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Article ; Online: A common protein C inhibitor exosite partially controls the heparin induced activation and inhibition of serine proteases.

Siddiqui, Urfi / Khan, Abdul Burhan / Ahmad, Tahif / Rehman, Ahmed Abdur / Jairajpuri, Mohamad Aman

International journal of biological macromolecules

2024 Volume 266, Issue Pt 2, Page(s) 131065

Abstract: Protein C inhibitor (PCI) maintains hemostasis by inhibiting both procoagulant and anticoagulant serine proteases, and plays important roles in coagulation, fibrinolysis, reproduction, and anti-angiogenesis. The reactive site loop of PCI traps and ... ...

Abstract	Protein C inhibitor (PCI) maintains hemostasis by inhibiting both procoagulant and anticoagulant serine proteases, and plays important roles in coagulation, fibrinolysis, reproduction, and anti-angiogenesis. The reactive site loop of PCI traps and irreversibly inhibits the proteases like APC (activating protein C), thrombin (FIIa) and factor Xa (FXa). Previous studies on antithrombin (ATIII) had identified Tyr253 and Glu255 as functional exosites that interact and aid in the inhibition of factor IXa and FXa. Presence of exosite in PCI is not known, however a sequence comparison with the PCI from different vertebrate species and ATIII identified Glu239 to be absolutely conserved. PCI residues analogous to ATIII exosite residues were mutated to R238A and E239A. Purified variant PCI in the presence of heparin (10 μg/ml) showed a 2-4 fold decrease in the rate of inhibition of the proteases. However, the stoichiometry of inhibition of FIIa, APC, and FXa by native PCI, R238A and E239A variants were found to be close to 1.0, which also indicated the formation of stable complexes based on SDS-PAGE and western blot analysis with thrombin and APC. Our findings revealed the possible presence of an exosite in PCI that influences the protease inhibition rates.
Language	English
Publishing date	2024-03-21
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2024.131065
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Article ; Online: Using serpins cysteine protease cross-specificity to possibly trap SARS-CoV-2 Mpro with reactive center loop chimera.

Jairajpuri, Mohamad Aman / Ansari, Shoyab

Clinical science (London, England : 1979)

2020 Volume 134, Issue 17, Page(s) 2235–2241

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) ...

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.
MeSH term(s)	Antiviral Agents/pharmacology ; Antiviral Agents/therapeutic use ; Betacoronavirus/drug effects ; Betacoronavirus/enzymology ; Blotting, Western ; COVID-19 ; Coronavirus 3C Proteases ; Coronavirus Infections/drug therapy ; Coronavirus Infections/virology ; Cysteine Endopeptidases/chemistry ; Electrophoresis, Polyacrylamide Gel ; Humans ; Pandemics ; Pneumonia, Viral/drug therapy ; Pneumonia, Viral/virology ; SARS-CoV-2 ; Serpins/pharmacology ; Serpins/therapeutic use ; Viral Nonstructural Proteins/antagonists & inhibitors ; Viral Nonstructural Proteins/chemistry
Chemical Substances	Antiviral Agents ; Serpins ; Viral Nonstructural Proteins ; Cysteine Endopeptidases (EC 3.4.22.-) ; Coronavirus 3C Proteases (EC 3.4.22.28)
Keywords	covid19
Language	English
Publishing date	2020-09-01
Publishing country	England
Document type	Letter
ZDB-ID	206835-7
ISSN	1470-8736 ; 0301-0538 ; 0009-0360 ; 0143-5221
ISSN (online)	1470-8736
ISSN	0301-0538 ; 0009-0360 ; 0143-5221
DOI	10.1042/CS20200767
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Article ; Online: Naringin binds to protein disulfide isomerase to inhibit its activity and modulate the blood coagulation rates: Implications in controlling thrombosis.

Khan, Abdul Burhan / Siddiqui, Urfi / Fatima, Sana / Rehman, Ahmed Abdur / Jairajpuri, Mohamad Aman

International journal of biological macromolecules

2023 Volume 252, Page(s) 126241

Abstract: Currently used antithrombotic drugs are beset with several drawbacks which necessitates the need for new and cheaper alternatives. Protein disulfide isomerase (PDI) is secreted in the blood plasma in cellular stress conditions and initiates the thrombus ... ...

