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Aranda-Chan V, Cárdenas-Guerra RE, Otero-Pedraza A, Pacindo-Cabrales EE, Flores-Pucheta CI, Montes-Flores O, Arroyo R, Ortega-López J. Insights into Peptidyl-Prolyl cis- trans Isomerases from Clinically Important Protozoans: From Structure to Potential Biotechnological Applications. Pathogens 2024; 13:644. [PMID: 39204244 PMCID: PMC11357558 DOI: 10.3390/pathogens13080644] [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: 06/10/2024] [Revised: 07/26/2024] [Accepted: 07/28/2024] [Indexed: 09/03/2024] Open
Abstract
Peptidyl-prolyl cis/trans isomerases (PPIases) are present in a wide variety of microorganisms, including protozoan parasites such as Trypanosoma cruzi, Trypanosoma brucei, Trichomonas vaginalis, Leishmania major, Leishmania donovani, Plasmodium falciparum, Plasmodium vivax, Entamoeba histolytica, Giardia intestinalis, Cryptosporidium parvum, and Cryptosporidium hominis, all of which cause important neglected diseases. PPIases are classified as cyclophilins, FKBPs, or parvulins and play crucial roles in catalyzing the cis-trans isomerization of the peptide bond preceding a proline residue. This activity assists in correct protein folding. However, experimentally, the biological structure-function characterization of PPIases from these protozoan parasites has been poorly addressed. The recombinant production of these enzymes is highly relevant for this ongoing research. Thus, this review explores the structural diversity, functions, recombinant production, activity, and inhibition of protozoan PPIases. We also highlight their potential as biotechnological tools for the in vitro refolding of other recombinant proteins from these parasites. These applications are invaluable for the development of diagnostic and therapeutic tools.
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Affiliation(s)
- Verónica Aranda-Chan
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Av. IPN # 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, Mexico City 07360, Mexico; (V.A.-C.); (R.E.C.-G.); (A.O.-P.); (E.E.P.-C.); (C.I.F.-P.); (O.M.-F.)
| | - Rosa Elena Cárdenas-Guerra
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Av. IPN # 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, Mexico City 07360, Mexico; (V.A.-C.); (R.E.C.-G.); (A.O.-P.); (E.E.P.-C.); (C.I.F.-P.); (O.M.-F.)
| | - Alejandro Otero-Pedraza
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Av. IPN # 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, Mexico City 07360, Mexico; (V.A.-C.); (R.E.C.-G.); (A.O.-P.); (E.E.P.-C.); (C.I.F.-P.); (O.M.-F.)
| | - Esdras Enoc Pacindo-Cabrales
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Av. IPN # 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, Mexico City 07360, Mexico; (V.A.-C.); (R.E.C.-G.); (A.O.-P.); (E.E.P.-C.); (C.I.F.-P.); (O.M.-F.)
| | - Claudia Ivonne Flores-Pucheta
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Av. IPN # 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, Mexico City 07360, Mexico; (V.A.-C.); (R.E.C.-G.); (A.O.-P.); (E.E.P.-C.); (C.I.F.-P.); (O.M.-F.)
| | - Octavio Montes-Flores
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Av. IPN # 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, Mexico City 07360, Mexico; (V.A.-C.); (R.E.C.-G.); (A.O.-P.); (E.E.P.-C.); (C.I.F.-P.); (O.M.-F.)
| | - Rossana Arroyo
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Av. IPN # 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, Mexico City 07360, Mexico;
| | - Jaime Ortega-López
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Av. IPN # 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, Mexico City 07360, Mexico; (V.A.-C.); (R.E.C.-G.); (A.O.-P.); (E.E.P.-C.); (C.I.F.-P.); (O.M.-F.)
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2
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Kim G, Yoon KS, Ha J, Kang I, Choe W. The PPIase Activity of CypB Is Essential for the Activation of Both AKT/mTOR and XBP1s Signaling Pathways during the Differentiation of 3T3-L1 Preadipocytes. Nutrients 2024; 16:2465. [PMID: 39125345 PMCID: PMC11313753 DOI: 10.3390/nu16152465] [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: 06/24/2024] [Revised: 07/24/2024] [Accepted: 07/26/2024] [Indexed: 08/12/2024] Open
Abstract
In this study, we undertook an extensive investigation to determine how CypB PPIase activity affects preadipocyte differentiation and lipid metabolism. Our findings revealed that inhibition of CypB's PPIase activity suppressed the expression of crucial proteins involved in adipocyte differentiation and induced changes in proteins regulating the cell cycle. Furthermore, we clarified the impact of CypB's PPIase activity on lipid metabolism via the AKT/mTOR signaling pathway. Additionally, we demonstrated the involvement of CypB's PPIase activity in lipid metabolism through the XBP1s pathway. These discoveries offer invaluable insights for devising innovative therapeutic strategies aimed at treating and averting obesity and its related health complications. Targeting CypB's PPIase activity may emerge as a promising avenue for addressing obesity-related conditions. Furthermore, our research opens up opportunities for creating new therapeutic strategies by enhancing our comprehension of the processes involved in cellular endoplasmic reticulum stress.
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Affiliation(s)
- Gyuhui Kim
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea; (G.K.); (K.-S.Y.); (J.H.); (I.K.)
| | - Kyung-Sik Yoon
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea; (G.K.); (K.-S.Y.); (J.H.); (I.K.)
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Joohun Ha
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea; (G.K.); (K.-S.Y.); (J.H.); (I.K.)
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Insug Kang
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea; (G.K.); (K.-S.Y.); (J.H.); (I.K.)
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Wonchae Choe
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea; (G.K.); (K.-S.Y.); (J.H.); (I.K.)
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea
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3
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Stauffer WT, Goodman AZ, Gallay PA. Cyclophilin inhibition as a strategy for the treatment of human disease. Front Pharmacol 2024; 15:1417945. [PMID: 39045055 PMCID: PMC11264201 DOI: 10.3389/fphar.2024.1417945] [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: 04/16/2024] [Accepted: 06/14/2024] [Indexed: 07/25/2024] Open
Abstract
Cyclophilins (Cyps), characterized as peptidyl-prolyl cis-trans isomerases (PPIases), are highly conserved and ubiquitous, playing a crucial role in protein folding and cellular signaling. This review summarizes the biochemical pathways mediated by Cyps, including their involvement in pathological states such as viral replication, inflammation, and cancer progression, to underscore the therapeutic potential of Cyp inhibition. The exploration of Cyp inhibitors (CypI) in this review, particularly non-immunosuppressive cyclosporine A (CsA) derivatives, highlights their significance as therapeutic agents. The structural and functional nuances of CsA derivatives are examined, including their efficacy, mechanism of action, and the balance between therapeutic benefits and off-target effects. The landscape of CypI is evaluated to emphasize the clinical need for targeted approaches to exploit the complex biology of Cyps and to propose future directions for research that may enhance the utility of non-immunosuppressive CsA derivatives in treating diseases where Cyps play a key pathological role.
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Affiliation(s)
| | | | - Philippe A. Gallay
- Department of Immunology & Microbiology, The Scripps Research Institute, La Jolla, CA, United States
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4
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Çiftçi YC, Yurtsever Y, Akgül B. Long non-coding RNA-mediated modulation of endoplasmic reticulum stress under pathological conditions. J Cell Mol Med 2024; 28:e18561. [PMID: 39072992 DOI: 10.1111/jcmm.18561] [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: 03/23/2024] [Revised: 06/12/2024] [Accepted: 06/27/2024] [Indexed: 07/30/2024] Open
Abstract
Endoplasmic reticulum (ER) stress, which ensues from an overwhelming protein folding capacity, activates the unfolded protein response (UPR) in an effort to restore cellular homeostasis. As ER stress is associated with numerous diseases, it is highly important to delineate the molecular mechanisms governing the ER stress to gain insight into the disease pathology. Long non-coding RNAs, transcripts with a length of over 200 nucleotides that do not code for proteins, interact with proteins and nucleic acids, fine-tuning the UPR to restore ER homeostasis via various modes of actions. Dysregulation of specific lncRNAs is implicated in the progression of ER stress-related diseases, presenting these molecules as promising therapeutic targets. The comprehensive analysis underscores the importance of understanding the nuanced interplay between lncRNAs and ER stress for insights into disease mechanisms. Overall, this review consolidates current knowledge, identifies research gaps and offers a roadmap for future investigations into the multifaceted roles of lncRNAs in ER stress and associated diseases to shed light on their pivotal roles in the pathogenesis of related diseases.
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Affiliation(s)
- Yusuf Cem Çiftçi
- Noncoding RNA Laboratory, Department of Molecular Biology and Genetics, Izmir Institute of Technology, Izmir, Turkey
| | - Yiğit Yurtsever
- Noncoding RNA Laboratory, Department of Molecular Biology and Genetics, Izmir Institute of Technology, Izmir, Turkey
| | - Bünyamin Akgül
- Noncoding RNA Laboratory, Department of Molecular Biology and Genetics, Izmir Institute of Technology, Izmir, Turkey
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5
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Mortoni A, Castelli E, Recca T, Quadrelli P. Structure of prolylrapamycin: confirmation through a revised and detailed NMR assignment study. J Antibiot (Tokyo) 2024; 77:345-352. [PMID: 38504121 PMCID: PMC11128375 DOI: 10.1038/s41429-024-00714-6] [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: 02/24/2023] [Revised: 02/15/2024] [Accepted: 02/21/2024] [Indexed: 03/21/2024]
Abstract
A complete and detailed characterization of Rapamycin (1) and Prolylrapamycin (2) has been conducted by homo- and hetero-nuclear NMR experiments in DMSO-d6 along with HRMS and FT-IR spectra and DSCs analyses. The NMR experiments allowed the assignment of every single proton and carbon atom belonging to the two structures and the definitive confirm of the presence of a pyrrolidine ring in Prolylrapamycin (2) in place of the piperidine ring that characterizes the structure of Sirolimus.
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Affiliation(s)
| | | | - Teresa Recca
- Centro Grandi Strumenti (CGS), Università degli Studi di Pavia, Via Bassi 21, 27100, Pavia, Italy
| | - Paolo Quadrelli
- Dipartimento di Chimica, Università degli Studi di Pavia, Viale Taramelli 12, 27100, Pavia, Italy.
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6
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Lin GH, Yu TA, Chang CF, Hsu CH. Proline Isomerization and Molten Globular Property of TgPDCD5 Secreted from Toxoplasma gondii Confers Its Regulation of Heparin Sulfate Binding. JACS AU 2024; 4:1763-1774. [PMID: 38818051 PMCID: PMC11134355 DOI: 10.1021/jacsau.3c00577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 06/01/2024]
Abstract
Toxoplasmosis, caused by Toxoplasma gondii, poses risks to vulnerable populations. TgPDCD5, a secreted protein of T. gondii, induces apoptosis through heparan sulfate-mediated endocytosis. The entry mechanism of TgPDCD5 has remained elusive. Here, we present the solution structure of TgPDCD5 as a helical bundle with an extended N-terminal helix, exhibiting molten globule characteristics. NMR perturbation studies reveal heparin/heparan sulfate binding involving the heparan sulfate/heparin proteoglycans-binding motif and the core region, influenced by proline isomerization of P107 residue. The heterogeneous proline recruits a cyclophilin TgCyp18, accelerating interconversion between conformers and regulating heparan/heparin binding. These atomic-level insights elucidate the binary switch's functionality, expose novel heparan sulfate-binding surfaces, and illuminate the unconventional cellular entry of pathogenic TgPDCD5.
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Affiliation(s)
- Gloria
Meng-Hsuan Lin
- Department
of Agricultural Chemistry, National Taiwan
University, Taipei 10617, Taiwan
- Genome
and Systems Biology Degree Program, National
Taiwan University and Academia Sinica, Taipei 10617, Taiwan
| | - Tsun-Ai Yu
- Genomic
Research Center, Academia Sinica, Taipei 115201, Taiwan
| | - Chi-Fon Chang
- Genomic
Research Center, Academia Sinica, Taipei 115201, Taiwan
| | - Chun-Hua Hsu
- Department
of Agricultural Chemistry, National Taiwan
University, Taipei 10617, Taiwan
- Genome
and Systems Biology Degree Program, National
Taiwan University and Academia Sinica, Taipei 10617, Taiwan
- Institute
of Biochemical Sciences, National Taiwan
University, Taipei 115201, Taiwan
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7
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Stewart R, Sharma S, Wu T, Okuda S, Xie G, Zhou XZ, Shilton B, Lu KP. The role of the master cancer regulator Pin1 in the development and treatment of cancer. Front Cell Dev Biol 2024; 12:1343938. [PMID: 38745861 PMCID: PMC11091292 DOI: 10.3389/fcell.2024.1343938] [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: 11/24/2023] [Accepted: 03/28/2024] [Indexed: 05/16/2024] Open
Abstract
This review examines the complex role of Pin1 in the development and treatment of cancer. Pin1 is the only peptidyl-prolyl isomerase (PPIase) that can recognize and isomerize phosphorylated Ser/Thr-Pro peptide bonds. Pin1 catalyzes a structural change in phosphorylated Ser/Thr-Pro motifs that can modulate protein function and thereby impact cell cycle regulation and tumorigenesis. The molecular mechanisms by which Pin1 contributes to oncogenesis are reviewed, including Pin1 overexpression and its correlation with poor cancer prognosis, and the contribution of Pin1 to aggressive tumor phenotypes involved in therapeutic resistance is discussed, with an emphasis on cancer stem cells, the epithelial-to-mesenchymal transition (EMT), and immunosuppression. The therapeutic potential of Pin1 inhibition in cancer is discussed, along with the promise and the difficulties in identifying potent, drug-like, small-molecule Pin1 inhibitors. The available evidence supports the efficacy of targeting Pin1 as a novel cancer therapeutic by analyzing the role of Pin1 in a complex network of cancer-driving pathways and illustrating the potential of synergistic drug combinations with Pin1 inhibitors for treating aggressive and drug-resistant tumors.
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Affiliation(s)
- Robert Stewart
- Department of Biochemistry, Western University, London, ON, Canada
| | - Shaunik Sharma
- Department of Biochemistry, Western University, London, ON, Canada
| | - Timothy Wu
- Department of Biochemistry, Western University, London, ON, Canada
| | - Sho Okuda
- Department of Biochemistry, Western University, London, ON, Canada
| | - George Xie
- Department of Biochemistry, Western University, London, ON, Canada
| | - Xiao Zhen Zhou
- Department of Biochemistry, Western University, London, ON, Canada
- Robarts Research Institute, Western University, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
- Lawson Health Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Brian Shilton
- Department of Biochemistry, Western University, London, ON, Canada
| | - Kun Ping Lu
- Department of Biochemistry, Western University, London, ON, Canada
- Robarts Research Institute, Western University, London, ON, Canada
- Lawson Health Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Department of Oncology, Western University, London, ON, Canada
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8
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Ai T, Liu H, Wan J, Lu B, Yu X, Liu J, Yimamu A, Aishan S, Liu C, Qin R. Proteomics Analysis Reveals the Underlying Factors of Mucilage Disappearance in Brasenia schreberi and Its Influence on Nutrient Accumulation. Foods 2024; 13:518. [PMID: 38397495 PMCID: PMC10888037 DOI: 10.3390/foods13040518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/31/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Brasenia schreberi J.F. Gmel (BS) is rich in mucilage, which has diverse biological activities, and is utilized in the food and pharmaceutical industries due to its nutritional value. Proteomics analysis was employed to investigate the cause of mucilage disappearance in BS and its effect on nutrient accumulation. Among the 2892 proteins identified, 840 differentially expressed proteins (DEPs) were found to be involved in mucilage development. By comparing the expression patterns and functions and pathway enrichment, the DEPs mainly contributed to carbon and energy metabolism, polysaccharide metabolism, and photosynthesis. Our study also revealed positive correlations between mucilage accumulation and tryptophan metabolism, with high levels of indole-3-acetic (IAA) contributing to mucilage accumulation. Furthermore, environmental changes and particularly excessive nutrients were found to be detrimental to mucilage synthesis. Overall, in the absence of various stimuli in the growing environment, BS accumulates more nutrients within the plant itself instead of producing mucilage.
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Affiliation(s)
- Tingyang Ai
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China; (T.A.); (H.L.); (J.W.); (B.L.); (X.Y.); (J.L.); (A.Y.); (S.A.)
| | - Hong Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China; (T.A.); (H.L.); (J.W.); (B.L.); (X.Y.); (J.L.); (A.Y.); (S.A.)
| | - Jiawei Wan
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China; (T.A.); (H.L.); (J.W.); (B.L.); (X.Y.); (J.L.); (A.Y.); (S.A.)
| | - Bojie Lu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China; (T.A.); (H.L.); (J.W.); (B.L.); (X.Y.); (J.L.); (A.Y.); (S.A.)
| | - Xiujuan Yu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China; (T.A.); (H.L.); (J.W.); (B.L.); (X.Y.); (J.L.); (A.Y.); (S.A.)
| | - Jiao Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China; (T.A.); (H.L.); (J.W.); (B.L.); (X.Y.); (J.L.); (A.Y.); (S.A.)
| | - Aidiya Yimamu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China; (T.A.); (H.L.); (J.W.); (B.L.); (X.Y.); (J.L.); (A.Y.); (S.A.)
| | - Saimire Aishan
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China; (T.A.); (H.L.); (J.W.); (B.L.); (X.Y.); (J.L.); (A.Y.); (S.A.)
| | - Caixiang Liu
- Department of Biological Magnetic Resonance Spectroscopy, Innovation Academy of Precision Measurement Science and Technology Innovation, Chinese Academy of Sciences, Wuhan 430071, China
| | - Rui Qin
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China; (T.A.); (H.L.); (J.W.); (B.L.); (X.Y.); (J.L.); (A.Y.); (S.A.)
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9
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Zhuang S, Chakraborty P, Zweckstetter M. Regulation of tau by peptidyl-prolyl isomerases. Curr Opin Struct Biol 2024; 84:102739. [PMID: 38061261 DOI: 10.1016/j.sbi.2023.102739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/06/2023] [Accepted: 11/13/2023] [Indexed: 02/09/2024]
Abstract
Tau is an intrinsically disordered protein found abundantly in axons, where it binds to microtubules. Since tau is a central player in the dynamic microtubule network, it is highly regulated by post-translational modifications. Abnormal hyperphosphorylation and aggregation of tau characterize a group of diseases called tauopathies. A specific protein family of cis/trans peptidyl-prolyl isomerases (PPIases) can interact with tau to regulate its aggregation and neuronal resilience. Structural interactions between tau and specific PPIases have been determined, establishing possible mechanisms for tau regulation and modification. While there have been numerous in vivo studies evaluating the impact of PPIase expression on tau biology/pathology, the direct roles of PPIases have yet to be fully characterized. Different PPIases correlate to either increased or decreased levels of tau-associated degeneration. Therefore, the ability of PPIases to structurally modify and regulate tau should be further investigated due to its potential therapeutic implications for Alzheimer's disease and other tauopathies.
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Affiliation(s)
- Shannon Zhuang
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075 Göttingen, Germany
| | - Pijush Chakraborty
- Department for NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077 Göttingen, Germany
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075 Göttingen, Germany; Department for NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077 Göttingen, Germany.
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10
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Rodríguez-Vega A, Dutra-Tavares AC, Souza TP, Semeão KA, Filgueiras CC, Ribeiro-Carvalho A, Manhães AC, Abreu-Villaça Y. Nicotine Exposure in a Phencyclidine-Induced Mice Model of Schizophrenia: Sex-Selective Medial Prefrontal Cortex Protein Markers of the Combined Insults in Adolescent Mice. Int J Mol Sci 2023; 24:14634. [PMID: 37834084 PMCID: PMC10572990 DOI: 10.3390/ijms241914634] [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: 07/19/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
Tobacco misuse as a comorbidity of schizophrenia is frequently established during adolescence. However, comorbidity markers are still missing. Here, the method of label-free proteomics was used to identify deregulated proteins in the medial prefrontal cortex (prelimbic and infralimbic) of male and female mice modelled to schizophrenia with a history of nicotine exposure during adolescence. Phencyclidine (PCP), used to model schizophrenia (SCHZ), was combined with an established model of nicotine minipump infusions (NIC). The combined insults led to worse outcomes than each insult separately when considering the absolute number of deregulated proteins and that of exclusively deregulated ones. Partially shared Reactome pathways between sexes and between PCP, NIC and PCPNIC groups indicate functional overlaps. Distinctively, proteins differentially expressed exclusively in PCPNIC mice reveal unique effects associated with the comorbidity model. Interactome maps of these proteins identified sex-selective subnetworks, within which some proteins stood out: for females, peptidyl-prolyl cis-trans isomerase (Fkbp1a) and heat shock 70 kDa protein 1B (Hspa1b), both components of the oxidative stress subnetwork, and gamma-enolase (Eno2), a component of the energy metabolism subnetwork; and for males, amphiphysin (Amph), a component of the synaptic transmission subnetwork. These are proposed to be further investigated and validated as markers of the combined insult during adolescence.
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Affiliation(s)
- Andrés Rodríguez-Vega
- Laboratório de Neurofisiologia, Departamento de Ciências Fisiológicas, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro 20550-170, RJ, Brazil; (A.R.-V.); (A.C.D.-T.); (T.P.S.); (K.A.S.); (C.C.F.); (A.C.M.)
| | - Ana Carolina Dutra-Tavares
- Laboratório de Neurofisiologia, Departamento de Ciências Fisiológicas, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro 20550-170, RJ, Brazil; (A.R.-V.); (A.C.D.-T.); (T.P.S.); (K.A.S.); (C.C.F.); (A.C.M.)
| | - Thainá P. Souza
- Laboratório de Neurofisiologia, Departamento de Ciências Fisiológicas, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro 20550-170, RJ, Brazil; (A.R.-V.); (A.C.D.-T.); (T.P.S.); (K.A.S.); (C.C.F.); (A.C.M.)
| | - Keila A. Semeão
- Laboratório de Neurofisiologia, Departamento de Ciências Fisiológicas, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro 20550-170, RJ, Brazil; (A.R.-V.); (A.C.D.-T.); (T.P.S.); (K.A.S.); (C.C.F.); (A.C.M.)
| | - Claudio C. Filgueiras
- Laboratório de Neurofisiologia, Departamento de Ciências Fisiológicas, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro 20550-170, RJ, Brazil; (A.R.-V.); (A.C.D.-T.); (T.P.S.); (K.A.S.); (C.C.F.); (A.C.M.)
| | - Anderson Ribeiro-Carvalho
- Departamento de Ciências, Faculdade de Formação de Professores da Universidade do Estado do Rio de Janeiro, São Gonçalo 24435-005, RJ, Brazil;
| | - Alex C. Manhães
- Laboratório de Neurofisiologia, Departamento de Ciências Fisiológicas, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro 20550-170, RJ, Brazil; (A.R.-V.); (A.C.D.-T.); (T.P.S.); (K.A.S.); (C.C.F.); (A.C.M.)
| | - Yael Abreu-Villaça
- Laboratório de Neurofisiologia, Departamento de Ciências Fisiológicas, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro 20550-170, RJ, Brazil; (A.R.-V.); (A.C.D.-T.); (T.P.S.); (K.A.S.); (C.C.F.); (A.C.M.)
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11
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Long CC, Antevska A, Mast DH, Okyem S, Sweedler JV, Do TD. Nonenzymatic Posttranslational Modifications and Peptide Cleavages Observed in Peptide Epimers. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:1898-1907. [PMID: 37102735 PMCID: PMC10524105 DOI: 10.1021/jasms.3c00092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Posttranslational modifications (PTMs) play vital roles in cellular homeostasis and are implicated in various pathological conditions. This work uses two ion mobility spectrometry-mass spectrometry (IMS-MS) modalities, drift-tube IMS (DT-IMS) and trapped IMS (TIMS), to characterize three important nonenzymatic PTMs that induce no mass loss: l/d isomerization, aspartate/isoaspartate isomerization, and cis/trans proline isomerization. These PTMs are assessed in a single peptide system, the recently discovered pleurin peptides, Plrn2, from Aplysia californica. We determine that the DT-IMS-MS/MS can capture and locate asparagine deamidation into aspartate and its subsequent isomerization to isoaspartate, a key biomarker for age-related diseases. Additionally, nonenzymatic peptide cleavage via in-source fragmentation is evaluated for differences in the intensities and patterns of fragment peaks between these PTMs. Peptide fragments resulting from in-source fragmentation, preceded by peptide denaturation by liquid chromatography (LC) mobile phase, exhibited cis/trans proline isomerization. Finally, the effects of differing the fragmentation voltage at the source and solution-based denaturation conditions on in-source fragmentation profiles are evaluated, confirming that LC denaturation and in-source fragmentation profoundly impact N-terminal peptide bond cleavages of Plrn2 and the structures of their fragment ions. With that, LC-IMS-MS/MS coupled with in-source fragmentation could be a robust method to identify three important posttranslational modifications: l/d isomerization, Asn-deamidation leading to Asp/IsoAsp isomerization, and cis/trans proline isomerization.
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Affiliation(s)
- Connor C. Long
- Department of Biochemistry, Cellular, and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | | | - David H. Mast
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, 61801
| | - Samuel Okyem
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, 61801
| | - Jonathan V. Sweedler
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, 61801
| | - Thanh D. Do
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996, USA
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12
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Wang R, Lu KP, Zhou XZ. Function and regulation of cis P-tau in the pathogenesis and treatment of conventional and nonconventional tauopathies. J Neurochem 2023; 166:904-914. [PMID: 37638382 DOI: 10.1111/jnc.15909] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 06/02/2023] [Accepted: 06/22/2023] [Indexed: 08/29/2023]
Abstract
Conventional tauopathies are a group of disease characterized by tau inclusions in the brains, including Alzheimer's disease (AD), Pick's disease (PiD), progressive supranuclear palsy (PSP), corticobasal degeneration (CBD), and certain types of frontotemporal dementia (FTD), among which AD is the most prevalent. Extensive post-translational modifications, especially hyperphosphorylation, and abnormal aggregation of tau protein underlie tauopathy. Cis-trans isomerization of protein plays an important role in protein folding, function, and degradation, which is regulated by peptidyl-proline isomerases (PPIases). Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (Pin1), the only PPIase found to isomerize Pro following phosphorylated Ser or Thr residues, alters phosphorylated tau protein conformation at pT231-P motif. The cis P-tau but not trans P-tau serves as an early driver of multiple neurodegenerative disease, encompassing AD, traumatic brain injury (TBI), chronic traumatic encephalopathy (CTE), and vascular contributions to cognitive impairment and dementia (VCID). Cis but not trans P-tau is resistant to protein dephosphorylation and degradation, and also prone to protein aggregation. Cis P-tau loses its ability to stabilize microtubule, causing and spreading tauopathy mainly in axons, a pathological process called cistauosis. The conformation-specific monoclonal antibody that targets only the cis P-tau serves as a very early diagnosis method and a potential treatment of not only conventional tauopathies but also nonconventional tauopathies such as VCID, with clinical trials ongoing. Notably, cis P-tau antibody is the only clinical-stage Alzheimer's therapeutic that has shown the efficacy in animal models of not only AD but also TBI and stroke, which are very early stages of dementia. Here we review the identification and pathological consequences of cis pt231-tau, the role of its regulator Pin1, as well as the clinical implication of cis pt231-tau conformation-specific antibody in conventional and nonconventional tauopathies.
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Affiliation(s)
- Ruizhi Wang
- Departments of Biochemistry and Oncology, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
- Robarts Research Institute, Western University, London, Ontario, Canada
| | - Kun Ping Lu
- Departments of Biochemistry and Oncology, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
- Robarts Research Institute, Western University, London, Ontario, Canada
| | - Xiao Zhen Zhou
- Departments of Biochemistry and Oncology, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
- Department of Pathology and Laboratory Medicine, and Oncology, Western University, London, Ontario, Canada
- Lawson Health Research Institute, Western University, London, Ontario, Canada
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13
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Muñoz-Muñoz PLA, Mares-Alejandre RE, Meléndez-López SG, Ramos-Ibarra MA. Structural Insights into the Giardia lamblia Target of Rapamycin Homolog: A Bioinformatics Approach. Int J Mol Sci 2023; 24:11992. [PMID: 37569368 PMCID: PMC10418948 DOI: 10.3390/ijms241511992] [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: 06/02/2023] [Revised: 07/18/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
TOR proteins, also known as targets of rapamycin, are serine/threonine kinases involved in various signaling pathways that regulate cell growth. The protozoan parasite Giardia lamblia is the causative agent of giardiasis, a neglected infectious disease in humans. In this study, we used a bioinformatics approach to examine the structural features of GTOR, a G. lamblia TOR-like protein, and predict functional associations. Our findings confirmed that it shares significant similarities with functional TOR kinases, including a binding domain for the FKBP-rapamycin complex and a kinase domain resembling that of phosphatidylinositol 3-kinase-related kinases. In addition, it can form multiprotein complexes such as TORC1 and TORC2. These results provide valuable insights into the structure-function relationship of GTOR, highlighting its potential as a molecular target for controlling G. lamblia cell proliferation. Furthermore, our study represents a step toward rational drug design for specific anti-giardiasis therapeutic agents.
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Affiliation(s)
| | - Rosa E. Mares-Alejandre
- Biotechnology and Biosciences Research Group, School of Chemical Sciences and Engineering, Autonomous University of Baja California, Tijuana 22390, Mexico; (P.L.A.M.-M.); (S.G.M.-L.); (M.A.R.-I.)
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14
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Debowski AW, Bzdyl NM, Thomas DR, Scott NE, Jenkins CH, Iwasaki J, Kibble EA, Khoo CA, Scheuplein NJ, Seibel PM, Lohr T, Metters G, Bond CS, Norville IH, Stubbs KA, Harmer NJ, Holzgrabe U, Newton HJ, Sarkar-Tyson M. Macrophage infectivity potentiator protein, a peptidyl prolyl cis-trans isomerase, essential for Coxiella burnetii growth and pathogenesis. PLoS Pathog 2023; 19:e1011491. [PMID: 37399210 DOI: 10.1371/journal.ppat.1011491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 06/14/2023] [Indexed: 07/05/2023] Open
Abstract
Coxiella burnetii is a Gram-negative intracellular pathogen that causes the debilitating disease Q fever, which affects both animals and humans. The only available human vaccine, Q-Vax, is effective but has a high risk of severe adverse reactions, limiting its use as a countermeasure to contain outbreaks. Therefore, it is essential to identify new drug targets to treat this infection. Macrophage infectivity potentiator (Mip) proteins catalyse the folding of proline-containing proteins through their peptidyl prolyl cis-trans isomerase (PPIase) activity and have been shown to play an important role in the virulence of several pathogenic bacteria. To date the role of the Mip protein in C. burnetii pathogenesis has not been investigated. This study demonstrates that CbMip is likely to be an essential protein in C. burnetii. The pipecolic acid derived compounds, SF235 and AN296, which have shown utility in targeting other Mip proteins from pathogenic bacteria, demonstrate inhibitory activities against CbMip. These compounds were found to significantly inhibit intracellular replication of C. burnetii in both HeLa and THP-1 cells. Furthermore, SF235 and AN296 were also found to exhibit antibiotic properties against both the virulent (Phase I) and avirulent (Phase II) forms of C. burnetii Nine Mile Strain in axenic culture. Comparative proteomics, in the presence of AN296, revealed alterations in stress responses with H2O2 sensitivity assays validating that Mip inhibition increases the sensitivity of C. burnetii to oxidative stress. In addition, SF235 and AN296 were effective in vivo and significantly improved the survival of Galleria mellonella infected with C. burnetii. These results suggest that unlike in other bacteria, Mip in C. burnetii is required for replication and that the development of more potent inhibitors against CbMip is warranted and offer potential as novel therapeutics against this pathogen.
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Affiliation(s)
- Aleksandra W Debowski
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Nedlands, Western Australia, Australia
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | - Nicole M Bzdyl
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Nedlands, Western Australia, Australia
| | - David R Thomas
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
- Infection and Immunity Program, Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Nichollas E Scott
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | | | - Jua Iwasaki
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Nedlands, Western Australia, Australia
- Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Nedlands, Western Australia, Australia
- Centre for Child Health Research, University of Western Australia, Perth, Western Australia, Australia
| | - Emily A Kibble
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Nedlands, Western Australia, Australia
- School of Veterinary and Life Sciences, Murdoch University, Perth, WA, Australia
- DMTC Limited, Level 1, Kew, Australia
| | - Chen Ai Khoo
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Nicolas J Scheuplein
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Pamela M Seibel
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | - Theresa Lohr
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Georgie Metters
- Defence Science and Technology Laboratory, Porton Down, Salisbury, United Kingdom
- Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, United Kingdom
| | - Charles S Bond
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | - Isobel H Norville
- Defence Science and Technology Laboratory, Porton Down, Salisbury, United Kingdom
- Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, United Kingdom
| | - Keith A Stubbs
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | - Nicholas J Harmer
- Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, United Kingdom
- Living Systems Institute, Stocker Road Exeter, United Kingdom
| | - Ulrike Holzgrabe
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Hayley J Newton
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
- Infection and Immunity Program, Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Mitali Sarkar-Tyson
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Nedlands, Western Australia, Australia
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15
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Soto OB, Ramirez CS, Koyani R, Rodriguez-Palomares IA, Dirmeyer JR, Grajeda B, Roy S, Cox MB. Structure and function of the TPR-domain immunophilins FKBP51 and FKBP52 in normal physiology and disease. J Cell Biochem 2023:10.1002/jcb.30406. [PMID: 37087733 PMCID: PMC10903107 DOI: 10.1002/jcb.30406] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 03/22/2023] [Accepted: 04/04/2023] [Indexed: 04/24/2023]
Abstract
Coordinated cochaperone interactions with Hsp90 and associated client proteins are crucial for a multitude of signaling pathways in normal physiology, as well as in disease settings. Research on the molecular mechanisms regulated by the Hsp90 multiprotein complexes has demonstrated increasingly diverse roles for cochaperones throughout Hsp90-regulated signaling pathways. Thus, the Hsp90-associated cochaperones have emerged as attractive therapeutic targets in a wide variety of disease settings. The tetratricopeptide repeat (TPR)-domain immunophilins FKBP51 and FKBP52 are of special interest among the Hsp90-associated cochaperones given their Hsp90 client protein specificity, ubiquitous expression across tissues, and their increasingly important roles in neuronal signaling, intracellular calcium release, peptide bond isomerization, viral replication, steroid hormone receptor function, and cell proliferation to name a few. This review summarizes the current knowledge of the structure and molecular functions of TPR-domain immunophilins FKBP51 and FKBP52, recent findings implicating these immunophilins in disease, and the therapeutic potential of targeting FKBP51 and FKBP52 for the treatment of disease.
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Affiliation(s)
- Olga B. Soto
- Border Biomedical Research Center and Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968
| | - Christian S. Ramirez
- Border Biomedical Research Center and Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968
| | - Rina Koyani
- Border Biomedical Research Center and Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968
| | - Isela A. Rodriguez-Palomares
- Border Biomedical Research Center and Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968
| | - Jessica R. Dirmeyer
- Border Biomedical Research Center and Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968
| | - Brian Grajeda
- Border Biomedical Research Center and Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968
| | - Sourav Roy
- Border Biomedical Research Center and Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968
| | - Marc B. Cox
- Border Biomedical Research Center and Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Texas at El Paso, El Paso, TX 79968
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16
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Ramirez LM, Zweckstetter M. Molecular-level interplay between intrinsically disordered clients and Hsp90. Curr Opin Chem Biol 2023; 74:102304. [PMID: 37068388 DOI: 10.1016/j.cbpa.2023.102304] [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: 01/31/2023] [Revised: 03/13/2023] [Accepted: 03/15/2023] [Indexed: 04/19/2023]
Abstract
Proteostasis is maintained by a network of molecular chaperones, a prominent member of which is the 90-kilodalton heat shock protein Hsp90. The chaperone function of Hsp90 has been extensively reviewed previously, emphasizing its ATPase activity and remodeling of folded client proteins. Experimental evidence implicating Hsp90 in neurodegenerative diseases has bolstered interest in the noncanonical chaperoning of intrinsically disordered protein (IDPs), however the interplay between Hsp90 and its disordered clients remains poorly understood. In this review we describe recent advances that have contributed to our understanding of the intricate mechanisms characterizing Hsp90-mediated chaperoning of the IDPs tau and α-synuclein and survey emerging insights into the modulation of the chaperone-client interplay in the context of neurodegeneration.
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Affiliation(s)
- Lisa Marie Ramirez
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075 Gӧttingen, Germany
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075 Gӧttingen, Germany; Department for NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Gӧttingen, Germany.
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17
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Afsari F, McIntyre TM. D-2-Hydroxyglutarate Inhibits Calcineurin Phosphatase Activity to Abolish NF-AT Activation and IL-2 Induction in Stimulated Lymphocytes. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:504-514. [PMID: 36602551 PMCID: PMC11071645 DOI: 10.4049/jimmunol.2200050] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 12/08/2022] [Indexed: 01/06/2023]
Abstract
Gliomas expressing mutant isocitrate dehydrogenases excessively synthesize d-2-hydroxyglutarate (D2HG), suppressing immune surveillance. A portion of this D2HG is released from these tumor cells, but the way environmental D2HG inhibits lymphocyte function is undefined. We incubated human PBLs or Jurkat T cells with D2HG at concentrations present within and surrounding gliomas or its obverse l-2-hydroxyglutarate (L2HG) stereoisomer. We quantified each 2HG stereoisomer within washed cells by N-(p-toluenesulfonyl)-l-phenylalanyl chloride derivatization with stable isotope-labeled D2HG and L2HG internal standards, HPLC separation, and mass spectrometry. D2HG was present in quiescent cells and was twice as abundant as L2HG. Extracellular 2HG rapidly increased intracellular levels of the provided stereoisomer by a stereoselective, concentration-dependent process. IL-2 expression, even when elicited by A23187 and PMA, was abolished by D2HG in a concentration-dependent manner, with significant reduction at just twice its basal level. In contrast, L2HG was only moderately inhibitory. IL-2 expression is regulated by increased intracellular Ca2+ that stimulates calcineurin to dephosphorylate cytoplasmic phospho-NF-AT, enabling its nuclear translocation. D2HG abolished stimulated expression of a stably integrated NF-AT-driven luciferase reporter that precisely paralleled its concentration-dependent inhibition of IL-2. D2HG did not affect intracellular Ca2+. Rather, surface plasmon resonance showed D2HG, but not L2HG, bound calcineurin, and D2HG, but not L2HG, inhibited Ca2+-dependent calcineurin phosphatase activity in stimulated Jurkat extracts. Thus, D2HG is a stereoselective calcineurin phosphatase inhibitor that prevents NF-AT dephosphorylation and so abolishes IL-2 transcription in stimulated lymphocytes. This occurs at D2HG concentrations found within and adjacent to gliomas independent of its metabolic or epigenetic transcriptional regulation.
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Affiliation(s)
- Faezeh Afsari
- Department of Biological, Geological, and Environmental Sciences, Cleveland State University, Cleveland, OH, USA
| | - Thomas M. McIntyre
- Department of Biological, Geological, and Environmental Sciences, Cleveland State University, Cleveland, OH, USA
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
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18
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Dipten L, Amenti, Rajkrishna M. Molecular docking analysis of juglone with parvulin-type PPiase PrsA from Staphylococcus aureus. Bioinformation 2023; 19:48-52. [PMID: 37720298 PMCID: PMC10504509 DOI: 10.6026/97320630019048] [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: 01/01/2023] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 09/19/2023] Open
Abstract
Staphylococcus aureus is an opportunistic pathogen that causes variety of infections range from mild skin diseases to life-threatening sepsis. It is also notorious for acquiring resistance to numerous antibiotics. Parvulin-type peptidyl-prolyl cis-trans isomerase (PPiase) domain containing PrsA protein is considered as an essential folding factor for secreted proteins of Gram-positive bacteria. Therefore, it is considered as a potential target for anti-staphylococcal drug discovery. Juglone, plant-derived 1,4-naphthoquinone, shows confirmed antitumor and antibacterial activities. Destruction of bacterial biofilm, inhibition of enzyme expression, degradation of nucleic acids, and other pathways are likely the major possible mechanisms for Staphylococcus aureus inactivation by juglone. Selective inhibition of parvulin type PPiase by juglone has been proven biochemically. However, detail structural information of parvulin-juglone interaction and mechanism of enzymatic inhibition till unexplored. Past hypothesis on inactivation of parvulin type PPiase due to covalent attachment of juglone molecules to its cysteine residues is not acceptable for the S. aureus PrsA parvulin domain as that lacks cysteine. Docking studies showed that juglone binds to the active site residues of S. aureus PrsA parvulin domain involved in enzymatic reaction. Active site conserved histidine residue of parvulin may be involved in juglone interaction as it was found to be the common interactive residue in majority of docking complexes. Data shows Juglone possibly inhibits parvulin type PPiase through competitive inhibition mechanism. Subtle differences of juglone interactions with other orthologous parvulin domains will help to develop semisynthetic drug with higher specificity against S. aureus.
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Affiliation(s)
- Laskar Dipten
- Department of Biotechnology, Nagaland University, Dimapur, Nagaland-797112, India
| | - Amenti
- Department of Biotechnology, Nagaland University, Dimapur, Nagaland-797112, India
| | - Mondal Rajkrishna
- Department of Biotechnology, Nagaland University, Dimapur, Nagaland-797112, India
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19
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Barge S, Jade D, Ayyamperumal S, Manna P, Borah J, Nanjan CMJ, Nanjan MJ, Talukdar NC. Potential inhibitors for FKBP51: an in silico study using virtual screening, molecular docking and molecular dynamics simulation. J Biomol Struct Dyn 2022; 40:13799-13811. [PMID: 34709133 DOI: 10.1080/07391102.2021.1994877] [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] [Indexed: 12/29/2022]
Abstract
Over the years, FK506-binding proteins have been targeted for different pharmaceutical interests. The FK506-binding protein, encoded by the FKBP5 gene, is responsible for stress and metabolic-related disorders, including cancer. In addition, the FKBD-I domain of the protein is a potential target for endocrine-related physiological diseases. In the present study, a set of natural compounds from the ZINC database was screened against FKBP51 protein using in silico strategy, namely pharmacophore modeling, molecular docking, and molecular dynamic simulation. A protein-ligand-based pharmacophore model workflow was employed to identify small molecules. The resultant compounds were then assessed for their toxicity using ADMET prediction. Based on ADMET prediction, 4768 compounds were selected for molecular docking to elucidate their binding mode. Based on the binding energy, 857 compounds were selected, and their Similarity Tanimoto coefficient was calculated, followed by clustering according to Jarvis-Patrick clustering methods (Jarp). The clustered singletons resulted in 14 hit compounds. The top 05 hit compounds and 05 known compounds were then subjected to 100 ns MD simulation to check the stability of complexes. The study revealed that the selected complexes are stable throughout the 100 ns simulation; for FKBD-I (4TW6), crystal structure compared with FKBP-51 (1KT0) crystal structure. Finally, the binding free energies of the hit complexes were calculated using molecular mechanics energies combined with Poisson-Boltzmann. The data reveal that all the complexes show negative BFEs, indicating a good affinity of the hit compounds to the protein. The top five compounds are, therefore, potential inhibitors for FKBP51. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sagar Barge
- Biochemistry and Drug Discovery Lab, Institute of Advanced Study in Science and Technology, Assam, India.,Department of Molecular Biology and Biotechnology, Cotton University, Panbazar, Assam, India
| | - Dhananjay Jade
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, Ooty, Tamil Nadu, India
| | - Selvaraj Ayyamperumal
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, Ooty, Tamil Nadu, India
| | - Prasenjit Manna
- Biochemistry and Drug Discovery Lab, Institute of Advanced Study in Science and Technology, Assam, India
| | - Jagat Borah
- Biochemistry and Drug Discovery Lab, Institute of Advanced Study in Science and Technology, Assam, India
| | | | | | - Narayan Chandra Talukdar
- Biochemistry and Drug Discovery Lab, Institute of Advanced Study in Science and Technology, Assam, India.,Assam Down Town University, Panikhaiti, Guwahati, Assam, India
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20
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Dewanjee S, Chakraborty P, Bhattacharya H, Chacko L, Singh B, Chaudhary A, Javvaji K, Pradhan SR, Vallamkondu J, Dey A, Kalra RS, Jha NK, Jha SK, Reddy PH, Kandimalla R. Altered glucose metabolism in Alzheimer's disease: Role of mitochondrial dysfunction and oxidative stress. Free Radic Biol Med 2022; 193:134-157. [PMID: 36206930 DOI: 10.1016/j.freeradbiomed.2022.09.032] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/16/2022] [Accepted: 09/29/2022] [Indexed: 12/06/2022]
Abstract
Increasing evidence suggests that abnormal cerebral glucose metabolism is largely present in Alzheimer's disease (AD). The brain utilizes glucose as its main energy source and a decline in its metabolism directly reflects on brain function. Weighing on recent evidence, here we systematically assessed the aberrant glucose metabolism associated with amyloid beta and phosphorylated tau accumulation in AD brain. Interlink between insulin signaling and AD highlighted the involvement of the IRS/PI3K/Akt/AMPK signaling, and GLUTs in the disease progression. While shedding light on the mitochondrial dysfunction in the defective glucose metabolism, we further assessed functional consequences of AGEs (advanced glycation end products) accumulation, polyol activation, and other contributing factors including terminal respiration, ROS (reactive oxygen species), mitochondrial permeability, PINK1/parkin defects, lysosome-mitochondrial crosstalk, and autophagy/mitophagy. Combined with the classic plaque and tangle pathologies, glucose hypometabolism with acquired insulin resistance and mitochondrial dysfunction potentiate these factors to exacerbate AD pathology. To this end, we further reviewed AD and DM (diabetes mellitus) crosstalk in disease progression. Taken together, the present work discusses the emerging role of altered glucose metabolism, contributing impact of insulin signaling, and mitochondrial dysfunction in the defective cerebral glucose utilization in AD.
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Affiliation(s)
- Saikat Dewanjee
- Advanced Pharmacognosy Research Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700 032, West Bengal, India
| | - Pratik Chakraborty
- Advanced Pharmacognosy Research Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700 032, West Bengal, India
| | - Hiranmoy Bhattacharya
- Advanced Pharmacognosy Research Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700 032, West Bengal, India
| | - Leena Chacko
- BioAnalytical Lab, Meso Scale Discovery, 1601 Research Blvd, Rockville, MD, USA
| | - Birbal Singh
- ICAR-Indian Veterinary Research Institute (IVRI), Regional Station, Palampur, 176061, Himachal Pradesh, India
| | - Anupama Chaudhary
- Orinin-BioSystems, LE-52, Lotus Road 4, CHD City, Karnal, 132001, Haryana, India
| | - Kalpana Javvaji
- CSIR-Indian Institute of Chemical Technology, Uppal Road, Tarnaka, India
| | | | | | - Abhijit Dey
- Department of Life Sciences, Presidency University, Kolkata, 700073, India
| | - Rajkumar Singh Kalra
- Immune Signal Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, 9040495, Japan
| | - Niraj Kumar Jha
- Department of Biotechnology, School of Engineering & Technology (SET), Sharda University, UP, 201310, India; Department of Biotechnology Engineering and Food Technology, Chandigarh University, Mohali, 140413, India; Department of Biotechnology, School of Applied & Life Sciences (SALS), Uttaranchal University, Dehradun, 248007, India
| | - Saurabh Kumar Jha
- Department of Biotechnology, School of Engineering & Technology (SET), Sharda University, UP, 201310, India; Department of Biotechnology Engineering and Food Technology, Chandigarh University, Mohali, 140413, India; Department of Biotechnology, School of Applied & Life Sciences (SALS), Uttaranchal University, Dehradun, 248007, India
| | - P Hemachandra Reddy
- Internal Medicine Department, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Neuroscience & Pharmacology, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Neurology Departments School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Public Health Department of Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Department of Speech, Language and Hearing Sciences, School Health Professions, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Ramesh Kandimalla
- CSIR-Indian Institute of Chemical Technology, Uppal Road, Tarnaka, India; Department of Biochemistry, Kakatiya Medical College, Warangal, India.
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21
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Peterson AA, Rangwala AM, Thakur MK, Ward PS, Hung C, Outhwaite IR, Chan AI, Usanov DL, Mootha VK, Seeliger MA, Liu DR. Discovery and molecular basis of subtype-selective cyclophilin inhibitors. Nat Chem Biol 2022; 18:1184-1195. [PMID: 36163383 PMCID: PMC9596378 DOI: 10.1038/s41589-022-01116-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 07/19/2022] [Indexed: 11/25/2022]
Abstract
Although cyclophilins are attractive targets for probing biology and therapeutic intervention, no subtype-selective cyclophilin inhibitors have been described. We discovered novel cyclophilin inhibitors from the in vitro selection of a DNA-templated library of 256,000 drug-like macrocycles for cyclophilin D (CypD) affinity. Iterated macrocycle engineering guided by ten X-ray co-crystal structures yielded potent and selective inhibitors (half maximal inhibitory concentration (IC50) = 10 nM) that bind the active site of CypD and also make novel interactions with non-conserved residues in the S2 pocket, an adjacent exo-site. The resulting macrocycles inhibit CypD activity with 21- to >10,000-fold selectivity over other cyclophilins and inhibit mitochondrial permeability transition pore opening in isolated mitochondria. We further exploited S2 pocket interactions to develop the first cyclophilin E (CypE)-selective inhibitor, which forms a reversible covalent bond with a CypE S2 pocket lysine, and exhibits 30- to >4,000-fold selectivity over other cyclophilins. These findings reveal a strategy to generate isoform-selective small-molecule cyclophilin modulators, advancing their suitability as targets for biological investigation and therapeutic development.
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Affiliation(s)
- Alexander A Peterson
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Aziz M Rangwala
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Manish K Thakur
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Patrick S Ward
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Christie Hung
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Ian R Outhwaite
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Alix I Chan
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Dmitry L Usanov
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Vamsi K Mootha
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Markus A Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, USA.
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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22
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Carius Y, Ries F, Gries K, Trentmann O, Lancaster CRD, Willmund F. Structural features of chloroplast trigger factor determined at 2.6 Å resolution. Acta Crystallogr D Struct Biol 2022; 78:1259-1272. [PMID: 36189745 PMCID: PMC9527764 DOI: 10.1107/s2059798322009068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 09/11/2022] [Indexed: 11/21/2022] Open
Abstract
The folding of newly synthesized polypeptides requires the coordinated action of molecular chaperones. Prokaryotic cells and the chloroplasts of plant cells possess the ribosome-associated chaperone trigger factor, which binds nascent polypeptides at their exit stage from the ribosomal tunnel. The structure of bacterial trigger factor has been well characterized and it has a dragon-shaped conformation, with flexible domains responsible for ribosome binding, peptidyl-prolyl cis-trans isomerization (PPIase) activity and substrate protein binding. Chloroplast trigger-factor sequences have diversified from those of their bacterial orthologs and their molecular mechanism in plant organelles has been little investigated to date. Here, the crystal structure of the plastidic trigger factor from the green alga Chlamydomonas reinhardtii is presented at 2.6 Å resolution. Due to the high intramolecular flexibility of the protein, diffraction to this resolution was only achieved using a protein that lacked the N-terminal ribosome-binding domain. The eukaryotic trigger factor from C. reinhardtii exhibits a comparable dragon-shaped conformation to its bacterial counterpart. However, the C-terminal chaperone domain displays distinct charge distributions, with altered positioning of the helical arms and a specifically altered charge distribution along the surface responsible for substrate binding. While the PPIase domain shows a highly conserved structure compared with other PPIases, its rather weak activity and an unusual orientation towards the C-terminal domain points to specific adaptations of eukaryotic trigger factor for function in chloroplasts.
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Affiliation(s)
- Yvonne Carius
- Department of Structural Biology, Saarland University, Center of Human and Molecular Biology (ZHMB), Faculty of Medicine, Building 60, 66421 Homburg, Germany
| | - Fabian Ries
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Erwin-Schrödinger-Strasse 70, 67663 Kaiserslautern, Germany
| | - Karin Gries
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Erwin-Schrödinger-Strasse 70, 67663 Kaiserslautern, Germany
| | - Oliver Trentmann
- Molecular Botany, University of Kaiserslautern, Erwin-Schrödinger-Strasse 70, 67663 Kaiserslautern, Germany
| | - C. Roy D. Lancaster
- Department of Structural Biology, Saarland University, Center of Human and Molecular Biology (ZHMB), Faculty of Medicine, Building 60, 66421 Homburg, Germany
| | - Felix Willmund
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Erwin-Schrödinger-Strasse 70, 67663 Kaiserslautern, Germany
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23
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Singh AK, Saharan K, Baral S, Vasudevan D. The plant nucleoplasmin AtFKBP43 needs its extended arms for histone interaction. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194872. [PMID: 36058470 DOI: 10.1016/j.bbagrm.2022.194872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 08/20/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
The nucleoplasmin family of histone chaperones is a key player in governing the dynamic architecture of chromatin, thereby regulating various DNA-templated processes. The crystal structure of the N-terminal domain of Arabidopsis thaliana FKBP43 (AtFKBP43), an FK506-binding immunophilin protein, revealed a characteristic nucleoplasmin fold, thus confirming it to be a member of the FKBP nucleoplasmin class. Small-Angle X-ray Scattering (SAXS) analyses confirmed its pentameric nature in solution, and additional studies confirmed the nucleoplasmin fold to be highly stable. Unlike its homolog AtFKBP53, the AtFKBP43 nucleoplasmin core domain could not interact with histones and required the acidic arms, C-terminal to the core, for histone association. However, SAXS generated low-resolution envelope structure, ITC, and AUC results revealed that an AtFKBP43 pentamer with C-terminal extensions interacts with H2A/H2B dimer and H3/H4 tetramer in an equimolar ratio, like AtFKBP53. Put together, AtFKBP43 belongs to a hitherto unreported subclass of FKBP nucleoplasmins that requires the C-terminal acidic stretches emanating from the core domain for histone interaction.
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Affiliation(s)
| | - Ketul Saharan
- Institute of Life Sciences, Bhubaneswar 751023, India; Regional Centre for Biotechnology, Faridabad 121001, India
| | - Somanath Baral
- Institute of Life Sciences, Bhubaneswar 751023, India; School of Biotechnology, KIIT University, Bhubaneswar 751024, India
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24
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Schiene‐Fischer C, Fischer G, Braun M. Non-Immunosuppressive Cyclophilin Inhibitors. Angew Chem Int Ed Engl 2022; 61:e202201597. [PMID: 35290695 PMCID: PMC9804594 DOI: 10.1002/anie.202201597] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Indexed: 01/05/2023]
Abstract
Cyclophilins, enzymes with peptidyl-prolyl cis/trans isomerase activity, are relevant to a large variety of biological processes. The most abundant member of this enzyme family, cyclophilin A, is the cellular receptor of the immunosuppressive drug cyclosporine A (CsA). As a consequence of the pathophysiological role of cyclophilins, particularly in viral infections, there is a broad interest in cyclophilin inhibition devoid of immunosuppressive activity. This Review first gives an introduction into the physiological and pathophysiological roles of cyclophilins. The presentation of non-immunosuppressive cyclophilin inhibitors will commence with drugs based on chemical modifications of CsA. The naturally occurring macrocyclic sanglifehrins have become other lead structures for cyclophilin-inhibiting drugs. Finally, de novo designed compounds, whose structures are not derived from or inspired by natural products, will be presented. Relevant synthetic concepts will be discussed, but the focus will also be on biochemical studies, structure-activity relationships, and clinical studies.
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Affiliation(s)
- Cordelia Schiene‐Fischer
- Institute of Biochemistry and BiotechnologyMartin-Luther-University Halle-Wittenberg06099Halle (Saale)Germany
| | - Gunter Fischer
- Max Planck Institute for Biophysical Chemistry37077GöttingenGermany
| | - Manfred Braun
- Institute of Organic and Macromolecular ChemistryHeinrich-Heine-University Düsseldorf40225DüsseldorfGermany
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25
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Lee YM, Teoh DEJ, Yeung K, Liou YC. The kingdom of the prolyl-isomerase Pin1: The structural and functional convergence and divergence of Pin1. Front Cell Dev Biol 2022; 10:956071. [PMID: 36111342 PMCID: PMC9468764 DOI: 10.3389/fcell.2022.956071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 07/11/2022] [Indexed: 11/28/2022] Open
Abstract
More than 20 years since its discovery, our understanding of Pin1 function in various diseases continues to improve. Pin1 plays a crucial role in pathogenesis and has been implicated in metabolic disorders, cardiovascular diseases, inflammatory diseases, viral infection, cancer and neurodegenerative diseases such as Alzheimer’s, Parkinson’s and Huntington’s disease. In particular, the role of Pin1 in neurodegenerative diseases and cancer has been extensively studied. Our understanding of Pin1 in cancer also led to the development of cancer therapeutic drugs targeting Pin1, with some currently in clinical trial phases. However, identifying a Pin1-specific drug with good cancer therapeutic effect remains elusive, thus leading to the continued efforts in Pin1 research. The importance of Pin1 is highlighted by the presence of Pin1 orthologs across various species: from vertebrates to invertebrates and Kingdom Animalia to Plantae. Among these Pin1 orthologs, their sequence and structural similarity demonstrate the presence of conservation. Moreover, their similar functionality between species further highlights the conservancy of Pin1. As researchers continue to unlock the mysteries of Pin1 in various diseases, using different Pin1 models might shed light on how to better target Pin1 for disease therapeutics. This review aims to highlight the various Pin1 orthologs in numerous species and their divergent functional roles. We will examine their sequence and structural similarities and discuss their functional similarities and uniqueness to demonstrate the interconnectivity of Pin1 orthologs in multiple diseases.
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26
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Liang L, Liu Y, Kang B, Wang R, Sun MY, Wu Q, Meng XF, Lin JP. Large-scale comparison of machine learning algorithms for target prediction of natural products. Brief Bioinform 2022; 23:6675751. [PMID: 36007240 DOI: 10.1093/bib/bbac359] [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: 02/09/2022] [Revised: 07/26/2022] [Accepted: 07/31/2022] [Indexed: 11/13/2022] Open
Abstract
Natural products (NPs) and their derivatives are important resources for drug discovery. There are many in silico target prediction methods that have been reported, however, very few of them distinguish NPs from synthetic molecules. Considering the fact that NPs and synthetic molecules are very different in many characteristics, it is necessary to build specific target prediction models of NPs. Therefore, we collected the activity data of NPs and their derivatives from the public databases and constructed four datasets, including the NP dataset, the NPs and its first-class derivatives dataset, the NPs and all its derivatives and the ChEMBL26 compounds dataset. Conditions, including activity thresholds and input features, were explored to access the performance of eight machine learning methods of target prediction of NPs, including support vector machines (SVM), extreme gradient boosting, random forests, K-nearest neighbor, naive Bayes, feedforward neural networks (FNN), convolutional neural networks and recurrent neural networks. As a result, the NPs and all their derivatives datasets were selected to build the best NP-specific models. Furthermore, the consensus models, as well as the voting models, were additionally applied to improve the prediction performance. More evaluations were made on the external validation set and the results demonstrated that (1) the NP-specific model performed better on the target prediction of NPs than the traditional models training on the whole compounds of ChEMBL26. (2) The consensus model of FNN + SVM possessed the best overall performance, and the voting model can significantly improve recall and specificity.
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Affiliation(s)
- Lu Liang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Ye Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Bo Kang
- National Supercomputer Center in Tianjin, 10 Xinhuanxi Road, Tianjin Binhai New Area, Tianjin 300457, China
| | - Ru Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Meng-Yu Sun
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Qi Wu
- National Supercomputer Center in Tianjin, 10 Xinhuanxi Road, Tianjin Binhai New Area, Tianjin 300457, China
| | - Xiang-Fei Meng
- National Supercomputer Center in Tianjin, 10 Xinhuanxi Road, Tianjin Binhai New Area, Tianjin 300457, China
| | - Jian-Ping Lin
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China.,Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China.,Platform of Pharmaceutical Intelligence, Tianjin International Joint Academy of Biomedicine, Tianjin 300457, China
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27
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Thadem N, Rajesh M, Balaboina H, Das S. Synthesis of bridgehead-azacycles via dual C-N/C-C annulation of α-amino acids, aminals and maleimides. Org Biomol Chem 2022; 20:6368-6383. [PMID: 35861324 DOI: 10.1039/d2ob01117d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis of various bridged azacyclic adducts has recently become a reemerging topic due to their bioactive and natural product mimic profiles. Accordingly, herein, we report a method for easy access to succinamide-bridged azacyclic derivatives through the metal-free polarization-controlled dual C-N/C-C annulation of readily available α-amino acids, 2-amino benzaldehydes or pyrrole/indole-2-aldehyde and maleimide substrates. This cascade features a rare dipolarophile-induced diastereo-selective amidative annulation, followed by 3 + 2 cycloaddition as key steps.
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Affiliation(s)
- Nagender Thadem
- Department of Organic Synthesis & Process Chemistry, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Manda Rajesh
- Department of Organic Synthesis & Process Chemistry, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India.
| | - Harikrishna Balaboina
- Department of Organic Synthesis & Process Chemistry, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India.
| | - Saibal Das
- Department of Organic Synthesis & Process Chemistry, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
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28
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Trivedi A, Gosai J, Nakane D, Shrivastava A. Design Principles of the Rotary Type 9 Secretion System. Front Microbiol 2022; 13:845563. [PMID: 35620107 PMCID: PMC9127263 DOI: 10.3389/fmicb.2022.845563] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 01/17/2022] [Indexed: 01/05/2023] Open
Abstract
The Fo ATP synthase, the bacterial flagellar motor, and the bacterial type 9 secretion system (T9SS) are the three known proton motive force driven biological rotary motors. In this review, we summarize the current information on the nuts and bolts of T9SS. Torque generation by T9SS, its role in gliding motility of bacteria, and the mechanism via which a T9SS-driven swarm shapes the microbiota are discussed. The knowledge gaps in our current understanding of the T9SS machinery are outlined.
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Affiliation(s)
- Abhishek Trivedi
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, United States
- Center for Biological Physics, Arizona State University, Tempe, AZ, United States
| | - Jitendrapuri Gosai
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, United States
- Center for Biological Physics, Arizona State University, Tempe, AZ, United States
| | - Daisuke Nakane
- Department of Engineering Science, The University of Electro-Communications, Tokyo, Japan
| | - Abhishek Shrivastava
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, United States
- Center for Biological Physics, Arizona State University, Tempe, AZ, United States
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29
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Relitti N, Saraswati AP, Carullo G, Papa A, Monti A, Benedetti R, Passaro E, Brogi S, Calderone V, Butini S, Gemma S, Altucci L, Campiani G, Doti N. Design and Synthesis of New Oligopeptidic Parvulin Inhibitors. ChemMedChem 2022; 17:e202200050. [PMID: 35357776 PMCID: PMC9321596 DOI: 10.1002/cmdc.202200050] [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: 01/24/2022] [Revised: 03/28/2022] [Indexed: 11/12/2022]
Abstract
Pin1 catalyzes the cis-trans isomerization of pThr-Pro or pSer-Pro amide bonds of different proteins involved in several physio/pathological processes. In this framework, recent research activity is directed towards the identification of new selective Pin1 inhibitors. Here, we developed a set ( 5a - p ) of peptide-based Pin1 inhibitors. Direct-binding experiments allowed the identification of the peptide-based inhibitor 5k as a potent ligand of Pin1. Notably, 5k binds Pin1 with a higher affinity compared to Pin4. The comparative analysis of molecular models of Pin1 and Pin4 with the selected compound, gave a rational explanation of the biochemical activity, and pinpointed the chemical elements that, if opportunely modified, may further improve inhibitory potency, pharmacological properties and selectivity of future peptide-based Parvulin inhibitors. Since 5k showed a limited cell penetration and no antiproliferative activity, it was conjugated to a polyarginine stretch, known to promote cell penetration of peptides, to obtain R8-5k derivative, which displayed an anti-proliferative effect on cancer cell lines compared to non-tumor cells. The effect of R8 on cell proliferation was also investigated. This work doubts the application of the R8 strategy for the development of cell penetrating antiproliferative peptides since it is not inert.
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Affiliation(s)
- Nicola Relitti
- University of Siena: Universita degli Studi di Siena, DBCF, ITALY
| | | | - Gabriele Carullo
- University of Siena: Universita degli Studi di Siena, DBCF, 2, Aldo Moro, 53100 Siena Italy, 53100, Siena, ITALY
| | - Alessandro Papa
- University of Siena: Universita degli Studi di Siena, DBCF, ITALY
| | | | - Rosaria Benedetti
- University of Campania Luigi Vanvitelli: Universita degli Studi della Campania Luigi Vanvitelli, Medicine, ITALY
| | - Eugenia Passaro
- University of Pisa Department of Pharmaceutical Sciences: Universita degli Studi di Pisa Dipartimento di Farmacia, Pharmacy, ITALY
| | - Simone Brogi
- University of Pisa Department of Pharmaceutical Sciences: Universita degli Studi di Pisa Dipartimento di Farmacia, Pharmacy, ITALY
| | - Vincenzo Calderone
- University of Pisa Department of Pharmaceutical Sciences: Universita degli Studi di Pisa Dipartimento di Farmacia, Pharmacy, ITALY
| | - Stefania Butini
- University of Siena: Universita degli Studi di Siena, DBCF, ITALY
| | - Sandra Gemma
- University of Siena: Universita degli Studi di Siena, DBCF, ITALY
| | - Lucia Altucci
- University of Campania Luigi Vanvitelli: Universita degli Studi della Campania Luigi Vanvitelli, Medicine, ITALY
| | - Giuseppe Campiani
- Universita degli Studi di Siena, Dipartimento di Biotecnologie, Via Aldo Moro 2, 53100, Siena, ITALY
| | - Nunzianna Doti
- CNR: Consiglio Nazionale delle Ricerche, Bioimaging, ITALY
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30
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Braun M, Schiene-Fischer C, Fischer G. Non‐Immunosuppressive Cyclophilin Inhibitors. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202201597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Manfred Braun
- Heinrich-Heine-Universität Düsseldorf: Heinrich-Heine-Universitat Dusseldorf Organic CHemistry Universitätsstr. 1 40225 Düsseldorf GERMANY
| | - Cordelia Schiene-Fischer
- Martin-Luther-Universität Halle-Wittenberg: Martin-Luther-Universitat Halle-Wittenberg Institute of Biochemistry and Biotechnology, GERMANY
| | - Gunter Fischer
- Max-Planck-Institut für Biophysikalische Chemie Abteilung Meiosis: Max-Planck-Institut fur Multidisziplinare Naturwissenschaften Abteilung Meiosis Max Planck Institute for Biophysical Chemistry GERMANY
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Time-Dependent Changes in Protein Composition of Medial Prefrontal Cortex in Rats with Neuropathic Pain. Int J Mol Sci 2022; 23:ijms23020955. [PMID: 35055141 PMCID: PMC8781622 DOI: 10.3390/ijms23020955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/10/2022] [Accepted: 01/14/2022] [Indexed: 01/03/2023] Open
Abstract
Chronic pain is associated with time-dependent structural and functional reorganization of the prefrontal cortex that may reflect adaptive pain compensatory and/or maladaptive pain-promoting mechanisms. However, the molecular underpinnings of these changes and whether there are time-dependent relationships to pain progression are not well characterized. In this study, we analyzed protein composition in the medial prefrontal cortex (mPFC) of rats at two timepoints after spinal nerve ligation (SNL) using two-dimensional gel electrophoresis (2D-ELFO) and liquid chromatography with tandem mass spectrometry (LC–MS/MS). SNL, but not sham-operated, rats developed persistent tactile allodynia and thermal hyperalgesia, confirming the presence of experimental neuropathic pain. Two weeks after SNL (early timepoint), we identified 11 proteins involved in signal transduction, protein transport, cell homeostasis, metabolism, and apoptosis, as well as heat-shock proteins and chaperones that were upregulated by more than 1.5-fold compared to the sham-operated rats. Interestingly, there were only four significantly altered proteins identified at 8 weeks after SNL (late timepoint). These findings demonstrate extensive time-dependent modifications of protein expression in the rat mPFC under a chronic neuropathic pain state that might underlie the evolution of chronic pain characterized by early pain-compensatory and later aberrant mechanisms.
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Vakilian M. A review on the effect of prolyl isomerization on immune response aberration and hypersensitivity reactions: A unifying hypothesis. Clin Immunol 2021; 234:108896. [PMID: 34848356 DOI: 10.1016/j.clim.2021.108896] [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: 08/27/2021] [Revised: 11/19/2021] [Accepted: 11/21/2021] [Indexed: 12/01/2022]
Abstract
Little is known about the causes and mechanisms of ectopic immune responses, including different types of hypersensitivity, superantigens, and cytokine storms. Two of the most questionable phenomena observed in immunology are why the intensity and extent of immune responses to different antigens are different, and why some self-antigens are attacked as foreign. The secondary structure of the peptides involved in the immune system, such as the epitope-paratope interfaces plays a pivotal role in the resulting immune responses. Prolyl cis/trans isomerization plays a fundamental role in the form of the secondary structure and the folding of proteins. This review covers some of the emerging evidence indicating the impact of prolyl isomerization on protein conformation, aberration of immune responses, and the development of hypersensitivity reactions.
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Affiliation(s)
- Mehrdad Vakilian
- Department of Cell Biology, Genetics and Physiology, University of Malaga (UMA), The Institute of Biomedical Research in Malaga (IBIMA), Málaga, Spain.
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Kolos JM, Pomplun S, Jung S, Rieß B, Purder PL, Voll AM, Merz S, Gnatzy M, Geiger TM, Quist-Løkken I, Jatzlau J, Knaus P, Holien T, Bracher A, Meyners C, Czodrowski P, Krewald V, Hausch F. Picomolar FKBP inhibitors enabled by a single water-displacing methyl group in bicyclic [4.3.1] aza-amides. Chem Sci 2021; 12:14758-14765. [PMID: 34820091 PMCID: PMC8597852 DOI: 10.1039/d1sc04638a] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 10/22/2021] [Indexed: 01/30/2023] Open
Abstract
Methyl groups can have profound effects in drug discovery but the underlying mechanisms are diverse and incompletely understood. Here we report the stereospecific effect of a single, solvent-exposed methyl group in bicyclic [4.3.1] aza-amides, robustly leading to a 2 to 10-fold increase in binding affinity for FK506-binding proteins (FKBPs). This resulted in the most potent and efficient FKBP ligands known to date. By a combination of co-crystal structures, isothermal titration calorimetry (ITC), density-functional theory (DFT), and 3D reference interaction site model (3D-RISM) calculations we elucidated the origin of the observed affinity boost, which was purely entropically driven and relied on the displacement of a water molecule at the protein-ligand-bulk solvent interface. The best compounds potently occupied FKBPs in cells and enhanced bone morphogenic protein (BMP) signaling. Our results show how subtle manipulation of the solvent network can be used to design atom-efficient ligands for difficult, solvent-exposed binding pockets.
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Affiliation(s)
- Jürgen M Kolos
- Department of Chemistry, Technical University of Darmstadt Alarich-Weiss-Straße 4 64293 Darmstadt Germany .,Max Planck Institute of Psychiatry Kraepelinstr. 2-10 80804 München Germany
| | - Sebastian Pomplun
- Max Planck Institute of Psychiatry Kraepelinstr. 2-10 80804 München Germany
| | - Sascha Jung
- Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie Otto-Hahn-Straße 6 44227 Dortmund Germany
| | - Benedikt Rieß
- Max Planck Institute of Psychiatry Kraepelinstr. 2-10 80804 München Germany
| | - Patrick L Purder
- Department of Chemistry, Technical University of Darmstadt Alarich-Weiss-Straße 4 64293 Darmstadt Germany
| | - Andreas M Voll
- Department of Chemistry, Technical University of Darmstadt Alarich-Weiss-Straße 4 64293 Darmstadt Germany
| | - Stephanie Merz
- Department of Chemistry, Technical University of Darmstadt Alarich-Weiss-Straße 4 64293 Darmstadt Germany
| | - Monika Gnatzy
- Department of Chemistry, Technical University of Darmstadt Alarich-Weiss-Straße 4 64293 Darmstadt Germany
| | - Thomas M Geiger
- Department of Chemistry, Technical University of Darmstadt Alarich-Weiss-Straße 4 64293 Darmstadt Germany
| | - Ingrid Quist-Løkken
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology 7491 Trondheim Norway.,Department of Immunology and Transfusion Medicine, St. Olav's University Hospital 7030 Trondheim Norway.,Department of Hematology, St. Olav's University Hospital 7030 Trondheim Norway
| | - Jerome Jatzlau
- Institute for Chemistry and Biochemistry, Freie Universität Berlin 14195 Berlin Germany
| | - Petra Knaus
- Institute for Chemistry and Biochemistry, Freie Universität Berlin 14195 Berlin Germany
| | - Toril Holien
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology 7491 Trondheim Norway.,Department of Immunology and Transfusion Medicine, St. Olav's University Hospital 7030 Trondheim Norway.,Department of Hematology, St. Olav's University Hospital 7030 Trondheim Norway
| | - Andreas Bracher
- Research Department Cellular Biochemistry, