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Padín JF, Pérez-Ortiz JM, Redondo-Calvo FJ. Aprotinin (II): Inhalational Administration for the Treatment of COVID-19 and Other Viral Conditions. Int J Mol Sci 2024; 25:7209. [PMID: 39000315 PMCID: PMC11241800 DOI: 10.3390/ijms25137209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 07/16/2024] Open
Abstract
Aprotinin is a broad-spectrum inhibitor of human proteases that has been approved for the treatment of bleeding in single coronary artery bypass surgery because of its potent antifibrinolytic actions. Following the outbreak of the COVID-19 pandemic, there was an urgent need to find new antiviral drugs. Aprotinin is a good candidate for therapeutic repositioning as a broad-spectrum antiviral drug and for treating the symptomatic processes that characterise viral respiratory diseases, including COVID-19. This is due to its strong pharmacological ability to inhibit a plethora of host proteases used by respiratory viruses in their infective mechanisms. The proteases allow the cleavage and conformational change of proteins that make up their viral capsid, and thus enable them to anchor themselves by recognition of their target in the epithelial cell. In addition, the activation of these proteases initiates the inflammatory process that triggers the infection. The attraction of the drug is not only its pharmacodynamic characteristics but also the possibility of administration by the inhalation route, avoiding unwanted systemic effects. This, together with the low cost of treatment (≈2 Euro/dose), makes it a good candidate to reach countries with lower economic means. In this article, we will discuss the pharmacodynamic, pharmacokinetic, and toxicological characteristics of aprotinin administered by the inhalation route; analyse the main advances in our knowledge of this medication; and the future directions that should be taken in research in order to reposition this medication in therapeutics.
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Affiliation(s)
- Juan-Fernando Padín
- Department of Medical Sciences, School of Medicine at Ciudad Real, University of Castilla-La Mancha, 13971 Ciudad Real, Spain
| | - José Manuel Pérez-Ortiz
- Facultad HM de Ciencias de la Salud, Universidad Camilo José Cela, 28692 Madrid, Spain
- Instituto de Investigación Sanitaria HM Hospitales, 28015 Madrid, Spain
| | - Francisco Javier Redondo-Calvo
- Department of Medical Sciences, School of Medicine at Ciudad Real, University of Castilla-La Mancha, 13971 Ciudad Real, Spain
- Department of Anaesthesiology and Critical Care Medicine, University General Hospital, 13005 Ciudad Real, Spain
- Translational Research Unit, University General Hospital and Research Institute of Castilla-La Mancha (IDISCAM), 13005 Ciudad Real, Spain
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Storch E, Overeem LH, Terhart M, Fitzek MP, Lange KS, Reuter U, Raffaelli B. PACAP-38 and sex hormones in women with migraine: exploratory analysis of a cross-sectional, matched cohort study. J Headache Pain 2024; 25:98. [PMID: 38858641 PMCID: PMC11165852 DOI: 10.1186/s10194-024-01804-4] [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: 03/01/2024] [Accepted: 06/04/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND Endogeneous and exogeneous sex hormones can impact the frequency and severity of migraine attacks, but the underlying mechanisms are poorly understood. In this study, we investigate the relationship between female sex hormones and Pituitary Adenylate Cyclase-Activating Polypeptide-38 (PACAP-38) concentrations in plasma of women with migraine and healthy controls, aiming to elucidate potential hormonal influences on PACAP dynamics and their relevance to migraine pathophysiology. METHODS This analysis is part of a cross-sectional, matched-cohort study. We recruited two groups of women with episodic migraine: one with a regular menstrual cycle (M-RMC) and another undergoing combined oral contraceptive treatment (M-COC). Additionally, we included corresponding age-matched control groups without migraine for both categories (C-RMC and C-COC). For participants with a RMC, the study visits were scheduled during the perimenstrual period (menstrual cycle day 2 ± 2) and periovulatory period (day 13 ± 2). Participants using COC were examined at day 4 ± 2 of the hormone-free interval and between day 7-14 of the hormone intake phase. During these visits, PACAP-38 concentrations in plasma were measured using a commercial Enzyme-linked-immunosorbent assay (ELISA) kit. RESULTS The study included 120 women, with 30 participants in each group. Women with migraine and a RMC had significantly higher PACAP-38 plasma concentrations compared to healthy controls at both study visits [day 2 ± 2: M-RMC: 2547.41 pg/ml (IQR 814.27 - 4473.48) vs. C-RMC: 1129.49 pg/ml (IQR 257.34 - 2684.88), p = 0.025; day 13 ± 2: M-RMC: 3098.89 pg/ml (IQR 1186.29 - 4379.47) vs. C-RMC: 1626.89 (IQR 383.83 - 3038.36), p = 0.028]. In contrast, PACAP-38 levels were comparable between migraine and control groups receiving COC. Women with migraine and a RMC exhibited higher PACAP-38 concentrations during menstruation compared to those using COC during the hormone-free interval. CONCLUSION Systemic PACAP-38 concentrations in women vary based on the presence of migraine diagnosis and their hormonal status.
