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Rabaan AA, Alshahrani MA, Othman B, Alfaresi M, Almutawif YA, Eid HMA, Saif A, Alshehri AA. Investigation of potential ascorbate peroxidase inhibitors for anti-leishmaniasis therapy. Folia Microbiol (Praha) 2024:10.1007/s12223-024-01190-z. [PMID: 39153157 DOI: 10.1007/s12223-024-01190-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 08/06/2024] [Indexed: 08/19/2024]
Abstract
L eishmaniasis is a prevalent disease that impacts 98 countries and territories, mainly in Africa, Asia, and South America. It can cause substantial illness and death, particularly in its visceral manifestation that can be specifically targeted in the development of medications to combat leishmaniasis. This study has found natural compounds with possible inhibitory activity against APX using a reliable and accurate QSAR model. Despite the severe side effects of current treatments and the absence of an effective vaccination, these compounds show promise as a potential treatment for the disease. Nine hit compounds were found, and subsequent molecular docking was performed. Estradiol cypionate showed the lowest binding energy (- 10.5 kcal/mol), thus showing the strongest binding, and also had the strongest binding affinity, with a ΔGTotal of - 26.31 ± 3.01 kcal/mol, second only to the control molecule. Additionally, three hits viz. cloxacillin-sodium (- 16.57 ± 2.89 kcal/mol), cinchonidine (- 16.04 ± 3.27 kcal/mol), and quinine hydrochloride dihydrate (13.38 ± 1.06 kcal/mol) also showed significant binding affinity. Multiple interactions between drugs and active site residues demonstrated a substantial binding affinity with the target protein. The identified compounds exhibited drug-like effects and were orally bioavailable based on their ADME-toxicology features. Overall, estradiol cypionate, cloxacillin sodium, cinchonidine, and quinine hydrochloride dihydrate all exhibited inhibitory effects on the APX enzyme of Leishmania donovani. These results suggest that further investigation is needed to explore the potential of developing novel anti-leishmaniasis drugs using these compounds.
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Affiliation(s)
- Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, 31,311, Dhahran, Saudi Arabia.
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia, 11,533.
- Department of Public Health and Nutrition, The University of Haripur, Haripur, Pakistan, 22,610.
| | - Mohammed Abdulrahman Alshahrani
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran, Saudi Arabia, 61,441
| | - Basim Othman
- Department of Public Health, Faculty of Applied Medical Sciences,, Albaha University, Albaha, Saudi Arabia, 65,77
| | - Mubarak Alfaresi
- Department of Microbiology, National Reference Laboratory, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates, 92,323
- Department of Pathology, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates, 505,055
| | - Yahya A Almutawif
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Taibah University, Madinah, Saudi Arabia, 41,411
| | - Hamza M A Eid
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Taibah University, Madinah, Saudi Arabia, 41,411
| | - Ahmed Saif
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia, 62,223
| | - Ahmad A Alshehri
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran, Saudi Arabia, 61,441.
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Freeman SL, Oliveira ASF, Gallio AE, Rosa A, Simitakou MK, Arthur CJ, Mulholland AJ, Cherepanov P, Raven EL. Heme binding to the SARS-CoV-2 spike glycoprotein. J Biol Chem 2023; 299:105014. [PMID: 37414149 PMCID: PMC10416065 DOI: 10.1016/j.jbc.2023.105014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/12/2023] [Accepted: 07/01/2023] [Indexed: 07/08/2023] Open
Abstract
The target for humoral immunity, SARS-CoV-2 spike glycoprotein, has become the focus of vaccine research and development. Previous work demonstrated that the N-terminal domain (NTD) of SARS-CoV-2 spike binds biliverdin-a product of heme catabolism-causing a strong allosteric effect on the activity of a subset of neutralizing antibodies. Herein, we show that the spike glycoprotein is also able to bind heme (KD = 0.5 ± 0.2 μM). Molecular modeling indicated that the heme group fits well within the same pocket on the SARS-CoV-2 spike NTD. Lined by aromatic and hydrophobic residues (W104, V126, I129, F192, F194, I203, and L226), the pocket provides a suitable environment to stabilize the hydrophobic heme. Mutagenesis of N121 has a substantive effect on heme binding (KD = 3000 ± 220 μM), confirming the pocket as a major heme binding location of the viral glycoprotein. Coupled oxidation experiments in the presence of ascorbate indicated that the SARS-CoV-2 glycoprotein can catalyze the slow conversion of heme to biliverdin. The heme trapping and oxidation activities of the spike may allow the virus to reduce levels of free heme during infection to facilitate evasion of the adaptive and innate immunity.
