1
|
Sinha P, Yadav AK. In silico identification of cyclosporin derivatives as potential inhibitors for RdRp of rotavirus by molecular docking and molecular dynamic studies. J Biomol Struct Dyn 2024; 42:5001-5014. [PMID: 37517053 DOI: 10.1080/07391102.2023.2239918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/05/2023] [Indexed: 08/01/2023]
Abstract
Rotavirus is one of the most common gastrointestinal viral diseases. Till date, there are only two vaccines available in the markets, which are specifically to be administered to young babies. In this study, VP1 RdRp is selected as potential target to carry out inhibitory activities. Cyclosporin A (Cys A) derivatives were designed via FBDD, pharmacokinetics, molecular docking, molecular dynamics (MD) simulation and molecular mechanics generalized born surface area was applied on these compounds. The results from these investigations were analyzed and it was found that the considered derivatives in this study were nontoxic and docking results revealed that the derivatives made some important bonds inside the active site of the receptors within a catalytic triad (Serine-Histidine-Aspartate). After analyzing the mean values of root mean square density (RMSD), root mean square fluctuation (RMSF), radius of gyration (RoG) and solvent accessible surface area (SASA) at 100 ns MD simulation of the selected compounds, it was found that compound 1 exhibits RMSD of 0.74 ± 0.10 Å, RMSF of 0.85 ± 0.15 Å, RoG of 16.45 ± 0.40 Å, SASA of 66.55 ± 0.35 nm2 and ΔGbind of -32.76 ± 0.02 kcal/mol. Therefore, the study revealed that amongst the designed and reported compounds, compound 1 was more stable within the active region of the RdRp and also this compound possesses lower binding free energy as compared to other selected compounds and Cys A as well.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Prashasti Sinha
- Department of Physics, School of Physical & Decision Science, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh, India
| | - Anil Kumar Yadav
- Department of Physics, School of Physical & Decision Science, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh, India
| |
Collapse
|
2
|
Zhao X, Zhao X, Di W, Wang C. Inhibitors of Cyclophilin A: Current and Anticipated Pharmaceutical Agents for Inflammatory Diseases and Cancers. Molecules 2024; 29:1235. [PMID: 38542872 PMCID: PMC10974348 DOI: 10.3390/molecules29061235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/02/2024] [Accepted: 03/05/2024] [Indexed: 04/07/2024] Open
Abstract
Cyclophilin A, a widely prevalent cellular protein, exhibits peptidyl-prolyl cis-trans isomerase activity. This protein is predominantly located in the cytosol; additionally, it can be secreted by the cells in response to inflammatory stimuli. Cyclophilin A has been identified to be a key player in many of the biological events and is therefore involved in several diseases, including vascular and inflammatory diseases, immune disorders, aging, and cancers. It represents an attractive target for therapeutic intervention with small molecule inhibitors such as cyclosporin A. Recently, a number of novel inhibitors of cyclophilin A have emerged. However, it remains elusive whether and how many cyclophilin A inhibitors function in the inflammatory diseases and cancers. In this review, we discuss current available data about cyclophilin A inhibitors, including cyclosporin A and its derivatives, quinoxaline derivatives, and peptide analogues, and outline the most recent advances in clinical trials of these agents. Inhibitors of cyclophilin A are poised to enhance our comprehension of the molecular mechanisms that underpin inflammatory diseases and cancers associated with cyclophilin A. This advancement will aid in the development of innovative pharmaceutical treatments in the future.
Collapse
Affiliation(s)
- Xuemei Zhao
- School of Pharmaceutical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan 250000, China; (X.Z.); (W.D.)
| | - Xin Zhao
- School of Pharmaceutical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan 250000, China; (X.Z.); (W.D.)
| | - Weihua Di
- School of Pharmaceutical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan 250000, China; (X.Z.); (W.D.)
| | - Chang Wang
- School of Pharmaceutical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan 250000, China; (X.Z.); (W.D.)
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan 250000, China
| |
Collapse
|
3
|
Vankadari N, Ghosal D. Structural Insights into SARS-CoV-2 Nonstructural Protein 1 Interaction with Human Cyclophilin and FKBP1 to Regulate Interferon Production. J Phys Chem Lett 2024; 15:919-924. [PMID: 38241259 DOI: 10.1021/acs.jpclett.3c02959] [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: 01/21/2024]
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic caused by the SARS-CoV-2 coronavirus and the perpetual rise of new variants warrant investigation of the molecular and structural details of the infection process and modulation of the host defense by viral proteins. This Letter reports the combined experimental and computational approaches to provide key insights into the structural and functional basis of Nsp1's association with different cyclophilins and FKBPs in regulating COVID-19 infection. We demonstrated the real-time stability and functional dynamics of the Nsp1-CypA/FKBP1A complex and investigated the repurposing of potential inhibitors that could block these interactions. Overall, we provided insights into the inhibitory role Nsp1 in downstream interferon production, a key aspect for host defense that prevents the SARS-CoV-2 or related family of corona virus infection.