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Affiliation(s)
- Elisabeth Storch
- Department of Neurology, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Zu Berlin, Charitéplatz 1, Berlin, 10117, Germany
| | - Lucas H Overeem
- Department of Neurology, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Zu Berlin, Charitéplatz 1, Berlin, 10117, Germany
| | - Maria Terhart
- Department of Neurology, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Zu Berlin, Charitéplatz 1, Berlin, 10117, Germany
| | - Mira P Fitzek
- Department of Neurology, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Zu Berlin, Charitéplatz 1, Berlin, 10117, Germany
| | - Kristin S Lange
- Department of Neurology, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Zu Berlin, Charitéplatz 1, Berlin, 10117, Germany
- Clinician Scientist Program, Berlin Institute of Health at Charité (BIH), Berlin, Germany
| | - Uwe Reuter
- Department of Neurology, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Zu Berlin, Charitéplatz 1, Berlin, 10117, Germany
- Universitätsmedizin Greifswald, Greifswald, Germany
| | - Bianca Raffaelli
- Department of Neurology, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Zu Berlin, Charitéplatz 1, Berlin, 10117, Germany.
- Clinician Scientist Program, Berlin Institute of Health at Charité (BIH), Berlin, Germany.
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Needham LM, Saavedra C, Rasch JK, Sole-Barber D, Schweitzer BS, Fairhall AJ, Vollbrecht CH, Wan S, Podorova Y, Bergsten AJ, Mehlenbacher B, Zhang Z, Tenbrake L, Saimi J, Kneely LC, Kirkwood JS, Pfeifer H, Chapman ER, Goldsmith RH. Label-free detection and profiling of individual solution-phase molecules. Nature 2024; 629:1062-1068. [PMID: 38720082 DOI: 10.1038/s41586-024-07370-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 04/02/2024] [Indexed: 05/21/2024]
Abstract
Most chemistry and biology occurs in solution, in which conformational dynamics and complexation underlie behaviour and function. Single-molecule techniques1 are uniquely suited to resolving molecular diversity and new label-free approaches are reshaping the power of single-molecule measurements. A label-free single-molecule method2-16 capable of revealing details of molecular conformation in solution17,18 would allow a new microscopic perspective of unprecedented detail. Here we use the enhanced light-molecule interactions in high-finesse fibre-based Fabry-Pérot microcavities19-21 to detect individual biomolecules as small as 1.2 kDa, a ten-amino-acid peptide, with signal-to-noise ratios (SNRs) >100, even as the molecules are unlabelled and freely diffusing in solution. Our method delivers 2D intensity and temporal profiles, enabling the distinction of subpopulations in mixed samples. Notably, we observe a linear relationship between passage time and molecular radius, unlocking the potential to gather crucial information about diffusion and solution-phase conformation. Furthermore, mixtures of biomolecule isomers of the same molecular weight and composition but different conformation can also be resolved. Detection is based on the creation of a new molecular velocity filter window and a dynamic thermal priming mechanism that make use of the interplay between optical and thermal dynamics22,23 and Pound-Drever-Hall (PDH) cavity locking24 to reveal molecular motion even while suppressing environmental noise. New in vitro ways of revealing molecular conformation, diversity and dynamics can find broad potential for applications in the life and chemical sciences.
