scholarly journals Using serpins cysteine protease cross-specificity to possibly trap SARS-CoV-2 Mpro with reactive center loop chimera

2020 ◽  
Vol 134 (17) ◽  
pp. 2235-2241
Author(s):  
Mohamad Aman Jairajpuri ◽  
Shoyab Ansari
Keyword(s):  
Cysteine Protease ◽  
Active Site ◽  
Cleavage Site ◽  
Serine Proteases ◽  
Therapeutic Potential ◽  
Cysteine Proteases ◽  
Protease Inhibition ◽  
Reactive Center Loop ◽  
Main Protease ◽  
Reactive Center

Abstract Human serine protease inhibitors (serpins) are the main inhibitors of serine proteases, but some of them also have the capability to effectively inhibit cysteine proteases. Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) main protease (Mpro) is a chymotrypsin-type cysteine protease that is needed to produce functional proteins essential for virus replication and transcription. Serpin traps its target proteases by presenting a reactive center loop (RCL) as protease-specific cleavage site, resulting in protease inactivation. Mpro target sites with its active site serine and other flanking residues can possibly interact with serpins. Alternatively, RCL cleavage site of serpins with known evidence of inhibition of cysteine proteases can be replaced by Mpro target site to make chimeric proteins. Purified chimeric serpin can possibly inhibit Mpro that can be assessed indirectly by observing the decrease in ability of Mpro to cleave its chromogenic substrate. Chimeric serpins with best interaction and active site binding and with ability to form 1:1 serpin–Mpro complex in human plasma can be assessed by using SDS/PAGE and Western blot analysis with serpin antibody. Trapping SARS-CoV-2 Mpro cysteine protease using cross-class serpin cysteine protease inhibition activity is a novel idea with significant therapeutic potential.

A reactive center loop–based prediction platform to enhance the design of therapeutic SERPINs

2021 ◽  
Vol 118 (45) ◽  
pp. e2108458118
Author(s):  
Wariya Sanrattana ◽  
Thibaud Sefiane ◽  
Simone Smits ◽  
Nadine D. van Kleef ◽  
Marcel H. Fens ◽  
...  
Keyword(s):  
Cleavage Site ◽  
Serine Proteases ◽  
Protein C ◽  
Activated Protein C ◽  
Reactive Center Loop ◽  
Physiological Processes ◽  
Naturally Occurring ◽  
Reactive Center ◽  
Insight Into

Serine proteases are essential for many physiological processes and require tight regulation by serine protease inhibitors (SERPINs). A disturbed SERPIN–protease balance may result in disease. The reactive center loop (RCL) contains an enzymatic cleavage site between the P1 through P1’ residues that controls SERPIN specificity. This RCL can be modified to improve SERPIN function; however, a lack of insight into sequence–function relationships limits SERPIN development. This is complicated by more than 25 billion mutants needed to screen the entire P4 to P4’ region. Here, we developed a platform to predict the effects of RCL mutagenesis by using α1-antitrypsin as a model SERPIN. We generated variants for each of the residues in P4 to P4’ region, mutating them into each of the 20 naturally occurring amino acids. Subsequently, we profiled the reactivity of the resulting 160 variants against seven proteases involved in coagulation. These profiles formed the basis of an in silico prediction platform for SERPIN inhibitory behavior with combined P4 to P4’ RCL mutations, which were validated experimentally. This prediction platform accurately predicted SERPIN behavior against five out of the seven screened proteases, one of which was activated protein C (APC). Using these findings, a next-generation APC-inhibiting α1-antitrypsin variant was designed (KMPR/RIRA; / indicates the cleavage site). This variant attenuates blood loss in an in vivo hemophilia A model at a lower dosage than the previously developed variant AIKR/KIPP because of improved potency and specificity. We propose that this SERPIN-based RCL mutagenesis approach improves our understanding of SERPIN behavior and will facilitate the design of therapeutic SERPINs.

scholarly journals CHARACTERIZATION OF PARTIALLY PURIFIED CYSTEINE PROTEASE INHIBITOR FROM THE FRUITS AND SEEDS OF SOURSOP (ANNONA MURICATA)

