1
|
Kelley EH, Osipiuk J, Korbas M, Endres M, Bland A, Ehrman V, Joachimiak A, Olsen KW, Becker DP. N α -acetyl-L-ornithine deacetylase from Escherichia coli and a ninhydrin-based assay to enable inhibitor identification. Front Chem 2024; 12:1415644. [PMID: 39055043 PMCID: PMC11270798 DOI: 10.3389/fchem.2024.1415644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 05/14/2024] [Indexed: 07/27/2024] Open
Abstract
Bacteria are becoming increasingly resistant to antibiotics, therefore there is an urgent need for new classes of antibiotics to fight antibiotic resistance. Mammals do not express N ɑ -acetyl-L-ornithine deacetylase (ArgE), an enzyme that is critical for bacterial survival and growth, thus ArgE represents a promising new antibiotic drug target, as inhibitors would not suffer from mechanism-based toxicity. A new ninhydrin-based assay was designed and validated that included the synthesis of the substrate analog N 5, N 5-di-methyl N α-acetyl-L-ornithine (kcat/Km = 7.32 ± 0.94 × 104 M-1s-1). This new assay enabled the screening of potential inhibitors that absorb in the UV region, and thus is superior to the established 214 nm assay. Using this new ninhydrin-based assay, captopril was confirmed as an ArgE inhibitor (IC50 = 58.7 μM; Ki = 37.1 ± 0.85 μM), and a number of phenylboronic acid derivatives were identified as inhibitors, including 4-(diethylamino)phenylboronic acid (IC50 = 50.1 μM). Selected inhibitors were also tested in a thermal shift assay with ArgE using SYPRO Orange dye against Escherichia coli ArgE to observe the stability of the enzyme in the presence of inhibitors (captopril Ki = 35.9 ± 5.1 μM). The active site structure of di-Zn EcArgE was confirmed using X-ray absorption spectroscopy, and we reported two X-ray crystal structures of E. coli ArgE. In summary, we describe the development of a new ninhydrin-based assay for ArgE, the identification of captopril and phenylboronic acids as ArgE inhibitors, thermal shift studies with ArgE + captopril, and the first two published crystal structures of ArgE (mono-Zn and di-Zn).
Collapse
Affiliation(s)
- Emma H. Kelley
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Jerzy Osipiuk
- Structural Biology Center, Argonne National Laboratory, X-ray Science Division, Lemont, IL, United States
- eBERlight, Argonne National Laboratory, X-ray Science Division, Lemont, IL, United States
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, United States
| | | | - Michael Endres
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, United States
| | - Alayna Bland
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Victoria Ehrman
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Andrzej Joachimiak
- Structural Biology Center, Argonne National Laboratory, X-ray Science Division, Lemont, IL, United States
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, United States
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, United States
| | - Kenneth W. Olsen
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Daniel P. Becker
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| |
Collapse
|
2
|
Bütikofer M, Stadler GR, Kadavath H, Cadalbert R, Torres F, Riek R. Rapid Protein-Ligand Affinity Determination by Photoinduced Hyperpolarized NMR. J Am Chem Soc 2024; 146:17974-17985. [PMID: 38957136 PMCID: PMC11228983 DOI: 10.1021/jacs.4c04000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
The binding affinity determination of protein-ligand complexes is a cornerstone of drug design. State-of-the-art techniques are limited by lengthy and expensive processes. Building upon our recently introduced novel screening method utilizing photochemically induced dynamic nuclear polarization (photo-CIDNP) NMR, we provide the methodological framework to determine binding affinities within 5-15 min using 0.1 mg of protein. The accuracy of our method is demonstrated for the affinity constants of peptides binding to a PDZ domain and fragment ligands binding to the protein PIN1. The method can also be extended to measure the affinity of nonphoto-CIDNP-polarizable ligands in competition binding experiments. Finally, we demonstrate a strong correlation between the ligand-reduced signals in photo-CIDNP-based NMR fragment screening and the well-established saturation transfer difference (STD) NMR. Thus, our methodology measures protein-ligand affinities in the micro- to millimolar range in only a few minutes and informs on the binding epitope in a single-scan experiment, opening new avenues for early stage drug discovery approaches.