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Affiliation(s)
- Lisa-Maria Needham
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- School of the Biological Sciences, University of Cambridge, Cambridge, UK
| | - Carlos Saavedra
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Julia K Rasch
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Daniel Sole-Barber
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Beau S Schweitzer
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Alex J Fairhall
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Cecilia H Vollbrecht
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemistry and Biochemistry, Kalamazoo College, Kalamazoo, MI, USA
| | - Sushu Wan
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Yulia Podorova
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Anders J Bergsten
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Zhao Zhang
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, WI, USA
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, USA
| | - Lukas Tenbrake
- Institut für Angewandte Physik, Universität Bonn, Bonn, Germany
| | - Jovanna Saimi
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Lucy C Kneely
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Jackson S Kirkwood
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Hannes Pfeifer
- Institut für Angewandte Physik, Universität Bonn, Bonn, Germany
| | - Edwin R Chapman
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, WI, USA
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, USA
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Doiphode S, Lokhande KB, Ghosh P, Swamy KV, Nagar S. Dual inhibition of cyclooxygenase-2 (COX-2) and 5-lipoxygenase (5-LOX) by resveratrol derivatives in cancer therapy: in silico approach. J Biomol Struct Dyn 2023; 41:8571-8586. [PMID: 36282056 DOI: 10.1080/07391102.2022.2135599] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 10/08/2022] [Indexed: 10/31/2022]
Abstract
In a number of human cancers, both cycloxygenase-2 (COX-2) and 5-lipoxygenase (5-LOX) are up-regulated and co-expressed, promoting cancer cell proliferation and angiogenesis. Resveratrol (3,4',5-trihydroxy-trans-stilbene) is a natural polyphenolic phytoalexin found in a variety of plants that influences various signal-transduction pathways which control apoptosis, cell growth and cell division, metastasis, angiogenesis and inflammation, and has an impact on cancer stages ranging from initiation to progression. In this work, molecular docking and molecular dynamics simulation method are employed to design resveratrol derivatives for COX-2 and 5-LOX enzymes. By attaching several functional groups on four different places of the resveratrol scaffold, the R group enumeration approach was employed to build four libraries of resveratrol derivatives. Thus, R group enumeration is done to focus on the enhancement of potency of compounds and other chemical characteristics like solubility. Drug-like filters such as REOS 1, 2, 3 and PAINS were applied to the libraries, generating a total of 5557 compounds. Drug-like filters such as REOS and PAINS-1, 2 and 3 were applied to the libraries, generating a total of 5557 compounds. All of these compounds were docked with both enzymes using the Glide SP and XP docking methods. Enrichment calculations were performed using 40 compounds from XP docking along with resveratrol, and 1000 decoy compounds from the DUD-E database to validate the docking protocol. The stability of the complexes was further studied using molecular dynamics simulation, radius of gyration, MM/GBSA, H bond monitoring and electrostatic potential surface (EPS). ADMET properties of compounds were studied using SwissADME and pkCSM server.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sayali Doiphode
- Bioinformatics Centre, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Pune, India
| | - Kiran Bharat Lokhande
- Bioinformatics Centre, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Pune, India
| | - Payel Ghosh
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, India
| | - K V Swamy
- MIT School of Bioengineering Sciences & Research, MIT Art, Design and Technology University, Pune, India
| | - Shuchi Nagar
- Bioinformatics Centre, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Pune, India
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Needham LM, Saavedra C, Rasch JK, Sole-Barber D, Schweitzer BS, Fairhall AJ, Vollbrecht CH, Mehlenbacher B, Zhang Z, Tenbrake L, Pfeifer H, Chapman ER, Goldsmith RH. Label-free observation of individual solution phase molecules. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.24.534170. [PMID: 36993572 PMCID: PMC10055403 DOI: 10.1101/2023.03.24.534170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The vast majority of chemistry and biology occurs in solution, and new label-free analytical techniques that can help resolve solution-phase complexity at the single-molecule level can provide new microscopic perspectives of unprecedented detail. Here, we use the increased light-molecule interactions in high-finesse fiber Fabry-Pérot microcavities to detect individual biomolecules as small as 1.2 kDa with signal-to-noise ratios >100, even as the molecules are freely diffusing in solution. Our method delivers 2D intensity and temporal profiles, enabling the distinction of sub-populations in mixed samples. Strikingly, we observe a linear relationship between passage time and molecular radius, unlocking the potential to gather crucial information about diffusion and solution-phase conformation. Furthermore, mixtures of biomolecule isomers of the same molecular weight can also be resolved. Detection is based on a novel molecular velocity filtering and dynamic thermal priming mechanism leveraging both photo-thermal bistability and Pound-Drever-Hall cavity locking. This technology holds broad potential for applications in life and chemical sciences and represents a major advancement in label-free in vitro single-molecule techniques.
