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1.
Int J Mol Sci ; 23(7)2022 Mar 25.
Article in English | MEDLINE | ID: covidwho-1785730

ABSTRACT

Environmentally friendly and sustainable processes for the production of active pharmaceutical ingredients (APIs) gain increasing attention. Biocatalytic synthesis routes with enzyme cascades support many stated green production principles, for example, the reduced need for solvents or the biodegradability of enzymes. Multi-enzyme reactions have even more advantages such as the shift of the equilibrium towards the product side, no intermediate isolation, and the synthesis of complex molecules in one reaction pot. Despite the intriguing benefits, only a few enzyme cascades have been applied in the pharmaceutical industry so far. However, several new enzyme cascades are currently being developed in research that could be of great importance to the pharmaceutical industry. Here, we present multi-enzymatic reactions for API synthesis that are close to an industrial application. Their performances are comparable or exceed their chemical counterparts. A few enzyme cascades that are still in development are also introduced in this review. Economic and ecological considerations are made for some example cascades to assess their environmental friendliness and applicability.


Subject(s)
Biocatalysis
2.
J Am Chem Soc ; 144(9): 3761-3765, 2022 03 09.
Article in English | MEDLINE | ID: covidwho-1713117

ABSTRACT

The Covid-19 pandemic highlights the urgent need for cost-effective processes to rapidly manufacture antiviral drugs at scale. Here we report a concise biocatalytic process for Molnupiravir, a nucleoside analogue recently approved as an orally available treatment for SARS-CoV-2. Key to the success of this process was the development of an efficient biocatalyst for the production of N-hydroxy-cytidine through evolutionary adaption of the hydrolytic enzyme cytidine deaminase. This engineered biocatalyst performs >85 000 turnovers in less than 3 h, operates at 180 g/L substrate loading, and benefits from in situ crystallization of the N-hydroxy-cytidine product (85% yield), which can be converted to Molnupiravir by a selective 5'-acylation using Novozym 435.


Subject(s)
Antiviral Agents , COVID-19/drug therapy , Cytidine Deaminase/metabolism , Cytidine/analogs & derivatives , SARS-CoV-2 , Biocatalysis , Cytidine/biosynthesis , Cytidine/metabolism , Cytidine Deaminase/genetics , Escherichia coli/enzymology , Escherichia coli/genetics , Hydroxylamines , Metabolic Engineering , Protein Engineering , Uridine/metabolism
3.
Nature ; 602(7896): 343-348, 2022 02.
Article in English | MEDLINE | ID: covidwho-1671588

ABSTRACT

Carbapenems are antibiotics of last resort in the clinic. Owing to their potency and broad-spectrum activity, they are an important part of the antibiotic arsenal. The vital role of carbapenems is exemplified by the approval acquired by Merck from the US Food and Drug Administration (FDA) for the use of an imipenem combination therapy to treat the increased levels of hospital-acquired and ventilator-associated bacterial pneumonia that have occurred during the COVID-19 pandemic1. The C6 hydroxyethyl side chain distinguishes the clinically used carbapenems from the other classes of ß-lactam antibiotics and is responsible for their low susceptibility to inactivation by occluding water from the ß-lactamase active site2. The construction of the C6 hydroxyethyl side chain is mediated by cobalamin- or B12-dependent radical S-adenosylmethionine (SAM) enzymes3. These radical SAM methylases (RSMTs) assemble the alkyl backbone by sequential methylation reactions, and thereby underlie the therapeutic usefulness of clinically used carbapenems. Here we present X-ray crystal structures of TokK, a B12-dependent RSMT that catalyses three-sequential methylations during the biosynthesis of asparenomycin A. These structures, which contain the two metallocofactors of the enzyme and were determined in the presence and absence of a carbapenam substrate, provide a visualization of a B12-dependent RSMT that uses the radical mechanism that is shared by most of these enzymes. The structures provide insight into the stereochemistry of initial C6 methylation and suggest that substrate positioning governs the rate of each methylation event.