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Segun Adeola ◽  
Habeeb Bankole ◽  
Rahmon Kanmodi
Keyword(s):  
Cysteine Protease ◽  
Anticancer Agent ◽  
Therapeutic Potential ◽  
Cysteine Proteases ◽  
Exchange Chromatography ◽  
Size Exclusion ◽  
Cysteine Protease Inhibitor ◽  
Tropical Fruit ◽  
Isolation And Purification ◽  
Wide Range

Introduction: Soursop (Annona muricataLinn) is an edible lowland tropical fruit-bearing tree that is widely cultivated across regions of the world. It has been extensively researched as a result of its store of acetogenin; a potent anticancer agent. However, there is a dearth of information on the precise mechanism of action of acetogenin; thereby subjecting it to rigorous scrutiny. It is therefore imperative to investigate this plant in the hope of discovering a different class of anticancer agent inherent in it. Various studies have demonstrated that cysteine protease inhibitors (CPIs) have considerable therapeutic potential which can be utilized in a variety of disease states including cancer. Aim: Study was designed to isolate, purify and characterize CPI from the fruits and seeds of Soursop. Method: Isolation and purification of CPI was achieved by simple methods consisting of ammonium sulphate precipitation, anion exchange chromatography and size exclusion chromatography. Mode of inhibition, optimum pH and temperature, as well as the effect of metals on the enzyme activity were determined using spectrophotometry. Result: The purified CPI from seeds and fruits exhibited competitive and noncompetitive inhibition against papain respectively. However, maximal inhibitory activities for both fruit and seed samples were observed at similar optimal pH and temperature of 8 and 40°C respectively. Although, metal cations such as cobalt (Co2+), copper (Cu2+) and zinc (Zn2+) did not effect a considerable decrease on the inhibitory activity of the CPI; Lead (Pb2+), Magnesium (Mg2+) and manganese (Mn2+) significantly inhibited CPI at a very low concentration (1mM). Conclusion: The antagonistic properties exhibited by the purified CPI certainly indicate its likely suitability for pharmaceutical application in the treatment of some pathological conditions such as cancer in which uncontrolled proteolytic activities of cysteine proteases are implicated. There is an ample scope for further research on structure elucidation and protein engineering to facilitate its usage in wide range of application.

scholarly journals Equilibrium Between Tri- and Tetra-Coordinate Chalcogenuranes Is Critical for Cysteine Protease Inhibition

2020 ◽  
Author(s):  
Gabriela Dias SIlva ◽  
Rodrigo L O R Cunha ◽  
Mauricio Domingues Coutinho Neto
Keyword(s):  
Cysteine Protease ◽  
Density Functional ◽  
Active Form ◽  
Sulfhydryl Group ◽  
Cysteine Proteases ◽  
Inhibition Mechanism ◽  
Direct Reaction ◽  
Exchange Reactions ◽  
Protease Inhibition ◽  
Biological Media

<div>There have been significant advances in the biological use of hypervalent selenium and tellurium compounds as cysteine protease inhibitors over the recent past. However, the full understanding of their reaction mechanisms in aqueous medium and the mechanism of cysteine proteases inhibition is still elusive. Kinetic studies suggest an irreversible inhibition mechanism, which was explained by forming a covalent bond between the enzyme sulfhydryl group and the chalcogen atom at its hypervalent state (+4). However, it is still unclear the active form of the inhibitor present in the aqueous biological media. To uncover this question, we performed a theoretical investigation using density functional theory (DFT). This study investigated chloride ligand exchange reactions by oxygen and sulfur nucleophiles on hypervalent selenium and tellurium compounds. All tetra- and tri-coordinate chalcogen compounds and distinct protonation states of the nucleophiles were considered, totaling 34 unique species, 7</div><div>nucleophiles and 155 free energies rections. We discovered that chloride is easily replaced by a nonprotonated nucleophile (SH<sup>–</sup> or OH<sup>– </sup>) in R<sub>2</sub>SeCl<sub>2</sub> . We also found that</div><div>tri-coordinate species are more stable than their tetra-coordinate counterparts, with selenoxide (R<sub>2</sub>SeO) protonation being strongly exergonic in acid pH. These results suggest that the protonated selenoxide (R<sub>2</sub>SeOH<sup>+</sup>) is the most probable active chemical species in biological media. The computed energetic profiles paint a possible picture for the selenurane activity, with successive exergonic steps leading to a covalent inhibition of thiol dependent enzymes, like cysteine proteases. A second less exergonic pathway has also been uncovered, with a direct reaction to chalcogenonium cation (R<sub>2</sub>SeCl<sup>+</sup>) as the inhibition step. The trends observed for the telluranes were similar, albeit with</div><div>more exergonic reactions and a stronger trend to form bonds with oxygen species then selenuranes.</div><div><br></div>

