement with RDCs than any individual ensemble refinement, implying that differences in lattice confinement also limit the fit of RDCs to X-ray coordinates.

NMR Observation of Sulfhydryl Signals in SARS-CoV-2 Main Protease Aids Structural Studies.

The 68-kDa homodimeric 3C-like protease of SARS-CoV-2, Mpro (3CLpro /Nsp5), is a key antiviral drug target. NMR spectroscopy of this large system proved challenging and resonance assignments have remained incomplete. Here we present the near-complete (>97 %) backbone assignments of a C145A variant of Mpro (Mpro C145A ) both with, and without, the N-terminal auto-cleavage substrate sequence, in its native homodimeric state. We also present SILLY (Selective Inversion of thioL and Ligand for NOESY), a simple yet effective pseudo-3D NMR experiment that utilizes NOEs to identify interactions between Cys-thiol or aliphatic protons, and their spatially proximate backbone amides in a perdeuterated protein background. High protection against hydrogen exchange is observed for 10 of the 11 thiol groups in Mpro C145A , even those that are partially accessible to solvent. A combination of SILLY methods and high-resolution triple-resonance NMR experiments reveals site-specific interactions between Mpro , its substrate peptides, and other ligands, which present opportunities for competitive binding studies in future drug design efforts.

An Enzyme with High Catalytic Proficiency Utilizes Distal Site Substrate Binding Energy to Stabilize the Closed State but at the Expense of Substrate Inhibition.

Understanding the factors that underpin the enormous catalytic proficiencies of enzymes is fundamental to catalysis and enzyme design. Enzymes are, in part, able to achieve high catalytic proficiencies by utilizing the binding energy derived from nonreacting portions of the substrate. In particular, enzymes with substrates containing a nonreacting phosphodianion group coordinated in a distal site have been suggested to exploit this binding energy primarily to facilitate a conformational change from an open inactive form to a closed active form, rather than to either induce ground state destabilization or stabilize the transition state. However, detailed structural evidence for the model is limited. Here, we use ß-phosphoglucomutase (ßPGM) to investigate the relationship between binding a phosphodianion group in a distal site, the adoption of a closed enzyme form, and catalytic proficiency. ßPGM catalyzes the isomerization of ß-glucose 1-phosphate to glucose 6-phosphate via phosphoryl transfer reactions in the proximal site, while coordinating a phosphodianion group of the substrate(s) in a distal site. ßPGM has one of the largest catalytic proficiencies measured and undergoes significant domain closure during its catalytic cycle. We find that side chain substitution at the distal site results in decreased substrate binding that destabilizes the closed active form but is not sufficient to preclude the adoption of a fully closed, near-transition state conformation. Furthermore, we reveal that binding of a phosphodianion group in the distal site stimulates domain closure even in the absence of a transferring phosphoryl group in the proximal site, explaining the previously reported ß-glucose 1-phosphate inhibition. Finally, our results support a trend whereby enzymes with high catalytic proficiencies involving phosphorylated substrates exhibit a greater requirement to stabilize the closed active form.

Advances in NMR Spectroscopy of Weakly Aligned Biomolecular Systems.

The measurement and application of residual dipolar couplings (RDCs) in solution NMR studies of biological macromolecules has become well established over the past quarter of a century. Numerous methods for generating the requisite anisotropic orientational molecular distribution have been demonstrated, each with its specific strengths and weaknesses. In parallel, an enormous number of pulse schemes have been introduced to measure the many different types of RDCs, ranging from the most widely measured backbone amide 15N-1H RDCs, to 1H-1H RDCs and couplings between low-γ nuclei. Applications of RDCs range from structure validation and refinement to the determination of relative domain orientations, the measurement of backbone and domain motions, and de novo structure determination. Nevertheless, it appears that the power of the RDC methodology remains underutilized. This review aims to highlight the practical aspects of sample preparation and RDC measurement while describing some of the most straightforward applications that take advantage of the exceptionally precise information contained in such data. Some emphasis will be placed on more recent developments that enable the accurate measurement of RDCs in larger systems, which is key to the ongoing shift in focus of biological NMR spectroscopy from structure determination toward gaining improved understanding of how molecular flexibility drives protein function.