Subject(s)
Carbapenems/biosynthesis , Methyltransferases/chemistry , Methyltransferases/metabolism , S-Adenosylmethionine/metabolism , Streptomyces/enzymology , Thienamycins/biosynthesis , Vitamin B 12/metabolism , Binding Sites , Biocatalysis , Coenzymes/metabolism , Crystallography, X-Ray , Kinetics , Methylation , Models, Molecular , Protein Binding , Protein Domains , Streptomyces/metabolism , beta-Lactamase Inhibitors/metabolism , beta-Lactamases/chemistry , beta-Lactamases/metabolism
4.
Int J Mol Sci ; 23(1)2021 Dec 28.
Article in English | MEDLINE | ID: covidwho-1580696

ABSTRACT

The inhibition of key enzymes that may contain the viral replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have assumed central importance in drug discovery projects. Nonstructural proteins (nsps) are essential for RNA capping and coronavirus replication since it protects the virus from host innate immune restriction. In particular, nonstructural protein 16 (nsp16) in complex with nsp10 is a Cap-0 binding enzyme. The heterodimer formed by nsp16-nsp10 methylates the 5'-end of virally encoded mRNAs to mimic cellular mRNAs and thus it is one of the enzymes that is a potential target for antiviral therapy. In this study, we have evaluated the mechanism of the 2'-O methylation of the viral mRNA cap using hybrid quantum mechanics/molecular mechanics (QM/MM) approach. It was found that the calculated free energy barriers obtained at M062X/6-31+G(d,p) is in agreement with experimental observations. Overall, we provide a detailed molecular analysis of the catalytic mechanism involving the 2'-O methylation of the viral mRNA cap and, as expected, the results demonstrate that the TS stabilization is critical for the catalysis.


Subject(s)
Methyltransferases/metabolism , RNA Caps/chemistry , RNA Caps/metabolism , SARS-CoV-2/enzymology , SARS-CoV-2/genetics , Viral Nonstructural Proteins/metabolism , Viral Regulatory and Accessory Proteins/metabolism , Biocatalysis , Biomechanical Phenomena , Methylation , Methyltransferases/chemistry , Molecular Dynamics Simulation , Quantum Theory , RNA Processing, Post-Transcriptional , Viral Nonstructural Proteins/chemistry , Viral Regulatory and Accessory Proteins/chemistry
5.
Molecules ; 26(16)2021 Aug 07.
Article in English | MEDLINE | ID: covidwho-1399345

ABSTRACT

Ionic liquids have unique chemical properties that have fascinated scientists in many fields. The effects of adding ionic liquids to biocatalysts are many and varied. The uses of ionic liquids in biocatalysis include improved separations and phase behaviour, reduction in toxicity, and stabilization of protein structures. As the ionic liquid state of the art has progressed, concepts of what can be achieved in biocatalysis using ionic liquids have evolved and more beneficial effects have been discovered. In this review ionic liquids for whole-cell and isolated enzyme biocatalysis will be discussed with an emphasis on the latest developments, and a look to the future.


Subject(s)
Biocatalysis , Cells/metabolism , Enzymes/isolation & purification , Ionic Liquids/chemistry , Solubility
6.
Molecules ; 26(17)2021 Sep 02.
Article in English | MEDLINE | ID: covidwho-1390702