Collapse
Affiliation(s)
- Matthias Bütikofer
- Institute for Molecular Physical Science, Vladimir Prelog Weg 2, 8093 Zürich, Switzerland
| | - Gabriela R Stadler
- Institute for Molecular Physical Science, Vladimir Prelog Weg 2, 8093 Zürich, Switzerland
| | - Harindranath Kadavath
- Institute for Molecular Physical Science, Vladimir Prelog Weg 2, 8093 Zürich, Switzerland
| | - Riccardo Cadalbert
- Institute for Molecular Physical Science, Vladimir Prelog Weg 2, 8093 Zürich, Switzerland
| | - Felix Torres
- Institute for Molecular Physical Science, Vladimir Prelog Weg 2, 8093 Zürich, Switzerland
- NexMR AG, Wiesenstrasse 10A, 8952 Schlieren, Switzerland
| | - Roland Riek
- Institute for Molecular Physical Science, Vladimir Prelog Weg 2, 8093 Zürich, Switzerland
| |
Collapse
|
3
|
Gooran N, Kopra K. Fluorescence-Based Protein Stability Monitoring-A Review. Int J Mol Sci 2024; 25:1764. [PMID: 38339045 PMCID: PMC10855643 DOI: 10.3390/ijms25031764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
Proteins are large biomolecules with a specific structure that is composed of one or more long amino acid chains. Correct protein structures are directly linked to their correct function, and many environmental factors can have either positive or negative effects on this structure. Thus, there is a clear need for methods enabling the study of proteins, their correct folding, and components affecting protein stability. There is a significant number of label-free methods to study protein stability. In this review, we provide a general overview of these methods, but the main focus is on fluorescence-based low-instrument and -expertise-demand techniques. Different aspects related to thermal shift assays (TSAs), also called differential scanning fluorimetry (DSF) or ThermoFluor, are introduced and compared to isothermal chemical denaturation (ICD). Finally, we discuss the challenges and comparative aspects related to these methods, as well as future opportunities and assay development directions.
Collapse
Affiliation(s)
| | - Kari Kopra
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland;
| |
Collapse
|
4
|
Kelley EH, Minasov G, Konczak K, Shuvalova L, Brunzelle JS, Shukla S, Beulke M, Thabthimthong T, Olsen KW, Inniss NL, Satchell KJF, Becker DP. Biochemical and Structural Analysis of the Bacterial Enzyme Succinyl-Diaminopimelate Desuccinylase (DapE) from Acinetobacter baumannii. ACS OMEGA 2024; 9:3905-3915. [PMID: 38284080 PMCID: PMC10809365 DOI: 10.1021/acsomega.3c08231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 01/30/2024]
Abstract
There is an urgent need for new antibiotics given the rise of antibiotic resistance, and succinyl-diaminopimelate desuccinylase (DapE, E.C. 3.5.1.18) has emerged as a promising bacterial enzyme target. DapE from Haemophilus influenzae (HiDapE) has been studied and inhibitors identified, but it is essential to explore DapE from different species to assess selective versus broad-spectrum therapeutics. We have determined the structure of DapE from the ESKAPE pathogen Acinetobacter baumannii (AbDapE) and studied inhibition by known inhibitors of HiDapE. AbDapE is inhibited by captopril and sulfate comparable to HiDapE, but AbDapE was not significantly inhibited by a known indoline sulfonamide HiDapE inhibitor. Captopril and sulfate both stabilize HiDapE by increasing the thermal melting temperature (Tm) in thermal shift assays. By contrast, sulfate decreases the stability of the AbDapE enzyme, whereas captopril increases the stability. Further, we report two crystal structures of selenomethionine-substituted AbDapE in the closed conformation, one with AbDapE in complex with succinate derived from enzymatic hydrolysis of N6-methyl-l,l-SDAP substrate and acetate (PDB code 7T1Q, 2.25 Å resolution), and a crystal structure of AbDapE with bound succinate along with l-(S)-lactate, a product of degradation of citric acid from the crystallization buffer during X-ray irradiation (PDB code 8F8O, 2.10 Å resolution).