Concordance of X-ray and AlphaFold2 Models of SARS-CoV-2 Main Protease with Residual Dipolar Couplings Measured in Solution.

The 68-kDa homodimeric 3C-like protease of SARS-CoV-2, Mpro (3CLpro/Nsp5), is a promising antiviral drug target. We evaluate the concordance of models generated by the newly introduced AlphaFold2 structure prediction program with residual dipolar couplings (RDCs) measured in solution for 15N-1HN and 13C'-1HN atom pairs. The latter were measured using a new, highly precise TROSY-AntiTROSY Encoded RDC (TATER) experiment. Three sets of AlphaFold2 models were evaluated: (1) MproAF, generated using the standard AlphaFold2 input structural database; (2) MproAFD, where the AlphaFold2 implementation was modified to exclude all candidate template X-ray structures deposited after Jan 1, 2020; and (3) MproAFS, which excluded all structures homologous to coronaviral Mpro. Close agreement between all three sets of AlphaFold models and experimental RDC data is found for most of the protein. For residues in well-defined secondary structure, the agreement decreases somewhat upon Amber relaxation. For these regions, MproAF agreement exceeds that of most high-resolution X-ray structures. Residues from domain 2 that comprise elements of both the active site and the homo-dimerization interface fit less well across all structures. These results indicate novel opportunities for combining experimentation with molecular dynamics simulations, where solution RDCs provide highly precise input for QM/MM simulations of substrate binding/reaction trajectories.

Total Synthesis of Viridiofungins A and B.

The total synthesis of viridiofungins A (1) and B (2) via ß-lactone 3 in 13 steps is reported. Key steps included an HF-mediated rearrangement of cyclobutene diester 9 to form a bicyclic lactone 6, an olefin cross metathesis between disubstituted alkene 3 and alkene 4 in which isomerization was suppressed, and a novel ß-lactone ring opening to form the amide. Deprotection then gave either viridiofungin A (1) or B (2) in high yield.

Four-dimensional NOE-NOE spectroscopy of SARS-CoV-2 Main Protease to facilitate resonance assignment and structural analysis.

Resonance assignment and structural studies of larger proteins by nuclear magnetic resonance (NMR) can be challenging when exchange broadening, multiple stable conformations, and 1H back-exchange of the fully deuterated chain pose problems. These difficulties arise for the SARS-CoV-2 Main Protease, a homodimer of 2 × 306 residues. We demonstrate that the combination of four-dimensional (4D) TROSY-NOESY-TROSY spectroscopy and 4D NOESY-NOESY-TROSY spectroscopy provides an effective tool for delineating the 1H-1H dipolar relaxation network. In combination with detailed structural information obtained from prior X-ray crystallography work, such data are particularly useful for extending and validating resonance assignments as well as for probing structural features.

The Role of Optimism and Psychosocial Factors in Athletes Recovery From ACL Injury: A Longitudinal Study.

Despite a growing interest into the role of psychosocial factors during the recovery period following sports injuries, there remains a paucity of longitudinal studies examining the indirect relationships between psychosocial factors, psychological responses, and recovery outcomes. The purpose of this study was to construct and test a conceptual model which examined the indirect relationships between optimism, psychosocial factors, rehabilitation adherence, and perceived knee function up to 12 months post anterior cruciate ligament (ACL) surgery. A prospective, longitudinal, and repeated measures design was employed, wherein 81 injured athletes (M age 26.89, SD = 7.52) completed measures of optimism, psychosocial factors, rehabilitation adherence, and perceived knee function on seven occasions (pre-surgery to 1 year post-surgery). Bayesian structural equation modeling evaluated the hypothesized indirect relationships proposed within the conceptual model. The main findings from this study was empirical support for a time-ordered, conceptual model which demonstrated that pre-surgery optimism had a significant overall indirect effect on perceived knee function at 12 months post-surgery (sum of indirect; αß = 0.08, post. SD = 0.05, CI [0.01, 0.04]), as well as a specific indirect effect through secondary appraisal at 1 month post-surgery, efficacy at 2 months post-surgery, and rehabilitation adherence at 6 months post-surgery (αß = 0.03, post. SD = 0.03, CI [0.00, 0.10]). Collectively, this study provides support for a number of previously hypothesized, but not empirically examined, indirect relationships between optimism, psychosocial factors and recovery outcomes. In doing so, we provide a conceptual model which has the potential to help guide individualized treatment recommendations, as well as identify individuals at risk of compromised recovery outcomes following ACL surgery.