ABSTRACT

Human neutrophil elastase (HNE) is a uniquely destructive serine protease with the ability to unleash a wave of proteolytic activity by destroying the inhibitors of other proteases. Although this phenomenon forms an important part of the innate immune response to invading pathogens, it is responsible for the collateral host tissue damage observed in chronic conditions such as chronic obstructive pulmonary disease (COPD), and in more acute disorders such as the lung injuries associated with COVID-19 infection. Previously, a combinatorially selected activity-based probe revealed an unexpected substrate preference for oxidised methionine, which suggests a link to oxidative pathogen clearance by neutrophils. Here we use oxidised model substrates and inhibitors to confirm this observation and to show that neutrophil elastase is specifically selective for the di-oxygenated methionine sulfone rather than the mono-oxygenated methionine sulfoxide. We also posit a critical role for ordered solvent in the mechanism of HNE discrimination between the two oxidised forms methionine residue. Preference for the sulfone form of oxidised methionine is especially significant. While both host and pathogens have the ability to reduce methionine sulfoxide back to methionine, a biological pathway to reduce methionine sulfone is not known. Taken together, these data suggest that the oxidative activity of neutrophils may create rapidly cleaved elastase "super substrates" that directly damage tissue, while initiating a cycle of neutrophil oxidation that increases elastase tissue damage and further neutrophil recruitment.


Subject(s)
Immunity, Innate , Leukocyte Elastase/metabolism , Methionine/analogs & derivatives , Neutrophils/immunology , Biocatalysis , COVID-19/immunology , COVID-19/pathology , COVID-19/virology , Catalytic Domain/genetics , Enzyme Assays , Host-Pathogen Interactions/immunology , Humans , Leukocyte Elastase/antagonists & inhibitors , Leukocyte Elastase/genetics , Lung/immunology , Lung/pathology , Lung/virology , Methionine/metabolism , Molecular Dynamics Simulation , Neutrophil Infiltration , Neutrophils/enzymology , Oxidation-Reduction/drug effects , Proteolysis/drug effects , Pulmonary Disease, Chronic Obstructive/immunology , Pulmonary Disease, Chronic Obstructive/pathology , SARS-CoV-2/immunology , Substrate Specificity/immunology
7.
Nucleic Acids Res ; 49(9): 5382-5392, 2021 05 21.
Article in English | MEDLINE | ID: covidwho-1387965

ABSTRACT

The emergence of SARS-CoV-2 infection has posed unprecedented threat to global public health. The virus-encoded non-structural protein 14 (nsp14) is a bi-functional enzyme consisting of an exoribonuclease (ExoN) domain and a methyltransferase (MTase) domain and plays a pivotal role in viral replication. Here, we report the structure of SARS-CoV-2 nsp14-ExoN domain bound to its co-factor nsp10 and show that, compared to the SARS-CoV nsp10/nsp14-full-length complex, SARS-CoV-2 nsp14-ExoN retains an integral exoribonuclease fold and preserves an active configuration in the catalytic center. Analysis of the nsp10/nsp14-ExoN interface reveals a footprint in nsp10 extensively overlapping with that observed in the nsp10/nsp16 structure. A marked difference in the co-factor when engaging nsp14 and nsp16 lies in helix-α1', which is further experimentally ascertained to be involved in nsp14-binding but not in nsp16-engagement. Finally, we also show that nsp10/nsp14-ExoN is enzymatically active despite the absence of nsp14-MTase domain. These data demonstrate that SARS-CoV-2 nsp10/nsp14-ExoN functions as an exoribonuclease with both structural and functional integrity.


Subject(s)
Biocatalysis , Exoribonucleases/chemistry , Exoribonucleases/metabolism , SARS-CoV-2/chemistry , SARS-CoV-2/enzymology , Viral Nonstructural Proteins/chemistry , Viral Nonstructural Proteins/metabolism , Viral Regulatory and Accessory Proteins/chemistry , Viral Regulatory and Accessory Proteins/metabolism , Binding Sites , Crystallography, X-Ray , Exoribonucleases/genetics , Guanine , Methyltransferases/chemistry , Methyltransferases/deficiency , Methyltransferases/genetics , Methyltransferases/metabolism , Models, Molecular , Protein Domains/genetics , SARS-CoV-2/genetics , Viral Nonstructural Proteins/genetics , Viral Regulatory and Accessory Proteins/genetics
8.
J Phys Chem Lett ; 12(17): 4195-4202, 2021 May 06.
Article in English | MEDLINE | ID: covidwho-1387119