Collapse
Affiliation(s)
- Emma H. Kelley
- Department
of Chemistry and Biochemistry, Loyola University
Chicago, 1032 West Sheridan Road, Chicago, Illinois 60660, United States
| | - George Minasov
- Department
of Microbiology-Immunology, Northwestern
University, Feinberg School of Medicine, Chicago, Illinois 60611, United States
- Center
for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Katherine Konczak
- Department
of Chemistry and Biochemistry, Loyola University
Chicago, 1032 West Sheridan Road, Chicago, Illinois 60660, United States
| | - Ludmilla Shuvalova
- Department
of Pharmacology, Northwestern University,
Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Joseph S. Brunzelle
- Northwestern
Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, Illinois 60439, United States
| | - Shantanu Shukla
- Department
of Microbiology-Immunology, Northwestern
University, Feinberg School of Medicine, Chicago, Illinois 60611, United States
- Center
for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Megan Beulke
- Department
of Chemistry and Biochemistry, Loyola University
Chicago, 1032 West Sheridan Road, Chicago, Illinois 60660, United States
| | - Teerana Thabthimthong
- Department
of Chemistry and Biochemistry, Loyola University
Chicago, 1032 West Sheridan Road, Chicago, Illinois 60660, United States
| | - Kenneth W. Olsen
- Department
of Chemistry and Biochemistry, Loyola University
Chicago, 1032 West Sheridan Road, Chicago, Illinois 60660, United States
| | - Nicole L. Inniss
- Department
of Microbiology-Immunology, Northwestern
University, Feinberg School of Medicine, Chicago, Illinois 60611, United States
- Center
for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Karla J. F. Satchell
- Department
of Microbiology-Immunology, Northwestern
University, Feinberg School of Medicine, Chicago, Illinois 60611, United States
- Center
for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Daniel P. Becker
- Department
of Chemistry and Biochemistry, Loyola University
Chicago, 1032 West Sheridan Road, Chicago, Illinois 60660, United States
| |
Collapse
|
5
|
Habeeb Mohammad TS, Kelley EH, Reidl CT, Konczak K, Beulke M, Javier J, Olsen KW, Becker DP. Cyclobutanone Inhibitors of Diaminopimelate Desuccinylase (DapE) as Potential New Antibiotics. Int J Mol Sci 2024; 25:1339. [PMID: 38279338 PMCID: PMC10815964 DOI: 10.3390/ijms25021339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 01/28/2024] Open
Abstract
Based on our previous success in using cyclobutanone derivatives as enzyme inhibitors, we have designed and prepared a 37-member library of α-aminocyclobutanone amides and sulfonamides, screened for inhibition of the bacterial enzyme diaminopimelate desuccinylase (DapE), which is a promising antibiotic target, and identified several inhibitors with micromolar inhibitory potency. Molecular docking suggests binding of the deprotonated hydrate of the strained cyclobutanone, and thermal shift analysis with the most potent inhibitor (3y, IC50 = 23.1 µM) enabled determination of a Ki value of 10.2 +/- 0.26 µM and observed two separate Tm values for H. influenzae DapE (HiDapE).
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Daniel P. Becker
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, USA; (T.S.H.M.); (E.H.K.); (K.K.); (M.B.); (J.J.); (K.W.O.)
| |
Collapse
|
6
|
Jeong DE, Lee HS, Ku B, Kim CH, Kim SJ, Shin HC. Insights into the recognition mechanism in the UBR box of UBR4 for its specific substrates. Commun Biol 2023; 6:1214. [PMID: 38030679 PMCID: PMC10687169 DOI: 10.1038/s42003-023-05602-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 11/17/2023] [Indexed: 12/01/2023] Open
Abstract
The N-end rule pathway is a proteolytic system involving the destabilization of N-terminal amino acids, known as N-degrons, which are recognized by N-recognins. Dysregulation of the N-end rule pathway results in the accumulation of undesired proteins, causing various diseases. The E3 ligases of the UBR subfamily recognize and degrade N-degrons through the ubiquitin-proteasome system. Herein, we investigated UBR4, which has a distinct mechanism for recognizing type-2 N-degrons. Structural analysis revealed that the UBR box of UBR4 differs from other UBR boxes in the N-degron binding sites. It recognizes type-2 N-terminal amino acids containing an aromatic ring and type-1 N-terminal arginine through two phenylalanines on its hydrophobic surface. We also characterized the binding mechanism for the second ligand residue. This is the report on the structural basis underlying the recognition of type-2 N-degrons by the UBR box with implications for understanding the N-end rule pathway.