Glenohumeral Migration of Intraosseous Suture- Button after Acromioclavicular JointACJ Reconstruction - A Case Report.

INTRODUCTION: Acromioclavicular joint (ACJ) separation is a common sports injury. Suture- button repair is favoured technique with a complication rate of 20%. We are the first to report the migration of a suture button into the glenohumeral joint. CASE REPORT: A 28-year-old right-handed rugby player presented with symptoms of laxity and catching within the right shoulder 4 years after reconstruction using an ACJ Dog Bone TM Technique (Arthrex Inc.). Magnetic resonance imaging showed that the coracoid suture button had migrated into the glenohumeral joint. CONCLUSION: The patient was successfully treated with an arthroscopic examination of the glenohumeral joint and removal of the button. We outline the risk factors and treatment options involved in this unique presentation.

Allomorphy as a mechanism of post-translational control of enzyme activity.

Enzyme regulation is vital for metabolic adaptability in living systems. Fine control of enzyme activity is often delivered through post-translational mechanisms, such as allostery or allokairy. ß-phosphoglucomutase (ßPGM) from Lactococcus lactis is a phosphoryl transfer enzyme required for complete catabolism of trehalose and maltose, through the isomerisation of ß-glucose 1-phosphate to glucose 6-phosphate via ß-glucose 1,6-bisphosphate. Surprisingly for a gatekeeper of glycolysis, no fine control mechanism of ßPGM has yet been reported. Herein, we describe allomorphy, a post-translational control mechanism of enzyme activity. In ßPGM, isomerisation of the K145-P146 peptide bond results in the population of two conformers that have different activities owing to repositioning of the K145 sidechain. In vivo phosphorylating agents, such as fructose 1,6-bisphosphate, generate phosphorylated forms of both conformers, leading to a lag phase in activity until the more active phosphorylated conformer dominates. In contrast, the reaction intermediate ß-glucose 1,6-bisphosphate, whose concentration depends on the ß-glucose 1-phosphate concentration, couples the conformational switch and the phosphorylation step, resulting in the rapid generation of the more active phosphorylated conformer. In enabling different behaviours for different allomorphic activators, allomorphy allows an organism to maximise its responsiveness to environmental changes while minimising the diversion of valuable metabolites.

The structural validity of the IKDC and its relationship with quality of life following ACL reconstruction.

OBJECTIVE: The purpose of this study was to (a) examine the structural validity of the International Knee Documentation Committee Subjective Knee Form in light of previously reported dimensionality issues, and (b) examine the relationships between the IKDC and patients' knee-related quality of life 2-9 years after anterior cruciate ligament (ACL) reconstruction. METHODS: A prospective research design was employed, wherein 319 patients (mean age = 29.07, SD = 9.03) completed the IKDC before surgery, 191 patients (mean age = 29.71, SD = 9.36) completed the IKDC at 6 months post-surgery, and 132 patients (mean age = 34.34, SD = 7.89) completed the IKDC and the Anterior Cruciate Ligament Quality of Life Survey (ACL-QOL) at 2-9 years post-surgery. RESULTS: Bayesian structural equation modeling analysis confirmed the two-factor structure (symptom & knee articulation and activity level) represented the most accurate conceptualization of perceived knee function across the three time-points. Moreover, findings revealed that of the two IKDC subscales pre-operatively, activity level was most strongly associated with long-term quality of life at 2-9 years following surgery, whereas 2-9 years post-operatively, symptoms and knee articulation was most strongly associated with long-term quality of life. CONCLUSIONS: The IKDC provides clinicians with a convenient total score to assess patients' perceived knee function, but its unidimensional factor structure is a poor representation of its items and fails to detect discrepancies in patients' post-operative quality of life, such as the relative importance of perceived knee activity level before reconstructive surgery.