Abstract	Currently used antithrombotic drugs are beset with several drawbacks which necessitates the need for new and cheaper alternatives. Protein disulfide isomerase (PDI) is secreted in the blood plasma in cellular stress conditions and initiates the thrombus formation. A screening of library of natural compounds revealed that naringin had a high binding affinity for the PDI (-8.2 kcal/mol). Recombinant PDI was purified using the affinity chromatography. Incubation of purified PDI (3 μM) with naringin (0-100 μM, pH 7.4, 25 °C) partially modulated its conformation. Consequently, the fluorescence emission spectra of the PDI binding to naringin were assessed using the Stern-Volmer equation, which indicated an association constant of 2.78 × 10
MeSH term(s)	Humans ; Protein Disulfide-Isomerases/metabolism ; Blood Coagulation ; Thrombosis/metabolism ; Flavanones/pharmacology
Chemical Substances	Protein Disulfide-Isomerases (EC 5.3.4.1) ; naringin (N7TD9J649B) ; Flavanones
Language	English
Publishing date	2023-08-09
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2023.126241
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Article ; Online: Naringin binds to protein disulfide isomerase to inhibit its activity and modulate the blood coagulation rates: Implications in controlling thrombosis

Khan, Abdul Burhan / Siddiqui, Urfi / Fatima, Sana / Rehman, Ahmed Abdur / Jairajpuri, Mohamad Aman

International Journal of Biological Macromolecules. 2023, p.126241-

2023 , Page(s) 126241–

Abstract	Currently used antithrombotic drugs are beset with several drawbacks which necessitates the need for new and cheaper alternatives. Protein disulfide isomerase (PDI) is secreted in the blood plasma in cellular stress conditions and initiates the thrombus formation. A screening of library of natural compounds revealed that naringin had a high binding affinity for the PDI (−8.2 kcal/mol). Recombinant PDI was purified using the affinity chromatography. Incubation of purified PDI (3 μM) with naringin (0-100 μM, pH 7.4, 25 °C) partially modulated its conformation. Consequently, the fluorescence emission spectra of the PDI binding to naringin were assessed using the Stern-Volmer equation, which indicated an association constant of 2.78 × 10⁴ M⁻¹ suggesting an appreciable affinity for the naringin, with a unique binding site. An insulin turbidity assay showed that PDI activity is decreased in the presence of naringin indicating inhibition. Molecular dynamic simulation studies showed the changes in the PDI structure on binding to the naringin. Incubation of naringin (80 μM) in fresh human plasma along with exogenous PDI (175 nM) showed a significant delay in the intrinsic and extrinsic coagulation pathways. We show that naringin is able to modulate the PDI conformation and activity resulting in altered blood coagulation rates.
Keywords	affinity chromatography ; blood coagulation ; blood plasma ; coagulation ; equations ; fluorescence ; humans ; insulin ; naringin ; pH ; protein disulfide-isomerase ; thrombosis ; turbidity ; Protein disulfide isomerase ; Anticoagulant
Language	English
Publishing place	Elsevier B.V.
Document type	Article ; Online
Note	Pre-press version
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2023.126241
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Article: Using serpins cysteine protease cross-specificity to possibly trap SARS-CoV-2 Mpro with reactive center loop chimera

Jairajpuri, Mohamad Aman / Ansari, Shoyab

Clin Sci (Lond)

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.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #738221
Database	COVID19

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Article ; Online: Using serpins cysteine protease cross-specificity to possibly trap SARS-CoV-2 Mpro with reactive center loop chimera

Jairajpuri, Mohamad Aman / Ansari, Shoyab

Clinical Science

2020 Volume 134, Issue 17, Page(s) 2235–2241

Abstract: 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 ... ...

Abstract	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.
Keywords	General Medicine ; covid19
Language	English
Publisher	Portland Press Ltd.
Publishing country	uk
Document type	Article ; Online
ZDB-ID	760216-9
ISSN	0143-5221 ; 0144-9664
ISSN	0143-5221 ; 0144-9664
DOI	10.1042/cs20200767
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Identification and validation of two alternatively spliced novel isoforms of human α-1-antichymotrypsin.

Fatima, Sana / Gupta, Swati / Khan, Abdul Burhan / Rehman, Sayeed Ur / Jairajpuri, Mohamad Aman

Biochemical and biophysical research communications

2022 Volume 628, Page(s) 25–31

Abstract: α-1-antichymotrypsin (ACT) is a serine proteinase inhibitor that controls the activity of proteases like chymotrypsin, cathepsin G and mast cell chymase. Familial variants of ACT results in liver and lung diseases, but it is also reported to be ... ...