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Affiliation(s)
- Lisa-Maria Needham
- Department of Chemistry, University of Wisconsin-Madison, WI, USA
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Carlos Saavedra
- Department of Chemistry, University of Wisconsin-Madison, WI, USA
| | - Julia K. Rasch
- Department of Chemistry, University of Wisconsin-Madison, WI, USA
| | | | | | - Alex J. Fairhall
- Department of Chemistry, University of Wisconsin-Madison, WI, USA
| | | | | | - Zhao Zhang
- Howard Hughes Medical Institute and the Department of Neuroscience, University of Wisconsin-Madison, WI, USA
| | - Lukas Tenbrake
- Institut für Angewandte Physik, Universität Bonn, Wegelerstr. 8, 53115 Bonn, Germany
| | - Hannes Pfeifer
- Institut für Angewandte Physik, Universität Bonn, Wegelerstr. 8, 53115 Bonn, Germany
| | - Edwin R. Chapman
- Howard Hughes Medical Institute and the Department of Neuroscience, University of Wisconsin-Madison, WI, USA
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Structural and Functional Characterization of a New Bacterial Dipeptidyl Peptidase III Involved in Fruiting Body Formation in Myxobacteria. Int J Mol Sci 2022; 24:ijms24010631. [PMID: 36614072 PMCID: PMC9820243 DOI: 10.3390/ijms24010631] [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: 10/30/2022] [Revised: 12/24/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022] Open
Abstract
Dipeptidyl peptidase III (DPP III) is a zinc-dependent enzyme that specifically hydrolyzes dipeptides from the N-terminal of different-length peptides, and it is involved in a number of physiological processes. Here, DPP III with an atypical pentapeptide zinc binding motif (HELMH) was identified from Corallococcus sp. EGB. It was shown that the activity of recombined CoDPP III was optimal at 50 °C and pH 7.0 with high thermostability up to 60 °C. Unique to CoDPP III, the crystal structure of the ligand-free enzyme was determined as a dimeric and closed form. The relatively small inter-domain cleft creates a narrower entrance to the substrate binding site and the unfavorable binding of the bulky naphthalene ring. The ectopic expression of CoDPP III in M. xanthus DK1622 resulted in a 12 h head start in fruiting body development compared with the wild type. Additionally, the A-signal prepared from the starving DK1622-CoDPP III rescued the developmental defect of the asgA mutant, and the fruiting bodies were more numerous and closely packed. Our data suggested that CoDPP III played a role in the fruiting body development of myxobacteria through the accumulation of peptides and amino acids to act as the A-signal.
