Exploring glutathione lyases as biocatalysts: paving the way for enzymatic lignin depolymerization and future stereoselective Applications

Glutathione-dependent β-etherases and glutathione lyases are key-enzymes for the biocatalytic depolymerization of lignin. In the first step, the nucleophilic attack of glutathione to the common β-O-4-aryl-ether motif in lignin is catalyzed by β-etherases and afterwards the glutathione is removed again by the action of glutathione lyases. Given their potential impact for lignin valorization, in this paper novel glutathione lyases are reported and biocatalytically characterized based on lignin model compounds. As a result, an enzyme exhibiting increased thermostability and lowered enantioselectivity - key features for implementation of glutathione lyases in enzymatic lignin depolymerization processes - was identified. Furthermore, first mutational studies of these enzymes revealed the possibility to further alter the activity as well as enantioselectivity of glutathione lyases by means of protein engineering. From a practical perspective, one-pot multi-step processes combining β-etherases and glutathione lyases are successfully set-up, giving hints on the potential that the implementation of these biocatalysts may bring for biorefinery purposes

Phage Display-Derived Compounds Displace hACE2 from Its Complex with SARS-CoV-2 Spike Protein

Severe respiratory syndrome coronavirus-2 (SARS-CoV-2) is a highly contagious beta-class coronavirus. Although vaccinations have shown high efficacy, the emergence of novel variants of concern (VOCs) has already exhibited traits of immune evasion. Thus, the development of tailored antiviral medications for patients with incomplete, inefficient, or non-existent immunization, is essential. The attachment of viral surface proteins to the cell surface is the first crucial step in the viral replication cycle, which for SARS-CoV-2 is mediated by the high affinity interaction of the viral trimeric spike with the host cell surface-located human angiotensin converting enzyme-2 (hACE2). Here, we used a novel and efficient next generation sequencing (NGS) supported phage display strategy for the selection of a set of SARS-CoV-2 receptor binding domain (RBD)-targeting peptide ligands that bind to the target protein with low µM to nM dissociation constants. Compound CVRBDL-3 inhibits the SARS-CoV-2 spike protein association to hACE2 in a concentration-dependent manner for pre- as well as post-complex formation conditions. Further rational optimization yielded a CVRBDL-3 based divalent compound, which demonstrated inhibitory efficacy with an IC50 value of 47 nM. The obtained compounds were not only efficient for the different spike constructs from the originally isolated “wt” SARS-CoV-2, but also for B.1.1.7 mutant trimeric spike protein. Our work demonstrates that phage display-derived peptide ligands are potential fusion inhibitors of viral cell entry. Moreover, we show that rational optimization of a combination of peptide sequences is a potential strategy in the further development of therapeutics for the treatment of acute COVID-19

Exploring glutathione lyases as biocatalysts: paving the way for enzymatic lignin depolymerization and future stereoselective applications

Glutathione-dependent β-etherases and glutathione lyases are key-enzymes for the biocatalytic depolymerization of lignin. In the first step, the nucleophilic attack of glutathione to the common β-O-4-arylether motif in lignin is catalyzed by β-etherases and afterwards the glutathione is removed again by the action of glutathione lyases. Given their potential impact for lignin valorization, in this paper novel glutathione lyases are reported and biocatalytically characterized based on lignin model compounds. As a result, an enzyme exhibiting increased thermostability and lowered enantioselectivity – key features for implementation of glutathione lyases in enzymatic lignin depolymerization processes – was identified. Furthermore, first mutational studies of these enzymes revealed the possibility to further alter the activity as well as enantioselectivity of glutathione lyases by means of protein engineering. From a practical perspective, onepot multi-step processes combining β-etherases and glutathione lyases are successfully set-up, giving hints on the potential that the implementation of these biocatalysts may bring for biorefinery purposes

A So-Far Overlooked Secondary Conformation State in the Binding Mode of SARS-CoV-2 Spike Protein to Human ACE2 and Its Conversion Rate Are Crucial for Estimating Infectivity Efficacy of the Underlying Virus Variant