ABSTRACT

The catalytic reaction in SARS-CoV-2 main protease is activated by a proton transfer (PT) from Cys145 to His41. The same PT is likely also required for the covalent binding of some inhibitors. Here we use a multiscale computational approach to investigate the PT thermodynamics in the apo enzyme and in complex with two potent inhibitors, N3 and the α-ketoamide 13b. We show that with the inhibitors the free energy cost to reach the charge-separated state of the active-site dyad is lower, with N3 inducing the most significant reduction. We also show that a few key sites (including specific water molecules) significantly enhance or reduce the thermodynamic feasibility of the PT reaction, with selective desolvation of the active site playing a crucial role. The approach presented is a cost-effective procedure to identify the enzyme regions that control the activation of the catalytic reaction and is thus also useful to guide the design of inhibitors.


Subject(s)
Drug Design , Protease Inhibitors/chemistry , SARS-CoV-2/enzymology , Viral Matrix Proteins/antagonists & inhibitors , Antiviral Agents/chemistry , Antiviral Agents/metabolism , Biocatalysis , COVID-19/pathology , COVID-19/virology , Catalytic Domain , Humans , Molecular Dynamics Simulation , Protease Inhibitors/metabolism , Protons , Quantum Theory , SARS-CoV-2/isolation & purification , Thermodynamics , Viral Matrix Proteins/metabolism
9.
Org Biomol Chem ; 19(30): 6650-6656, 2021 08 05.
Article in English | MEDLINE | ID: covidwho-1343477

ABSTRACT

The exquisite chemodiversity of terpenoids is the product of the large diverse terpene synthase (TPS) superfamily. Here, by using structural and phylogenetic analyses and site-directed mutagenesis, we identified a residue (Cys440 in Nicotiana tabacum 5-epi-aristolochene synthase) proximal to an ion-binding motif common to all TPSs and named the preNSE/DTE residue, which determines the product specificity of sesquiterpene synthases from different plant species. In sesquiterpene synthases catalyzing 1,10-cyclization (1,10-cyclases) of farnesyl diphosphate, mutation of the residue in both specific and promiscuous 1,10-cyclases from different lineages leads to the accumulation of monocyclic germacrene A-11-ol, which is "short-circuited" from complex cyclization cascades, suggesting a key role of this residue in generating the first common intermediate of 1,10-cyclization. Altering this residue in a specific 1,11-cyclase results in alternative 1,10-cyclization products. Moreover, the preNSE/DTE residue can be harnessed to engineer highly specific sesquiterpene synthases for an improved proportion of high-value terpenoids, such as patchoulol, a main constituent of several traditional Chinese medicines that could treat SARS-CoV-2.


Subject(s)
Alkyl and Aryl Transferases/chemistry , Alkyl and Aryl Transferases/metabolism , Biocatalysis , Alkyl and Aryl Transferases/genetics , Catalytic Domain , Cyclization , Models, Molecular , Mutagenesis, Site-Directed , Phylogeny , Tobacco/enzymology
10.
Org Biomol Chem ; 19(30): 6650-6656, 2021 08 05.
Article in English | MEDLINE | ID: covidwho-1310820

ABSTRACT

The exquisite chemodiversity of terpenoids is the product of the large diverse terpene synthase (TPS) superfamily. Here, by using structural and phylogenetic analyses and site-directed mutagenesis, we identified a residue (Cys440 in Nicotiana tabacum 5-epi-aristolochene synthase) proximal to an ion-binding motif common to all TPSs and named the preNSE/DTE residue, which determines the product specificity of sesquiterpene synthases from different plant species. In sesquiterpene synthases catalyzing 1,10-cyclization (1,10-cyclases) of farnesyl diphosphate, mutation of the residue in both specific and promiscuous 1,10-cyclases from different lineages leads to the accumulation of monocyclic germacrene A-11-ol, which is "short-circuited" from complex cyclization cascades, suggesting a key role of this residue in generating the first common intermediate of 1,10-cyclization. Altering this residue in a specific 1,11-cyclase results in alternative 1,10-cyclization products. Moreover, the preNSE/DTE residue can be harnessed to engineer highly specific sesquiterpene synthases for an improved proportion of high-value terpenoids, such as patchoulol, a main constituent of several traditional Chinese medicines that could treat SARS-CoV-2.