Collapse
Affiliation(s)
- Naveen Vankadari
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3000, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3000, Australia
| | - Debnath Ghosal
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3000, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3000, Australia
| |
Collapse
|
4
|
de Pablo N, Meana C, Martínez‐García J, Martínez‐Vicente P, Albert M, Guerra S, Angulo A, Balsinde J, Balboa MA. Lipin-2 regulates the antiviral and anti-inflammatory responses to interferon. EMBO Rep 2023; 24:e57238. [PMID: 37929625 PMCID: PMC10702840 DOI: 10.15252/embr.202357238] [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: 03/24/2023] [Revised: 10/16/2023] [Accepted: 10/19/2023] [Indexed: 11/07/2023] Open
Abstract
Interferons (IFN) are crucial antiviral and immunomodulatory cytokines that exert their function through the regulation of a myriad of genes, many of which are not yet characterized. Here, we reveal that lipin-2, a phosphatidic acid phosphatase whose mutations produce an autoinflammatory syndrome known as Majeed syndrome in humans, is regulated by IFN in a STAT-1-dependent manner. Lipin-2 inhibits viral replication both in vitro and in vivo. Moreover, lipin-2 also acts as a regulator of inflammation in a viral context by reducing the signaling through TLR3 and the generation of ROS and release of mtDNA that ultimately activate the NLRP3 inflammasome. Inhibitors of mtDNA release from mitochondria restrict IL-1β production in lipin-2-deficient animals in a model of viral infection. Finally, analyses of databases from COVID-19 patients show that LPIN2 expression levels negatively correlate with the severity of the disease. Overall, these results uncover novel regulatory mechanisms of the IFN response driven by lipin-2 and open new perspectives for the future management of patients with LPIN2 mutations.
Collapse
Affiliation(s)
- Nagore de Pablo
- Instituto de Biología y Genética MolecularConsejo Superior de Investigaciones Científicas (CSIC)ValladolidSpain
| | - Clara Meana
- Instituto de Biología y Genética MolecularConsejo Superior de Investigaciones Científicas (CSIC)ValladolidSpain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM)Instituto de Salud Carlos IIIMadridSpain
| | - Javier Martínez‐García
- Instituto de Biología y Genética MolecularConsejo Superior de Investigaciones Científicas (CSIC)ValladolidSpain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM)Instituto de Salud Carlos IIIMadridSpain
| | - Pablo Martínez‐Vicente
- Immunology Unit, Department of Biomedical Sciences, Faculty of Medicine and Health SciencesUniversity of BarcelonaBarcelonaSpain
- Institut d'Investigacions Biomèdiques August Pi i SunyerBarcelonaSpain
| | - Manuel Albert
- Departamento de Medicina Preventiva y Salud Pública, Facultad de MedicinaUniversidad Autónoma de MadridMadridSpain
| | - Susana Guerra
- Departamento de Medicina Preventiva y Salud Pública, Facultad de MedicinaUniversidad Autónoma de MadridMadridSpain
| | - Ana Angulo
- Immunology Unit, Department of Biomedical Sciences, Faculty of Medicine and Health SciencesUniversity of BarcelonaBarcelonaSpain
- Institut d'Investigacions Biomèdiques August Pi i SunyerBarcelonaSpain
| | - Jesús Balsinde
- Instituto de Biología y Genética MolecularConsejo Superior de Investigaciones Científicas (CSIC)ValladolidSpain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM)Instituto de Salud Carlos IIIMadridSpain
| | - María A Balboa
- Instituto de Biología y Genética MolecularConsejo Superior de Investigaciones Científicas (CSIC)ValladolidSpain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM)Instituto de Salud Carlos IIIMadridSpain
| |
Collapse
|
5
|
Li Y, Liu T, Lai X, Xie H, Tang H, Wu S, Li Y. Rational design peptide inhibitors of Cyclophilin D as a potential treatment for acute pancreatitis. Medicine (Baltimore) 2023; 102:e36188. [PMID: 38050301 PMCID: PMC10695616 DOI: 10.1097/md.0000000000036188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/27/2023] [Indexed: 12/06/2023] Open
Abstract
Cyclophilin D (CypD) is a mitochondrial matrix peptidyl prolidase that regulates the mitochondrial permeability transition pore. Inhibition of CypD was suggested as a therapeutic strategy for acute pancreatitis. Peptide inhibitors emerged as novel binding ligand for blocking receptor activity. In this study, we present our computational approach for designing peptide inhibitors of CypD. The 3-D structure of random peptides were built, and docked into the active center of CypD using Rosetta script integrated FlexPepDock module. The peptide displayed the lowest binding energy against CypD was further selected for virtual iterative mutation based on virtual mutagenesis and molecular docking. Finally, the top 5 peptides with the lowest binding energy was selected for validating their affinity against CypD using inhibitory assay. We showed 4 out of the selected 5 peptides were capable for blocking the activity of CypD, while WACLQ display the strongest affinity against CypD, which reached 0.28 mM. The binding mechanism between WACLQ and CypD was characterized using molecular dynamics simulation. Here, we proved our approach can be a robust method for screening peptide inhibitors.