Since its outbreak in 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread with high transmission efficiency across the world, putting health care as well as economic systems under pressure. During the course of the pandemic, the originally identified SARS-CoV-2 variant has been multiple times replaced by various mutant versions, which showed enhanced fitness due to increased infection and transmission rates. In order to find an explanation for why SARS-CoV-2 and its emerging mutated versions showed enhanced transmission efficiency compared with SARS-CoV (2002), an enhanced binding affinity of the spike protein to human angiotensin converting enzyme 2 (hACE2) has been proposed by crystal structure analysis and was identified in cell culture models. Kinetic analysis of the interaction of various spike protein constructs with hACE2 was considered to be best described by a Langmuir-based 1:1 stoichiometric interaction. However, we demonstrate in this report that the SARS-CoV-2 spike protein interaction with hACE2 is best described by a two-step interaction, which is defined by an initial binding event followed by a slower secondary rate transition that enhances the stability of the complex by a factor of ~190 (primary versus secondary state) with an overall equilibrium dissociation constant (KD) of 0.20 nM. In addition, we show that the secondary rate transition is not only present in SARS-CoV-2 wild type (“wt”; Wuhan strain) but also found in the B.1.1.7 variant, where its transition rate is 5-fold increased.IMPORTANCE The current SARS-CoV-2 pandemic is characterized by the high infectivity of SARS-CoV-2 and its derived variants of concern (VOCs). It has been widely assumed that the reason for its increased cell entry compared with SARS-CoV (2002) is due to alterations in the viral spike protein, where single amino acid residue substitutions can increase affinity for hACE2. So far, the interaction of a single unit of the CoV-2 spike protein has been described using the 1:1 Langmuir interaction kinetic. However, we demonstrate here that there is a secondary state binding step that may be essential for novel VOCs in order to further increase their infectivity. These findings are important for quantitatively understanding the infection process of SARS-CoV-2 and characterization of emerging SARS-CoV-2 variants of spike proteins. Thus, they provide a tool for predicting the potential infectivity of the respective viral variants based on secondary rate transition and secondary complex stability

Development of an α-synuclein fibril and oligomer specific tracer for diagnosis of Parkinson's disease, dementia with Lewy bodies and multiple system atrophy

The development of specific disease-associated PET tracers is one of the major challenges, the realization of which in neurodegenerative diseases would enable not only the efficiency of diagnosis but also support the development of disease-modifying therapeutics. Parkinson's disease (PD) is the most common neurodegenerative movement disorder and is characterized by neuronal fibrillary inclusions composed of aggregated α-synuclein (α-syn). However, these deposits are not only found in PD, but also in other related diseases such as multiple system atrophy (MSA) and dementia with Lewy bodies (DLB), which are grouped under the term synucleinopathies. In this study, we used NGS-guided phage display selection to identify short peptides that bind aggregated α-syn. By surface plasmon resonance (SPR)-based affinity screening, we identified the peptide SVLfib-5 that recognizes aggregated α-syn with high complex stability and sequence specificity. Further analysis SPR showed that SVLfib-5 is not only specific for aggregated α-syn, but in particular recognizes fibrillary and oligomeric structures. Moreover, fluorescence microscopy of human brain tissue sections from PD, MSA, and DLB patients with SVLfib-5 allowed specific recognition of α-syn and a clear discrimination between diseased and non-diseased samples. These findings provide the basis for the further development of an α-syn PET tracer for early diagnosis and monitoring of disease progression and therapy progress

In Vitro Reconstitution of the Highly Active and Natively Folded Recombinant Human Superoxide Dismutase 1 Holoenzyme

SOD1 is an antioxidant enzyme that exists as a highly stable dimer in healthy humans. Each subunit contains an intramolecular disulfide bond and coordinates one zinc and one copper ion. The dimer is destabilized in the absence of the ions and disruption of the disulfide bond, which leads to the formation of small oligomers and subsequently larger insoluble aggregates. An acquired toxic function of destabilized SOD1 is postulated to be associated with amyotrophic lateral sclerosis (ALS), which is a neurodegenerative disease characterized by peripheral and central paralysis and by 3‐ to 5‐year median survival after diagnosis. In this study, we present a protocol for heterologous expression of human SOD1 in E. coli and total reconstitution of the holoenzyme, which exhibits the highest reported specific activity (four‐fold higher) of recombinant hSOD1. Biophysical characterization confirms the native state of this protein. The presented protocol provides highly active hSOD1 that will benefit in vitro investigations of this protein