Subject(s)
Alkyl and Aryl Transferases/chemistry , Alkyl and Aryl Transferases/metabolism , Biocatalysis , Alkyl and Aryl Transferases/genetics , Catalytic Domain , Cyclization , Models, Molecular , Mutagenesis, Site-Directed , Phylogeny , Tobacco/enzymology
11.
Nat Commun ; 12(1): 3287, 2021 06 02.
Article in English | MEDLINE | ID: covidwho-1253936

ABSTRACT

The SARS-CoV-2 nsp16/nsp10 enzyme complex modifies the 2'-OH of the first transcribed nucleotide of the viral mRNA by covalently attaching a methyl group to it. The 2'-O methylation of the first nucleotide converts the status of mRNA cap from Cap-0 to Cap-1, and thus, helps the virus evade immune surveillance in host cells. Here, we report two structures of nsp16/nsp10 representing pre- and post-release states of the RNA product (Cap-1). We observe overall widening of the enzyme upon product formation, and an inward twisting motion in the substrate binding region upon product release. These conformational changes reset the enzyme for the next round of catalysis. The structures also identify a unique binding mode and the importance of a divalent metal ion for 2'-O methylation. We also describe underlying structural basis for the perturbed enzymatic activity of a clinical variant of SARS-CoV-2, and a previous SARS-CoV outbreak strain.


Subject(s)
Magnesium/chemistry , RNA Caps/metabolism , RNA, Viral/metabolism , SARS-CoV-2/genetics , Viral Nonstructural Proteins/metabolism , Viral Regulatory and Accessory Proteins/metabolism , Amino Acid Sequence , Binding Sites , Biocatalysis , Cloning, Molecular , Crystallography, X-Ray , Escherichia coli/genetics , Escherichia coli/metabolism , Gene Expression Regulation, Viral , Humans , Magnesium/metabolism , Methylation , Methyltransferases , Models, Molecular , Protein Binding , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Interaction Domains and Motifs , RNA Caps/chemistry , RNA Caps/genetics , RNA, Viral/chemistry , RNA, Viral/genetics , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , S-Adenosylmethionine/chemistry , S-Adenosylmethionine/metabolism , SARS-CoV-2/enzymology , SARS-CoV-2/ultrastructure , Sequence Alignment , Sequence Homology, Amino Acid , Substrate Specificity , Viral Nonstructural Proteins/chemistry , Viral Nonstructural Proteins/genetics , Viral Regulatory and Accessory Proteins/chemistry , Viral Regulatory and Accessory Proteins/genetics
12.
Org Biomol Chem ; 19(20): 4380-4396, 2021 05 26.
Article in English | MEDLINE | ID: covidwho-1243316

ABSTRACT

CK2 is a protein kinase that plays important roles in many physio-pathological cellular processes. As such, the development of chemical probes for CK2 has received increasing attention in the past decade with more than 40 lead compounds developed. In this review, we aim to provide the reader with a comprehensive overview of the chemical probes acting outside the highly-conserved ATP-site developed to date. Such probes belong to different classes of molecules spanning from small molecules to peptides, act with a range of mechanisms of action and some of them present themselves as promising tools to investigate the biology of CK2 and therefore develop therapeutics for many disease areas including cancer and COVID-19.