Collapse
Affiliation(s)
- Da Eun Jeong
- Critical Disease Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Bioscience & Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Hye Seon Lee
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, Daejeon, 34141, Republic of Korea
| | - Bonsu Ku
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, Daejeon, 34141, Republic of Korea
| | - Cheol-Hee Kim
- Department of Bioscience & Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Seung Jun Kim
- Critical Disease Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon, 34113, Republic of Korea.
| | - Ho-Chul Shin
- Critical Disease Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejeon, 34134, Republic of Korea.
| |
Collapse
|
7
|
Patel HP, Martinez‐Ramirez G, Dobrzynski E, Iglesias AA, Liu D, Ballicora MA. A critical inter-subunit interaction for the transmission of the allosteric signal in the Agrobacterium tumefaciens ADP-glucose pyrophosphorylase. Protein Sci 2023; 32:e4747. [PMID: 37551561 PMCID: PMC10461462 DOI: 10.1002/pro.4747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/20/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023]
Abstract
ADP-glucose pyrophosphorylase is a key regulatory enzyme involved in starch and glycogen synthesis in plants and bacteria, respectively. It has been hypothesized that inter-subunit communications are important for the allosteric effect in this enzyme. However, no specific interactions have been identified as part of the regulatory signal. The enzyme from Agrobacterium tumefaciens is a homotetramer allosterically regulated by fructose 6-phosphate and pyruvate. Three pairs of distinct subunit-subunit interfaces are present. Here we focus on an interface that features two symmetrical interactions between Arg11 and Asp141 from one subunit with residues Asp141 and Arg11 of the neighbor subunit, respectively. Previously, scanning mutagenesis showed that a mutation at the Arg11 position disrupted the activation of the enzyme. Considering the distance of these residues from the allosteric and catalytic sites, we hypothesized that the interaction between Arg11 and Asp141 is critical for allosteric signaling rather than effector binding. To prove our hypothesis, we mutated those two sites (D141A, D141E, D141N, D141R, R11D, and R11K) and performed kinetic and binding analysis. Mutations that altered the charge affected the regulation the most. To prove that the interaction per se (rather than the presence of specific residues) is critical, we partially rescued the R11D protein by introducing a second mutation (R11D/D141R). This could not restore the activator effect on kcat , but it did rescue the effect on substrate affinity. Our results indicate the critical functional role of Arg11 and Asp141 to relay the allosteric signal in this subunit interface.
Collapse
Affiliation(s)
- Hiral P. Patel
- Department of Chemistry and BiochemistryLoyola University ChicagoChicagoIllinoisUSA
| | | | - Emily Dobrzynski
- Department of Chemistry and BiochemistryLoyola University ChicagoChicagoIllinoisUSA
| | | | - Dali Liu
- Department of Chemistry and BiochemistryLoyola University ChicagoChicagoIllinoisUSA
| | - Miguel A. Ballicora
- Department of Chemistry and BiochemistryLoyola University ChicagoChicagoIllinoisUSA
| |
Collapse
|
8
|
Liveris ZJ, Kelley EH, Simmons E, Konczak K, Lutz MR, Ballicora M, Olsen KW, Becker DP. Synthesis and characterization of the N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE) alternate substrate analog N,N-dimethyl-l,l-SDAP. Bioorg Med Chem 2023; 91:117415. [PMID: 37459673 DOI: 10.1016/j.bmc.2023.117415] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/26/2023] [Accepted: 07/11/2023] [Indexed: 08/01/2023]
Abstract
Growing antibiotic resistance by pathogenic bacteria has led to a global crisis. The bacterial enzyme N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE) provides a very attractive target for the discovery of a new class of antibiotics, as it resides exclusively in many pathogenic bacterial strains and is a key enzyme in the lysine biosynthetic pathway. This pathway is responsible for the production of lysine as well as meso-diaminopimelate (m-DAP), both of which are required for peptidoglycan cell-wall synthesis, and lysine for peptide synthesis. The enzyme DapE catalyzes the hydrolysis of N-succinyl-l,l-diaminopimelic acid (l,l-SDAP) to succinate and l,l-diaminopimelic acid (l,l-DAP), and due to its absence in humans, inhibition of DapE avoids mechanism-based side effects. We have executed the asymmetric synthesis of N,N-dimethyl-SDAP, an l,l-SDAP substrate analog and an analog of the synthetic substrate of our previously described DapE assay. Previous modeling studies advocated that N,N-dimethyl-SDAP might function as an inhibitor, however the compound behaves as a substrate, and we have demonstrated the use of N,N-dimethyl-SDAP as the substrate in a modified ninhydrin-based DapE assay. Thermal shift experiments of DapE in the presence of N,N-dimethyl-SDAP are consistent with a melt temperature (Tm) shifted by succinate, the product of enzymatic hydrolysis.