A cysteine protease inhibitor blocks SARS-CoV-2 infection of human and monkey cells

2020 ◽  
Author(s):  
Drake M. Mellott ◽  
Chien-Te Tseng ◽  
Aleksandra Drelich ◽  
Pavla Fajtová ◽  
Bala C. Chenna ◽  
...  
Keyword(s):  
Protease Inhibitor ◽  
Host Cell ◽  
Cysteine Protease ◽  
Cleavage Site ◽  
Cathepsin L ◽  
Cysteine Proteases ◽  
Protein Processing ◽  
Spike Protein ◽  
Cysteine Protease Inhibitor ◽  
Viral Infectivity

ABSTRACTK777 is a di-peptide analog that contains an electrophilic vinyl-sulfone moiety and is a potent, covalent inactivator of cathepsins. Vero E6, HeLa/ACE2, Caco-2, A549/ACE2, and Calu-3, cells were exposed to SARS-CoV-2, and then treated with K777. K777 reduced viral infectivity with EC50 values of inhibition of viral infection of: 74 nM for Vero E6, <80 nM for A549/ACE2, and 4 nM for HeLa/ACE2 cells. In contrast, Calu-3 and Caco-2 cells had EC50 values in the low micromolar range. No toxicity of K777 was observed for any of the host cells at 10-100 μM inhibitor. K777 did not inhibit activity of the papain-like cysteine protease and 3CL cysteine protease, encoded by SARS-CoV-2 at concentrations of ≤ 100 μM. These results suggested that K777 exerts its potent anti-viral activity by inactivation of mammalian cysteine proteases which are essential to viral infectivity. Using a propargyl derivative of K777 as an activity-based probe, K777 selectively targeted cathepsin B and cathepsin L in Vero E6 cells. However only cathepsin L cleaved the SARS-CoV-2 spike protein and K777 blocked this proteolysis. The site of spike protein cleavage by cathepsin L was in the S1 domain of SARS-CoV-2, differing from the cleavage site observed in the SARS CoV-1 spike protein. These data support the hypothesis that the antiviral activity of K777 is mediated through inhibition of the activity of host cathepsin L and subsequent loss of viral spike protein processing.SIGNIFICANCEThe virus causing COVID-19 is highly infectious and has resulted in a global pandemic. We confirm that a cysteine protease inhibitor, approved by the FDA as a clinical-stage compound, inhibits SARS-CoV-2 infection of several human and monkey cell lines with notable(nanomolar) efficacy. The mechanism of action of this inhibitor is identified as a specific inhibition of host cell cathepsin L. This in turn inhibits host cell processing of the coronaviral spike protein, a step required for cell entry. Neither of the coronaviral proteases are inhibited, and the cleavage site of spike protein processing is different from that reported in other coronaviruses. Hypotheses to explain the differential activity of the inhibitor with different cell types are discussed.

Quantum mechanics/molecular mechanics studies of the mechanism of cysteine protease inhibition by peptidyl-2,3-epoxyketones

2017 ◽  
Vol 19 (20) ◽  
pp. 12740-12748 ◽  
Author(s):  
Kemel Arafet ◽  
Silvia Ferrer ◽  
Florenci V. González ◽  
Vicent Moliner
Keyword(s):  
Quantum Mechanics ◽  
Life Cycle ◽  
Molecular Mechanics ◽  
Cysteine Protease ◽  
Therapeutic Targets ◽  
Cysteine Proteases ◽  
Protease Inhibition ◽  
Parasitic Protozoa

Cysteine proteases are the most abundant proteases in parasitic protozoa and they are essential enzymes to sustain the life cycle of several of them, thus becoming attractive therapeutic targets for the development of new inhibitors.