Subject(s)
Casein Kinase II/chemistry , Casein Kinase II/metabolism , Molecular Probes/metabolism , Animals , Biocatalysis , Drug Discovery , Humans
13.
Nucleic Acids Res ; 49(9): 5382-5392, 2021 05 21.
Article in English | MEDLINE | ID: covidwho-1217861

ABSTRACT

The emergence of SARS-CoV-2 infection has posed unprecedented threat to global public health. The virus-encoded non-structural protein 14 (nsp14) is a bi-functional enzyme consisting of an exoribonuclease (ExoN) domain and a methyltransferase (MTase) domain and plays a pivotal role in viral replication. Here, we report the structure of SARS-CoV-2 nsp14-ExoN domain bound to its co-factor nsp10 and show that, compared to the SARS-CoV nsp10/nsp14-full-length complex, SARS-CoV-2 nsp14-ExoN retains an integral exoribonuclease fold and preserves an active configuration in the catalytic center. Analysis of the nsp10/nsp14-ExoN interface reveals a footprint in nsp10 extensively overlapping with that observed in the nsp10/nsp16 structure. A marked difference in the co-factor when engaging nsp14 and nsp16 lies in helix-α1', which is further experimentally ascertained to be involved in nsp14-binding but not in nsp16-engagement. Finally, we also show that nsp10/nsp14-ExoN is enzymatically active despite the absence of nsp14-MTase domain. These data demonstrate that SARS-CoV-2 nsp10/nsp14-ExoN functions as an exoribonuclease with both structural and functional integrity.


Subject(s)
Biocatalysis , Exoribonucleases/chemistry , Exoribonucleases/metabolism , SARS-CoV-2/chemistry , SARS-CoV-2/enzymology , Viral Nonstructural Proteins/chemistry , Viral Nonstructural Proteins/metabolism , Viral Regulatory and Accessory Proteins/chemistry , Viral Regulatory and Accessory Proteins/metabolism , Binding Sites , Crystallography, X-Ray , Exoribonucleases/genetics , Guanine , Methyltransferases/chemistry , Methyltransferases/deficiency , Methyltransferases/genetics , Methyltransferases/metabolism , Models, Molecular , Protein Domains/genetics , SARS-CoV-2/genetics , Viral Nonstructural Proteins/genetics , Viral Regulatory and Accessory Proteins/genetics
14.
J Nanobiotechnology ; 19(1): 26, 2021 Jan 19.
Article in English | MEDLINE | ID: covidwho-1067241

ABSTRACT

With the rapid advancement and progress of nanotechnology, nanomaterials with enzyme-like catalytic activity have fascinated the remarkable attention of researchers, due to their low cost, high operational stability, adjustable catalytic activity, and ease of recycling and reuse. Nanozymes can catalyze the same reactions as performed by enzymes in nature. In contrast the intrinsic shortcomings of natural enzymes such as high manufacturing cost, low operational stability, production complexity, harsh catalytic conditions and difficulties of recycling, did not limit their wide applications. The broad interest in enzymatic nanomaterial relies on their outstanding properties such as stability, high activity, and rigidity to harsh environments, long-term storage and easy preparation, which make them a convenient substitute instead of the native enzyme. These abilities make the nanozymes suitable for multiple applications in sensing and imaging, tissue engineering, environmental protection, satisfactory tumor diagnostic and therapeutic, because of distinguished properties compared with other artificial enzymes such as high biocompatibility, low toxicity, size dependent catalytic activities, large surface area for further bioconjugation or modification and also smart response to external stimuli. This review summarizes and highlights latest progress in applications of metal and metal oxide nanomaterials with enzyme/multienzyme mimicking activities. We cover the applications of sensing, cancer therapy, water treatment and anti-bacterial efficacy. We also put forward the current challenges and prospects in this research area, hoping to extension of this emerging field. In addition to therapeutic potential of nanozymes for disease prevention, their practical effects in diagnostics, to monitor the presence of SARS-CoV-2 and related biomarkers for future pandemics will be predicted.