Collapse
Affiliation(s)
- Zachary J Liveris
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, United States
| | - Emma H Kelley
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, United States
| | - Emma Simmons
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, United States
| | - Katherine Konczak
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, United States
| | - Marlon R Lutz
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, United States
| | - Miguel Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, United States
| | - Kenneth W Olsen
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, United States
| | - Daniel P Becker
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, United States.
| |
Collapse
|
9
|
Machera SJ, Niedziółka-Jönsson J, Jönsson-Niedziółka M, Szot-Karpińska K. Determination of the Dissociation Constant for Polyvalent Receptors Using ELISA: A Case of M13 Phages Displaying Troponin T-Specific Peptides. ACS OMEGA 2023; 8:26253-26262. [PMID: 37521637 PMCID: PMC10373194 DOI: 10.1021/acsomega.3c02551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/27/2023] [Indexed: 08/01/2023]
Abstract
Phage-derived affinity peptides have become widespread thanks to their easy selection via phage display. Interactions between a target protein and its specific peptide are similar to those between antibodies and antigens. The strength of these non-covalent complexes may be described by the dissociation constant (Kd). In this paper, protein-specific peptides are exposed on the pIII protein present in the M13 bacteriophage virion with up to five copies. Therefore, one phage particle can bind from one to five ligands. Here, we discuss the dependences between phage-displayed peptides and their ligands in solution using a model system based on troponin T (TnT) binding phages. Moreover, a method of calculating Kd values from ELISA experiments was developed and is presented. The determined Kd values are in the picomolar range.
Collapse
|
10
|
Khan AM, Atia-Tul-Wahab, Farooq S, Ullah A, Choudhary MI. Repurposing of US-FDA approved drugs against SARS-CoV-2 main protease (M pro) by using STD-NMR spectroscopy, in silico studies and antiviral assays. Int J Biol Macromol 2023; 234:123540. [PMID: 36740128 PMCID: PMC9896891 DOI: 10.1016/j.ijbiomac.2023.123540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/21/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023]
Abstract
SARS-CoV-2 Main protease (Mpro) is a well-known drug target against SARS-CoV-2 infection. Identification of Mpro inhibitors is vigorously pursued due to its crucial role in viral replication. The present study was aimed to identify Mpro inhibitors via repurposing of US-FDA approved drugs by STD-NMR spectroscopy. In this study, 156 drugs and natural compounds were evaluated against Mpro. Among them, 10 drugs were found to be interacting with Mpro, including diltiazem HCl (1), mefenamic acid (2), losartan potassium (3), mexiletine HCl (4), glaucine HBr (5), trimebutine maleate (6), flurbiprofen (7), amantadine HCl (8), dextromethorphan (9), and lobeline HCl (10) in STD-NMR spectroscopy. Their interactions were compared with three standards (Repurposed anti-viral drugs), dexamethasone, chloroquine phosphate, and remdesivir. Thermal stability of Mpro and dissociation constant (Kd) of six interacting drugs were also determined using DSF. RMSD plots in MD simulation studies showed the formation of stable protein-ligand complexes. They were further examined for their antiviral activity by plaque reduction assay against SARS-CoV-2, which showed 55-100% reduction in viral plaques. This study demonstrates the importance of drug repurposing against emerging and neglected diseases. This study also exhibits successful application of STD-NMR spectroscopy combined with plaque reduction assay in rapid identification of potential anti-viral agents.
Collapse
Affiliation(s)
- Abdul Mateen Khan
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Atia-Tul-Wahab
- Dr. Panjwani Center for Molecular and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan.
| | - Saba Farooq
- National Institute of Virology, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Asmat Ullah
- Dr. Panjwani Center for Molecular and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - M Iqbal Choudhary
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan; Dr. Panjwani Center for Molecular and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan; Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
| |
Collapse
|
11
|
Production of a halotolerant endo-1,4-β-glucanase by a newly isolated Bacillus velezensis H1 on olive mill wastes without pretreatment: purification and characterization of the enzyme. Arch Microbiol 2022; 204:681. [DOI: 10.1007/s00203-022-03300-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/07/2022] [Accepted: 10/21/2022] [Indexed: 11/25/2022]
|