Homology modelling and structural analysis of human arylamine N-acetyltransferase NAT1: evidence for the conservation of a cysteine protease catalytic domain and an active-site loop

2001 ◽  
Vol 356 (2) ◽  
pp. 327-334 ◽  
Author(s):  
Fernando RODRIGUES-LIMA ◽  
Claudine DELOMÉNIE ◽  
Geoffrey H. GOODFELLOW ◽  
Denis M. GRANT ◽  
Jean-Marie DUPRET
Keyword(s):  
Crystal Structure ◽  
Cysteine Protease ◽  
Active Site ◽  
Catalytic Mechanism ◽  
Catalytic Domain ◽  
Homology Modelling ◽  
Metabolic Activation ◽  
Cysteine Proteases ◽  
Catalytic Triad ◽  
Quality Model

Arylamine N-acetyltransferases (EC 2.3.1.5) (NATs) catalyse the biotransformation of many primary arylamines, hydrazines and their N-hydroxylated metabolites, thereby playing an important role in both the detoxification and metabolic activation of numerous xenobiotics. The recently published crystal structure of the Salmonella typhimurium NAT (StNAT) revealed the existence of a cysteine protease-like (Cys-His-Asp) catalytic triad. In the present study, a three-dimensional homology model of human NAT1, based upon the crystal structure of StNAT [Sinclair, Sandy, Delgoda, Sim and Noble (2000) Nat. Struct. Biol. 7, 560–564], is demonstrated. Alignment of StNAT and NAT1, together with secondary structure predictions, have defined a consensus region (residues 29–131) in which 37% of the residues are conserved. Homology modelling provided a good quality model of the corresponding region in human NAT1. The location of the catalytic triad was found to be identical in StNAT and NAT1. Comparison of active-site structural elements revealed that a similar length loop is conserved in both species (residues 122–131 in NAT1 model and residues 122–133 in StNAT). This observation may explain the involvement of residues 125, 127 and 129 in human NAT substrate selectivity. Our model, and the fact that cysteine protease inhibitors do not affect the activity of NAT1, suggests that human NATs may have adapted a common catalytic mechanism from cysteine proteases to accommodate it for acetyl-transfer reactions.

scholarly journals IN Silico Approach of Some Selected Honey Constituents as SARS-CoV-2 Main Protease (COVID-19) Inhibitors

2020 ◽  
Author(s):  
Heba Hashem
Keyword(s):  
Active Site ◽  
Life Cycles ◽  
High Binding Energy ◽  
Protease Inhibition ◽  
Enzyme Active Site ◽  
Therapeutic Drugs ◽  
Main Protease ◽  
The World ◽  
Essential Enzyme ◽  
The Way

<p>The huge attack of coronavirus disease 2019 (COVID-19) over all the world forces the researcher around the world to study the crystal structure of the main protease M<sup>pro</sup> ( 3-chymotrypsin-like cysteine enzyme) which is the essential enzyme for coronavirus processing the polyproteins and its life cycles. And by the way, the inhibition of this enzyme active site becomes the target of all scientists of drug discovery in order to overcome this disease. In this study, we have used the molecular modeling approach to evaluate the activity of different active compounds from honeybee and propolis to inhibit the presented sars-cov-2 main protease via Schrödinger Maestro v10.1. the presented study resulted in six main compounds possess high binding energy with the receptor active site of COVID-19 main protease. we hope this study being the way for honeybee constitution as an effective ligand for sars-cov-2 main protease inhibition and be in the medicinal study of anti-COVID-19 therapeutic drugs.</p>

Proteases: a primer

2002 ◽  
Vol 38 ◽  
pp. 1-8 ◽  
Author(s):  
Nigel M Hooper
Keyword(s):  
Active Site ◽  
Serine Proteases ◽  
Cysteine Proteases ◽  
Aspartic Proteases ◽  
Peptide Bonds ◽  
Endogenous Inhibitors ◽  
Merops Database ◽  
Internal Peptide ◽  
Synthesis And Degradation

A protease can be defined as an enzyme that hydrolyses peptide bonds. Proteases can be divided into endopeptidases, which cleave internal peptide bonds in substrates, and exopeptidases, which cleave the terminal peptide bonds. Exopeptidases can be further subdivided into aminopeptidases and carboxypeptidases. The Schechter and Berger nomenclature provides a model for describing the interactions between the peptide substrate and the active site of a protease. Proteases can also be classified as aspartic proteases, cysteine proteases, metalloproteases, serine proteases and threonine proteases, depending on the nature of the active site. Different inhibitors can be used experimentally to distinguish between these classes of protease. The MEROPs database groups proteases into families on the basis of similarities in sequence and structure. Protease activity can be regulated in vivo by endogenous inhibitors, by the activation of zymogens and by altering the rate of their synthesis and degradation.