Two-site recognition of Staphylococcus aureus peptidoglycan by lysostaphin SH3b.

Lysostaphin is a bacteriolytic enzyme targeting peptidoglycan, the essential component of the bacterial cell envelope. It displays a very potent and specific activity toward staphylococci, including methicillin-resistant Staphylococcus aureus. Lysostaphin causes rapid cell lysis and disrupts biofilms, and is therefore a therapeutic agent of choice to eradicate staphylococcal infections. The C-terminal SH3b domain of lysostaphin recognizes peptidoglycans containing a pentaglycine crossbridge and has been proposed to drive the preferential digestion of staphylococcal cell walls. Here we elucidate the molecular mechanism underpinning recognition of staphylococcal peptidoglycan by the lysostaphin SH3b domain. We show that the pentaglycine crossbridge and the peptide stem are recognized by two independent binding sites located on opposite sides of the SH3b domain, thereby inducing a clustering of SH3b domains. We propose that this unusual binding mechanism allows synergistic and structurally dynamic recognition of S. aureus peptidoglycan and underpins the potent bacteriolytic activity of this enzyme.

Total Synthesis and Stereochemical Reassignment of Citrafungin A.

The stereoselective 12-step total synthesis of the reassigned structure for citrafungin A (1a) via cyclobutene diester 10 is described. Key steps involved a formal [2 + 2]-cycloaddition, oxa-Michael/cyclobutanone ring-opening cascade to secure the alkyl citrate core, and asymmetric vinylzinc addition to form the C6 stereocenter. In addition, no oxidative adjustments are required to secure the citrate oxidation level.

Observation of ß-Amyloid Peptide Oligomerization by Pressure-Jump NMR Spectroscopy.

Brain tissue of Alzheimer's disease patients invariably contains deposits of insoluble, fibrillar aggregates of peptide fragments of the amyloid precursor protein (APP), typically 40 or 42 residues in length and referred to as Aß40 and Aß42. However, it remains unclear whether these fibrils or oligomers constitute the toxic species. Depending on sample conditions, oligomers can form in a few seconds or less. These oligomers are invisible to solution NMR spectroscopy, but they can be rapidly (<1 s) resolubilized and converted to their NMR-visible monomeric constituents by raising the hydrostatic pressure to a few kbar. Hence, utilizing pressure-jump NMR, the oligomeric state can be studied at residue-specific resolution by monitoring its signals in the monomeric state. Oligomeric states of Aß40 exhibit a high degree of order, reflected by slow longitudinal 15N relaxation (T1 > 5 s) for residues 18-21 and 31-34, whereas the N-terminal 10 residues relax much faster (T1 ≤ 1.5 s), indicative of extensive internal motions. Transverse relaxation rates rapidly increase to ca. 1000 s-1 after the oligomerization is initiated.

Phosphite binding by the HtxB periplasmic binding protein depends on the protonation state of the ligand.

Phosphorus acquisition is critical for life. In low phosphate conditions, some species of bacteria have evolved mechanisms to import reduced phosphorus compounds, such as phosphite and hypophosphite, as alternative phosphorus sources. Uptake is facilitated by high-affinity periplasmic binding proteins (PBPs) that bind cargo in the periplasm and shuttle it to an ATP-binding cassette (ABC)-transporter in the bacterial inner membrane. PtxB and HtxB are the PBPs responsible for binding phosphite and hypophosphite, respectively. They recognize the P-H bond of phosphite/hypophosphite via a conserved P-H...π interaction, which confers nanomolar dissociation constants for their respective ligands. PtxB also has a low-level binding affinity for phosphate and hypophosphite, whilst HtxB can facilitate phosphite uptake in vivo. However, HtxB does not bind phosphate, thus the HtxBCDE transporter has recently been successfully exploited for biocontainment of genetically modified organisms by phosphite-dependent growth. Here we use a combination of X-ray crystallography, NMR and Microscale Thermophoresis to show that phosphite binding to HtxB depends on the protonation state of the ligand, suggesting that pH may effect the efficiency of phosphite uptake by HtxB in biotechnology applications.