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Affiliation(s)
- Samuel L Freeman
- School of Chemistry, Cantock's Close, University of Bristol, Bristol, United Kingdom
| | - A Sofia F Oliveira
- School of Chemistry, Cantock's Close, University of Bristol, Bristol, United Kingdom
| | - Andrea E Gallio
- School of Chemistry, Cantock's Close, University of Bristol, Bristol, United Kingdom
| | - Annachiara Rosa
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Maria K Simitakou
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Christopher J Arthur
- School of Chemistry, Cantock's Close, University of Bristol, Bristol, United Kingdom
| | - Adrian J Mulholland
- School of Chemistry, Cantock's Close, University of Bristol, Bristol, United Kingdom
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom; Department of Infectious Disease, St-Mary's Campus, Imperial College London, United Kingdom.
| | - Emma L Raven
- School of Chemistry, Cantock's Close, University of Bristol, Bristol, United Kingdom.
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Zhao J, de Serrano V, Dumarieh R, Thompson M, Ghiladi RA, Franzen S. The Role of the Distal Histidine in H2O2 Activation and Heme Protection in both Peroxidase and Globin Functions. J Phys Chem B 2012; 116:12065-77. [DOI: 10.1021/jp300014b] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Junjie Zhao
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United
States
| | - Vesna de Serrano
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United
States
| | - Rania Dumarieh
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United
States
| | - Matt Thompson
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United
States
| | - Reza A. Ghiladi
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United
States
| | - Stefan Franzen
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United
States
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Euglena gracilis ascorbate peroxidase forms an intramolecular dimeric structure: its unique molecular characterization. Biochem J 2010; 426:125-34. [PMID: 20015051 DOI: 10.1042/bj20091406] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Euglena gracilis lacks a catalase and contains a single APX (ascorbate peroxidase) and enzymes related to the redox cycle of ascorbate in the cytosol. In the present study, a full-length cDNA clone encoding the Euglena APX was isolated and found to contain an open reading frame encoding a protein of 649 amino acids with a calculated molecular mass of 70.5 kDa. Interestingly, the enzyme consisted of two entirely homologous catalytic domains, designated APX-N and APX-C, and an 102 amino acid extension in the N-terminal region, which had a typical class II signal proposed for plastid targeting in Euglena. A computer-assisted analysis indicated a novel protein structure with an intramolecular dimeric structure. The analysis of cell fractionation showed that the APX protein is distributed in the cytosol, but not the plastids, suggesting that Euglena APX becomes mature in the cytosol after processing of the precursor. The kinetics of the recombinant mature FL (full-length)-APX and the APX-N and APX-C domains with ascorbate and H2O2 were almost the same as that of the native enzyme. However, the substrate specificity of the mature FL-APX and the native enzyme was different from that of APX-N and APX-C. The mature FL-APX, but not the truncated forms, could reduce alkyl hydroperoxides, suggesting that the dimeric structure is correlated with substrate recognition. In Euglena cells transfected with double-stranded RNA, the silencing of APX expression resulted in a significant increase in the cellular level of H2O2, indicating the physiological importance of APX to the metabolism of H2O2.
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Nonaka D, Wariishi H, Welinder KG, Fujii H. Paramagnetic 13C and 15N NMR Analyses of the Push and Pull Effects in Cytochrome c Peroxidase and Coprinus cinereus Peroxidase Variants: Functional Roles of Highly Conserved Amino Acids around Heme. Biochemistry 2009; 49:49-57. [DOI: 10.1021/bi9017285] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Daisuke Nonaka
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Myodaiji, Okazaki 444-8787, Japan
| | - Hiroyuki Wariishi
- Faculty of Agriculture, Kyushu University, Hakozaki, Fukuoka 821-8581, Japan
| | - Karen G. Welinder
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark
| | - Hiroshi Fujii
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Myodaiji, Okazaki 444-8787, Japan
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