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Ye P, Duan W, Leng YQ, Wang YK, Tan X, Wang WZ. DPP3: From biomarker to therapeutic target of cardiovascular diseases. Front Cardiovasc Med 2022; 9:974035. [PMID: 36312232 PMCID: PMC9605584 DOI: 10.3389/fcvm.2022.974035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 09/26/2022] [Indexed: 11/13/2022] Open
Abstract
Cardiovascular disease is the leading cause of death globally among non-communicable diseases, which imposes a serious socioeconomic burden on patients and the healthcare system. Therefore, finding new strategies for preventing and treating cardiovascular diseases is of great significance in reducing the number of deaths and disabilities worldwide. Dipeptidyl peptidase 3 (DPP3) is the first zinc-dependent peptidase found among DPPs, mainly distributes within the cytoplasm. With the unique HEXXGH catalytic sequence, it is associated with the degradation of oligopeptides with 4 to 10 amino acids residues. Accumulating evidences have demonstrated that DPP3 plays a significant role in almost all cellular activities and pathophysiological mechanisms. Regarding the role of DPP3 in cardiovascular diseases, it is currently mainly used as a biomarker for poor prognosis in patients with cardiovascular diseases, suggesting that the level of DPP3 concentration in plasma is closely linked to the mortality of diseases such as cardiogenic shock and heart failure. Interestingly, it has been reported recently that DPP3 regulates blood pressure by interacting with the renin-angiotensin system. In addition, DPP3 also participates in the processes of pain signaling, inflammation, and oxidative stress. But the exact mechanism by which DPP3 affects cardiovascular function is not clear. Hence, this review summarizes the recent advances in the structure and catalytic activity of DPP3 and its extensive biological functions, especially its role as a therapeutic target in cardiovascular diseases. It will provide a theoretical basis for exploring the potential value of DPP3 as a therapeutic target for cardiovascular diseases.
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Affiliation(s)
- Peng Ye
- Department of Marine Biomedicine and Polar Medicine, Naval Medical Center, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Wei Duan
- Department of Marine Biomedicine and Polar Medicine, Naval Medical Center, Naval Medical University (Second Military Medical University), Shanghai, China,Key Laboratory of Medical Electrophysiology of Ministry of Education, Medical Electrophysiology Key Lab of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, China
| | - Yue-Qi Leng
- Department of Marine Biomedicine and Polar Medicine, Naval Medical Center, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Yang-Kai Wang
- Department of Marine Biomedicine and Polar Medicine, Naval Medical Center, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Xing Tan
- Department of Marine Biomedicine and Polar Medicine, Naval Medical Center, Naval Medical University (Second Military Medical University), Shanghai, China,Xing Tan
| | - Wei-Zhong Wang
- Department of Marine Biomedicine and Polar Medicine, Naval Medical Center, Naval Medical University (Second Military Medical University), Shanghai, China,*Correspondence: Wei-Zhong Wang
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Palaniraj S, Murugesan R, Narayan S. Aprotinin – Conjugated biocompatible porous nanocomposite for dentine remineralization and biofilm degradation. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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9
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Survey of Dipeptidyl Peptidase III Inhibitors: From Small Molecules of Microbial or Synthetic Origin to Aprotinin. Molecules 2022; 27:molecules27093006. [PMID: 35566358 PMCID: PMC9101112 DOI: 10.3390/molecules27093006] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/23/2022] [Accepted: 05/05/2022] [Indexed: 11/30/2022] Open
Abstract
Dipeptidyl peptidase III (DPP III) was originally thought to be a housekeeping enzyme that contributes to intracellular peptide catabolism. More specific roles for this cytosolic metallopeptidase, in the renin-angiotensin system and oxidative stress regulation, were confirmed, or recognized, only recently. To prove indicated (patho)physiological functions of DPP III in cancer progression, cataract formation and endogenous pain modulation, or to reveal new ones, selective and potent inhibitors are needed. This review encompasses natural and synthetic compounds with experimentally proven inhibitory activity toward mammalian DPP III. Except for the polypeptide aprotinin, all others are small molecules and include flavonoids, coumarin and benzimidazole derivatives. Presented are current strategies for the discovery or development of DPP III inhibitors, and mechanisms of inhibitory actions. The most potent inhibitors yet reported (propioxatin A and B, Tyr-Phe- and Phe-Phe-NHOH, and JMV-390) are active in low nanomolar range and contain hydroxamic acid moiety. High inhibitory potential possesses oligopeptides from the hemorphin group, valorphin and tynorphin, which are poor substrates of DPP III. The crystal structure of human DPP III-tynorphin complex enabled the design of the transition-state peptidomimetics inhibitors, effective in low micromolar concentrations. A new direction in the field is the development of fluorescent inhibitor for monitoring DPP III activity.
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Molecular Dynamics Simulations Study of the Interactions between Human Dipeptidyl-Peptidase III and Two Substrates. Molecules 2021; 26:molecules26216492. [PMID: 34770898 PMCID: PMC8587566 DOI: 10.3390/molecules26216492] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 10/24/2021] [Accepted: 10/25/2021] [Indexed: 01/14/2023] Open
Abstract
Human dipeptidyl-peptidase III (hDPP III) is capable of specifically cleaving dipeptides from the N-terminal of small peptides with biological activity such as angiotensin II (Ang II, DRVYIHPF), and participates in blood pressure regulation, pain modulation, and the development of cancers in human biological activities. In this study, 500 ns molecular dynamics simulations were performed on free-hDPP III (PDB code: 5E33), hDPP III-Ang II (PDB code: 5E2Q), and hDPP III-IVYPW (PDB code: 5E3C) to explore how these two peptides affect the catalytic efficiency of enzymes in terms of the binding mode and the conformational changes. Our results indicate that in the case of the hDPP III-Ang II complex, subsite S1 became small and hydrophobic, which might be propitious for the nucleophile to attack the substrate. The structures of the most stable conformations of the three systems revealed that Arg421-Lys423 could form an α-helix with the presence of Ang II, but only part of the α-helix was produced in hDPP III-IVYPW. As the hinge structure in hDPP III, the conformational changes that took place in the Arg421-Lys423 residue could lead to the changes in the shape and space of the catalytic subsites, which might allow water to function as a nucleophile to attack the substrate. Our results may provide new clues to enable the design of new inhibitors for hDPP III in the future.
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Lokhande KB, Doiphode S, Vyas R, Swamy KV. Molecular docking and simulation studies on SARS-CoV-2 M pro reveals Mitoxantrone, Leucovorin, Birinapant, and Dynasore as potent drugs against COVID-19. J Biomol Struct Dyn 2020; 39:7294-7305. [PMID: 32815481 PMCID: PMC7484567 DOI: 10.1080/07391102.2020.1805019] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The outbreak of novel coronavirus (COVID-19), which began from Wuhan City, Hubei, China, and declared as a Public Health Emergency of International Concern by World Health Organization (WHO) on 30th January 2020. The present study describes how the available drug candidates can be used as a potential SARS-CoV-2 Mpro inhibitor by molecular docking and molecular dynamic simulation studies. Drug repurposing strategy is applied by using the library of antiviral and FDA approved drugs retrieved from the Selleckchem Inc. (Houston, TX, http://www.selleckchem.com) and DrugBank database respectively. Computational methods like molecular docking and molecular dynamics simulation were used. The molecular docking calculations were performed using LeadIT FlexX software. The molecular dynamics simulations of 100 ns were performed to study conformational stability for all complex systems. Mitoxantrone and Leucovorin from FDA approved drug library and Birinapant and Dynasore from anti-viral drug libraries interact with SARS-CoV-2 Mpro at higher efficiency as a result of the improved steric and hydrophobic environment in the binding cavity to make stable complex. Also, the molecular dynamics simulations of 100 ns revealed the mean RMSD value of 2.25 Å for all the complex systems. This shows that lead compounds bound tightly within the Mpro cavity and thus having conformational stability. Glutamic acid (Glu166) of Mpro is a key residue to hold and form a stable complex of reported lead compounds by forming hydrogen bonds and salt bridge. Our findings suggest that Mitoxantrone, Leucovorin, Birinapant, and Dynasore represents potential inhibitors of SARS-CoV-2 Mpro.
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Affiliation(s)
- Kiran Bharat Lokhande
- Bioinformatics Research Laboratory, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Patil Vidyapeeth, Pune, India
| | - Sayali Doiphode
- Bioinformatics Research Laboratory, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Patil Vidyapeeth, Pune, India
| | - Renu Vyas
- Bioinformatics Research Group, MIT School of Bioengineering Science and Research, MIT- ADT University, Pune, India
| | - K Venkateswara Swamy
- Bioinformatics Research Laboratory, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Patil Vidyapeeth, Pune, India.,Bioinformatics Research Group, MIT School of Bioengineering Science and Research, MIT- ADT University, Pune, India
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