Abstract	α-1-antichymotrypsin (ACT) is a serine proteinase inhibitor that controls the activity of proteases like chymotrypsin, cathepsin G and mast cell chymase. Familial variants of ACT results in liver and lung diseases, but it is also reported to be associated with several other disease conditions. ACT is mainly synthesized in the liver using four coding exons, namely E1, E2, E3 and E4 encoding a 423 amino acid protein that also includes a 23 amino acid signal peptide. It is found to be associated with amyloid plaques and is elevated during inflammatory response and modulates cytokine based signal transduction pathways, independent of its anti-protease activity. Therefore, the multispecificity of ACT and its non-inhibitory roles in diseased conditions warrants an assessment of possible existence of the other isoforms. Consequently, scanning of introns, 5' and 3' region of the ACT gene using computational tools like FGENESH and FEX did indicate the presence of coding regions. Using a combined approach of bioinformatics and molecular biology, we have found one novel exon located in the intronic region between exons E1 and E2, that splices with exon E2 and replaces N-terminal exon E1, generating an ACT isoform with a novel 151 base pair N-terminus. This isoform was found to lack the signal sequence and is smaller in size but its reactive centre loop remains intact. A truncated transcript was also confirmed with an extension of the E3 by a 12 nucleotide intronic region including a stop codon. Modelling studies show that due to removal of E4 this isoform lacks the RCL. Novel isoform ACT-N lacks E1 but has a conserved RCL. However, due to loss of strands of β-sheet A, it may also be inactive, but with ability to bind the target proteases. The novel truncated ACT-T isoform lacks the RCL and may have a non-inhibitory role. These hypothesis will need further work for functional validation.
MeSH term(s)	Alternative Splicing ; Amino Acid Sequence ; Amino Acids/metabolism ; Cathepsin G/metabolism ; Chymases/metabolism ; Chymotrypsin/metabolism ; Codon, Terminator ; Cytokines/metabolism ; Humans ; Nucleotides/metabolism ; Protein Isoforms/metabolism ; Protein Sorting Signals ; Serine Proteinase Inhibitors/genetics ; Serpins
Chemical Substances	Amino Acids ; Codon, Terminator ; Cytokines ; Nucleotides ; Protein Isoforms ; Protein Sorting Signals ; SERPINA3 protein, human ; Serine Proteinase Inhibitors ; Serpins ; Chymotrypsin (EC 3.4.21.1) ; Cathepsin G (EC 3.4.21.20) ; Chymases (EC 3.4.21.39)
Language	English
Publishing date	2022-08-26
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	205723-2
ISSN	1090-2104 ; 0006-291X ; 0006-291X
ISSN (online)	1090-2104 ; 0006-291X
ISSN	0006-291X
DOI	10.1016/j.bbrc.2022.08.061
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Article: Identification and validation of two alternatively spliced novel isoforms of human alpha-1-antichymotrypsin

Fatima, Sana / Gupta, Swati / Khan, Abdul Burhan / Rehman, Sayeed ur / Jairajpuri, Mohamad Aman

Biochemical and biophysical research communications. 2022 Aug. 21,

2022

Abstract	α-1-antichymotrypsin (ACT) is a serine proteinase inhibitor that controls the activity of proteases like chymotrypsin, cathepsin G and mast cell chymase. Familial variants of ACT results in liver and lung diseases, but it is also reported to be associated with several other disease conditions. ACT is mainly synthesized in the liver using four coding exons, namely E1, E2, E3 and E4 encoding a 423 amino acid protein that also includes a 23 amino acid signal peptide. It is found to be associated with amyloid plaques and is elevated during inflammatory response and modulates cytokine based signal transduction pathways, independent of its anti-protease activity. Therefore, the multispecificity of ACT and its non-inhibitory roles in diseased conditions warrants an assessment of possible existence of the other isoforms. Consequently, scanning of introns, 5′ and 3′ region of the ACT gene using computational tools like FGENESH and FEX did indicate the presence of coding regions. Using a combined approach of bioinformatics and molecular biology, we have found one novel exon located in the intronic region between exons E1 and E2, that splices with exon E2 and replaces N-terminal exon E1, generating an ACT isoform with a novel 151 base pair N-terminus. This isoform was found to lack the signal sequence and is smaller in size but its reactive centre loop remains intact. A truncated transcript was also confirmed with an extension of the E3 by a 12 nucleotide intronic region including a stop codon. Modelling studies show that due to removal of E4 this isoform lacks the RCL. Novel isoform ACT-N lacks E1 but has a conserved RCL. However, due to loss of strands of β-sheet A, it may also be inactive, but with ability to bind the target proteases. The novel truncated ACT-T isoform lacks the RCL and may have a non-inhibitory role. These hypothesis will need further work for functional validation.
Keywords	amino acids ; amyloid ; bioinformatics ; cathepsin G ; chymotrypsin ; cytokines ; exons ; humans ; inflammation ; introns ; liver ; lungs ; mast cells ; molecular biology ; research ; serine proteinase inhibitors ; signal peptide ; signal transduction ; stop codon
Language	English
Dates of publication	2022-0821
Publishing place	Elsevier Inc.
Document type	Article
Note	Pre-press version
ZDB-ID	205723-2
ISSN	0006-291X ; 0006-291X
ISSN (online)	0006-291X
ISSN	0006-291X
DOI	10.1016/j.bbrc.2022.08.061
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Article ; Online: Contrasting conformational dynamics of β-sheet A and helix F with implications in neuroserpin inhibition and aggregation.