In Vitro Reconstitution of the Highly Active and Natively Folded Recombinant Human Superoxide Dismutase 1 Holoenzyme

SOD1 is an antioxidant enzyme that exists as a highly stable dimer in healthy humans. Each subunit contains an intramolecular disulfide bond and coordinates one zinc and one copper ion. The dimer is destabilized in the absence of the ions and disruption of the disulfide bond, which leads to the formation of small oligomers and subsequently larger insoluble aggregates. An acquired toxic function of destabilized SOD1 is postulated to be associated with amyotrophic lateral sclerosis (ALS), which is a neurodegenerative disease characterized by peripheral and central paralysis and by 3‐ to 5‐year median survival after diagnosis. In this study, we present a protocol for heterologous expression of human SOD1 in E. coli and total reconstitution of the holoenzyme, which exhibits the highest reported specific activity (four‐fold higher) of recombinant hSOD1. Biophysical characterization confirms the native state of this protein. The presented protocol provides highly active hSOD1 that will benefit in vitro investigations of this protein

Discovery of all-D-peptide inhibitors of SARS CoV 2 3C-like protease

During the replication process of SARS-CoV-2 the main protease of the virus (3-chymotrypsin-like protease (3CLpro)) plays a pivotal role and is essential for the life cycle of the pathogen. Numerous studies have been conducted so far, which have confirmed 3CLpro as an attractive drug target to combat COVID-19. We describe a novel and efficient next generation sequencing (NGS) supported phage display selection strategy for the identification of a set of SARS-CoV-2 3CLpro targeting peptide ligands that inhibit the 3CL protease, in a competitive or non-competetive mode, in the low µM range. From the most efficient L-peptides obtained from the phage display, we designed all-D-peptides based on the retro-inverso (ri) principle. They had IC50 values also in the low µM range, and in combination even in the sub-micromolar range. The inhibition modes of these D-ri peptides were the same as their respective L-peptide versions. Our results demonstrate that retro-inverso obtained all-D-peptides interact with high-affinity and inhibit the SARS-CoV-2 3CL protease, thus reinforcing their potential as therapeutic agents. The here described D-ri peptides address limitations associated with current L-peptide inhibitors and are promising lead compounds. Further optimization regarding pharmacokinetic properties will allow the development of even more potent D-peptides to be used for the prevention and treatment of COVID-19

Discovery of all-D-peptide inhibitors of SARS CoV 2 3C-like protease

During the replication process of SARS-CoV-2 the main protease of the virus (3-chymotrypsin-like protease (3CLpro)) plays a pivotal role and is essential for the life cycle of the pathogen. Numerous studies have been conducted so far, which have confirmed 3CLpro as an attractive drug target to combat COVID-19. We describe a novel and efficient next generation sequencing (NGS) supported phage display selection strategy for the identification of a set of SARS-CoV-2 3CLpro targeting peptide ligands that inhibit the 3CL protease, in a competitive or non-competetive mode, in the low µM range. From the most efficient L-peptides obtained from the phage display, we designed all-D-peptides based on the retro-inverso (ri) principle. They had IC50 values also in the low µM range, and in combination even in the sub-micromolar range. The inhibition modes of these D-ri peptides were the same as their respective L-peptide versions. Our results demonstrate that retro-inverso obtained all-D-peptides interact with high-affinity and inhibit the SARS-CoV-2 3CL protease, thus reinforcing their potential as therapeutic agents. The here described D-ri peptides address limitations associated with current L-peptide inhibitors and are promising lead compounds. Further optimization regarding pharmacokinetic properties will allow the development of even more potent D-peptides to be used for the prevention and treatment of COVID-19