scholarly journals Cohesin cleavage by separase is enhanced by a substrate motif distinct from the cleavage site

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Laura E. Rosen ◽  
Joseph E. Klebba ◽  
Jonathan B. Asfaha ◽  
Chloe M. Ghent ◽  
Melody G. Campbell ◽  
...  
Keyword(s):  
Substrate Specificity ◽  
Chromosome Segregation ◽  
Cysteine Protease ◽  
Active Site ◽  
Cleavage Site ◽  
Specific Substrate ◽  
Substrate Docking ◽  
Substrate Cleavage ◽  
Docking Interaction ◽  
Substrate Motif

AbstractChromosome segregation begins when the cysteine protease, separase, cleaves the Scc1 subunit of cohesin at the metaphase-to-anaphase transition. Separase is inhibited prior to metaphase by the tightly bound securin protein, which contains a pseudosubstrate motif that blocks the separase active site. To investigate separase substrate specificity and regulation, here we develop a system for producing recombinant, securin-free human separase. Using this enzyme, we identify an LPE motif on the Scc1 substrate that is distinct from the cleavage site and is required for rapid and specific substrate cleavage. Securin also contains a conserved LPE motif, and we provide evidence that this sequence blocks separase engagement of the Scc1 LPE motif. Our results suggest that rapid cohesin cleavage by separase requires a substrate docking interaction outside the active site. This interaction is blocked by securin, providing a second mechanism by which securin inhibits cohesin cleavage.

scholarly journals Equilibrium Between Tri- and Tetra-Coordinate Chalcogenuranes Is Critical for Cysteine Protease Inhibition

2020 ◽  
Author(s):  
Gabriela Dias SIlva ◽  
Rodrigo L O R Cunha ◽  
Mauricio Domingues Coutinho Neto
Keyword(s):  
Cysteine Protease ◽  
Density Functional ◽  
Active Form ◽  
Sulfhydryl Group ◽  
Cysteine Proteases ◽  
Inhibition Mechanism ◽  
Direct Reaction ◽  
Exchange Reactions ◽  
Protease Inhibition ◽  
Biological Media

<div>There have been significant advances in the biological use of hypervalent selenium and tellurium compounds as cysteine protease inhibitors over the recent past. However, the full understanding of their reaction mechanisms in aqueous medium and the mechanism of cysteine proteases inhibition is still elusive. Kinetic studies suggest an irreversible inhibition mechanism, which was explained by forming a covalent bond between the enzyme sulfhydryl group and the chalcogen atom at its hypervalent state (+4). However, it is still unclear the active form of the inhibitor present in the aqueous biological media. To uncover this question, we performed a theoretical investigation using density functional theory (DFT). This study investigated chloride ligand exchange reactions by oxygen and sulfur nucleophiles on hypervalent selenium and tellurium compounds. All tetra- and tri-coordinate chalcogen compounds and distinct protonation states of the nucleophiles were considered, totaling 34 unique species, 7</div><div>nucleophiles and 155 free energies rections. We discovered that chloride is easily replaced by a nonprotonated nucleophile (SH<sup>–</sup> or OH<sup>– </sup>) in R<sub>2</sub>SeCl<sub>2</sub> . We also found that</div><div>tri-coordinate species are more stable than their tetra-coordinate counterparts, with selenoxide (R<sub>2</sub>SeO) protonation being strongly exergonic in acid pH. These results suggest that the protonated selenoxide (R<sub>2</sub>SeOH<sup>+</sup>) is the most probable active chemical species in biological media. The computed energetic profiles paint a possible picture for the selenurane activity, with successive exergonic steps leading to a covalent inhibition of thiol dependent enzymes, like cysteine proteases. A second less exergonic pathway has also been uncovered, with a direct reaction to chalcogenonium cation (R<sub>2</sub>SeCl<sup>+</sup>) as the inhibition step. The trends observed for the telluranes were similar, albeit with</div><div>more exergonic reactions and a stronger trend to form bonds with oxygen species then selenuranes.</div><div><br></div>

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