An effective cis-ß-octahedral Mn(iii) SALPN catalyst for the Mukaiyama-Isayama hydration of α,ß-unsaturated esters.

Two cis-ß-MnIIISALPN catalysts were synthesised and tested in the Mukaiyama-Isayama hydration of α,ß-unsaturated esters. The MnIIIEtOSALPN(acac) complex 7 is the most active and catalyses hydration with little or no detectable undesired alkene reduction. This catalyst is superior for alkene hydration compared to the originally reported Mn(dpm)3 catalyst.

Return to sport after lower limb arthroplasty - why not for all?

BACKGROUND: Total hip and knee replacements are being performed in increasing numbers in progressively younger patients with higher activity demands. Many such patients have expectations of returning to athletic activity post-operatively yet are not always able to do so and the reasons behind this have not been extensively examined. We hypothesise that any reasons for a failure to return to athletic activity post-operatively are multi-factorial. AIM: To quantify the return to athletic activity following lower limb joint arthroplasty and understand qualitative reasons for altered activity participation. METHODS: A single centre, single surgeon retrospective questionnaire for hip and knee arthroplasty patients under age 60 years, minimum two years post-surgery with exclusion criteria of multiple degenerative joint involvement and multiple medical co-morbidities. Outcomes were validated joint-specific (Oxford hip and knee) and lifestyle questionnaires [short form 12 (SF-12) and University of California, Los Angeles (UCLA)] and an activity questionnaire assessing ability participation in athletic activity post-operatively. Statistical analysis was performed on the validated outcome data, including comparison between hip and knee replacements. Frequency tables were produced to quantify the different athletic activities participated in by patients. RESULTS: Responses were received from 64 patients (80% response rate). There was a statistically significant improvement in Oxford hip and knee scores following surgery. SF-12 scores also improved for all patients, but no statistically significant difference was seen between joints (P = 0.88). Mean UCLA scores pre-operatively were 7.67 and at two years post-operatively were 7.69, with no statistically significant change (P = 0.91). All patients reported high satisfaction and improved ability to perform athletic activity at a higher frequency compared to pre-operatively. The most common reasons for changing activity participation were not wanting to stress their joint replacement or instructions by other doctors or the lead surgeon. There was no difference in the responses to the questionnaire based on type of joint replacement (P = 0.995). CONCLUSION: Patients receiving a joint replacement are able to participate in athletic activity to high levels and are satisfied with their outcomes. Reasons for non-participation are multi-factorial.

Synthesis of Alkyl Citrates (-)-CJ-13,981, (-)-CJ-13,982, and (-)-L-731,120 via a Cyclobutene Diester.

An efficient and step-economic new approach to alkyl citrate natural products from a cyclobutene diester is presented. The key sequence involves a formal [2 + 2]-cycloaddition of a silylketene acetal with dimethylacetylene dicarboxylate to provide the cyclobutene diester 14 with 4.5:1 stereoselectivity. Exposure of diester 14 in acidic methanol effected a hydrolysis, intramolecular oxy-Michael reaction, and cyclobutanone methanolysis cascade to give the triester 15. Iodination and elimination then afforded a key alkyl citrate alkene intermediate, which was converted into the natural products (-)-CJ-13,982 (1), (-)-CJ-13,981 (2), and (-)-L-731,120 (3) via a cross-metathesis and subsequent reduction.

Clinical and radiological outcome for Trufit Plug in the treatment of chondral and osteochondral lesions at a minimum of 2 years.

The aim of this study was to evaluate the functional and radiological outcome of TruFit plugs. We retrospectively reviewed 10 patients who underwent treatment for a symptomatic chondral/osteochondral lesion using one or more Trufit Plugs. Full incorporation of the bony portion of the plug occurred in only 3 and partial incorporation in 7 lesions. The remaining portion of these 7 lesions looked cystic on MRI. The significance of this cystic change is not clear. Though all 10 patients showed some improvement on the IKDC scoring system but the amount of the improvement was small.