Subject(s)
Biomimetic Materials/chemistry , Metals/chemistry , Nanomedicine/methods , Nanostructures/chemistry , Oxides/chemistry , Animals , Anti-Bacterial Agents/chemistry , Anti-Bacterial Agents/therapeutic use , Biocatalysis , Biomimetic Materials/therapeutic use , Biosensing Techniques/methods , Biotechnology/methods , COVID-19 Testing/methods , Environmental Monitoring/methods , Humans , Metals/therapeutic use , Nanotechnology/methods , Neoplasms/diagnosis , Neoplasms/therapy , Oxides/therapeutic use
15.
Chem Soc Rev ; 50(3): 1968-2009, 2021 Feb 15.
Article in English | MEDLINE | ID: covidwho-978525

ABSTRACT

With recent outbreaks of COVID-19 and Ebola, health and healthcare have once more shown to be heavily burdened by the lack of generally effective anti-viral therapies. Initial scientific ventures towards finding anti-viral agents are soon to be followed by challenges regarding their mass production. Biocatalysis offers mild, highly selective, and environmentally benign synthetic strategies for the production of pharmaceuticals in a sustainable fashion. Here we summarise biocatalytic methods that have been applied to the production of FDA-approved anti-viral drugs and their intermediates. Exemplary are the enzymatic asymmetric synthesis of amino acid components, the fermentative production of structurally complex intermediates of anti-influenza drugs and the fully enzymatic, large-scale synthesis of a potential block-buster HIV drug. With many enzyme classes being uncharted with regards to the synthesis of anti-viral agents, there is still a large unopened toolbox waiting to be unlocked. Additionally, by discussing biocatalytic strategies towards potential anti-viral agents against SARS-CoV-2, we hope to contribute to the development of novel synthetic routes to aid in the mass production of a future treatment of COVID-19.


Subject(s)
Antiviral Agents/chemical synthesis , Antiviral Agents/therapeutic use , COVID-19/drug therapy , Antiviral Agents/chemistry , Antiviral Agents/pharmacology , Biocatalysis , COVID-19/virology , Drug Approval/legislation & jurisprudence , SARS-CoV-2/drug effects , SARS-CoV-2/isolation & purification , United States , United States Food and Drug Administration
16.
Int J Biol Macromol ; 165(Pt A): 1438-1446, 2020 Dec 15.
Article in English | MEDLINE | ID: covidwho-843655

ABSTRACT

There are several families of cysteine proteinases with different folds - for example the (chymo)trypsin fold family and papain-like fold family - but in both families the hydrolase activity of cysteine proteinases requires a cysteine residue as the catalytic nucleophile. In this work, we have analyzed the topology of the active site regions in 146 three-dimensional structures of proteins belonging to the Papain-like Cysteine Proteinase (PCP) superfamily, which includes papain as a typical representative of this protein superfamily. All analyzed enzymes contain a unique structurally closed conformation - a "PCP-Zone" - which can be divided into two groups, Class A and Class B. Eight structurally conserved amino acids of the PCP-Zone form a common Structural Core. The Structural Core, catalytic nucleophile, catalytic base and residue Xaa - which stabilizes the side-chain conformation of the catalytic base - make up a PCP Structural Catalytic Core (PCP-SCC). The PCP-SCC of Class A and Class B are divided into 5 and 2 types, respectively. Seven variants of the mutual arrangement of the amino-acid side chains of the catalytic triad - nucleophile, base and residue Xaa - within the same fold clearly demonstrate how enzymes with the papain-like fold adapt to the need to perform diverse functions in spite of their limited structural diversity. The roles of both the PCP-Zone of SARS-CoV-2-PLpro described in this study and the NBCZone of SARS-CoV-2-3CLpro presented in our earlier article (Denesyuk AI, Johnson MS, Salo-Ahen OMH, Uversky VN, Denessiouk K. Int J Biol Macromol. 2020;153:399-411) that are in contacts with inhibitors are discussed.


Subject(s)
Catalytic Domain , Papain/chemistry , Papain/metabolism , Biocatalysis , Models, Molecular
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