Ansari, Shoyab / Ray, Arjun / Ali, Mohammad Farhan / Bano, Shadabi / Jairajpuri, Mohamad Aman

International journal of biological macromolecules

2021 Volume 176, Page(s) 117–125

Abstract: Neuroserpin (NS) is an inhibitory protein of serpin super family, its shutter region variants have high propensity to aggregate leading to pathological disorders like familial encephalopathy with NS inclusion bodies (FENIB). Helix F and β-sheet A of NS ... ...

Abstract	Neuroserpin (NS) is an inhibitory protein of serpin super family, its shutter region variants have high propensity to aggregate leading to pathological disorders like familial encephalopathy with NS inclusion bodies (FENIB). Helix F and β-sheet A of NS participate in the tissue plasminogen activator (tPA) inhibition but the mechanism is not yet completely understood. A microsecond (μs) molecular dynamics simulation of the helix F and strand 3A variants showed predominant fluctuations in the loop connecting the strands of β-sheet A. Therefore to understand the role of helix F and strand 3A of β-sheet A, cysteine was incorporated at the position N182 in stand 3A (N182C) and position W154 (W154C) in the helix F using site-directed mutagenesis. Purified variants were further labeled with Alexa Fluor488 C
MeSH term(s)	Fluorescent Dyes ; Humans ; Maleimides ; Molecular Dynamics Simulation ; Mutagenesis, Site-Directed ; Neuropeptides/antagonists & inhibitors ; Neuropeptides/chemistry ; Neuropeptides/genetics ; Protein Aggregates ; Protein Conformation ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Recombinant Proteins/chemistry ; Recombinant Proteins/genetics ; Serpins/chemistry ; Serpins/genetics ; Tissue Plasminogen Activator/pharmacology ; Neuroserpin
Chemical Substances	Alexa Fluor 488 C5-maleimide ; Fluorescent Dyes ; Maleimides ; Neuropeptides ; Protein Aggregates ; Recombinant Proteins ; Serpins ; Tissue Plasminogen Activator (EC 3.4.21.68)
Language	English
Publishing date	2021-01-28
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2021.01.171
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Article ; Online: Genetically encoded FRET-based optical sensor for Hg

Soleja, Neha / Jairajpuri, Mohamad Aman / Queen, Aarfa / Mohsin, Mohd

Journal of industrial microbiology & biotechnology

2019 Volume 46, Issue 12, Page(s) 1669–1683

Abstract: Due to the potential toxicity of mercury, there is an immediate need to understand its uptake, transport and flux within living cells. Conventional techniques used to analyze ... ...

Abstract	Due to the potential toxicity of mercury, there is an immediate need to understand its uptake, transport and flux within living cells. Conventional techniques used to analyze Hg
MeSH term(s)	Biological Transport ; Cell Survival ; Escherichia coli/chemistry ; Fluorescence Resonance Energy Transfer ; HEK293 Cells ; Humans ; Intracellular Space/chemistry ; Mercury/analysis ; Saccharomyces cerevisiae/chemistry
Chemical Substances	Mercury (FXS1BY2PGL)
Language	English
Publishing date	2019-09-17
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1482484-X
ISSN	1476-5535 ; 1367-5435
ISSN (online)	1476-5535
ISSN	1367-5435
DOI	10.1007/s10295-019-02235-w
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