Collapse
Affiliation(s)
- Yuehong Li
- Department of Critical Care Medicine, Longyan First Affiliated Hospital of Fujian Medical University, Longyan, China
| | - Ting Liu
- Department of Critical Care Medicine, Longyan First Affiliated Hospital of Fujian Medical University, Longyan, China
| | - Xiaoyan Lai
- Department of Critical Care Medicine, Longyan First Affiliated Hospital of Fujian Medical University, Longyan, China
| | - Huifang Xie
- Department of Critical Care Medicine, Longyan First Affiliated Hospital of Fujian Medical University, Longyan, China
| | - Heng Tang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Shuangchan Wu
- Institute of Medical Research, Northwestern Polytechnical University, Xian, Shanxi Province, China
| | - Yongshun Li
- Department of Critical Care Medicine, Longyan First Affiliated Hospital of Fujian Medical University, Longyan, China
| |
Collapse
|
6
|
Manna S, Das K, Santra S, Nosova EV, Zyryanov GV, Halder S. Structural and Synthetic Aspects of Small Ring Oxa- and Aza-Heterocyclic Ring Systems as Antiviral Activities. Viruses 2023; 15:1826. [PMID: 37766233 PMCID: PMC10536032 DOI: 10.3390/v15091826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 08/17/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
Antiviral properties of different oxa- and aza-heterocycles are identified and properly correlated with their structural features and discussed in this review article. The primary objective is to explore the activity of such ring systems as antiviral agents, as well as their synthetic routes and biological significance. Eventually, the structure-activity relationship (SAR) of the heterocyclic compounds, along with their salient characteristics are exhibited to build a suitable platform for medicinal chemists and biotechnologists. The synergistic conclusions are extremely important for the introduction of a newer tool for the future drug discovery program.
Collapse
Affiliation(s)
- Sibasish Manna
- Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur 440010, India
| | - Koushik Das
- Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur 440010, India
| | - Sougata Santra
- Department of Organic and Biomolecular Chemistry, Chemical Engineering Institute, Ural Federal University, 19 Mira Street, 620002 Yekaterinburg, Russia; (S.S.); (E.V.N.); (G.V.Z.)
| | - Emily V. Nosova
- Department of Organic and Biomolecular Chemistry, Chemical Engineering Institute, Ural Federal University, 19 Mira Street, 620002 Yekaterinburg, Russia; (S.S.); (E.V.N.); (G.V.Z.)
- I. Ya. Postovskiy Institute of Organic Synthesis, Ural Division of the Russian Academy of Sciences, 22 S. Kovalevskoy Street, 620219 Yekaterinburg, Russia
| | - Grigory V. Zyryanov
- Department of Organic and Biomolecular Chemistry, Chemical Engineering Institute, Ural Federal University, 19 Mira Street, 620002 Yekaterinburg, Russia; (S.S.); (E.V.N.); (G.V.Z.)
- I. Ya. Postovskiy Institute of Organic Synthesis, Ural Division of the Russian Academy of Sciences, 22 S. Kovalevskoy Street, 620219 Yekaterinburg, Russia
| | - Sandipan Halder
- Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur 440010, India
| |
Collapse
|
7
|
Kanna M, Nakatsu Y, Yamamotoya T, Encinas J, Ito H, Okabe T, Asano T, Sakaguchi T. Roles of peptidyl prolyl isomerase Pin1 in viral propagation. Front Cell Dev Biol 2022; 10:1005325. [PMID: 36393854 PMCID: PMC9642847 DOI: 10.3389/fcell.2022.1005325] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/13/2022] [Indexed: 07/30/2023] Open
Abstract
Peptidyl-prolyl isomerase (PPIase) is a unique enzyme that promotes cis-trans isomerization of a proline residue of a target protein. Peptidyl-prolyl cis-trans isomerase NIMA (never in mitosis A)-interacting 1 (Pin1) is a PPIase that binds to the pSer/pThr-Pro motif of target proteins and isomerizes their prolines. Pin1 has been reported to be involved in cancer development, obesity, aging, and Alzheimer's disease and has been shown to promote the growth of several viruses including SARS-CoV-2. Pin1 enhances the efficiency of viral infection by promoting uncoating and integration of the human immunodeficiency virus. It has also been shown that Pin1 interacts with hepatitis B virus proteins and participates in viral replication. Furthermore, Pin1 promotes not only viral proliferation but also the progression of virus-induced tumorigenesis. In this review, we focus on the effects of Pin1 on the proliferation of various viruses and discuss the underlying molecular mechanisms.
Collapse
Affiliation(s)
- Machi Kanna
- Department of Biomedical Chemistry, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima City, Japan
| | - Yusuke Nakatsu
- Department of Biomedical Chemistry, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima City, Japan
| | - Takeshi Yamamotoya
- Department of Biomedical Chemistry, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima City, Japan
| | | | - Hisanaka Ito
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Japan
| | - Takayoshi Okabe
- Drug Discovery Initiative, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Japan
| | - Tomoichiro Asano
- Department of Biomedical Chemistry, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima City, Japan
| | - Takemasa Sakaguchi
- Department of Virology, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima City, Japan
| |
Collapse
|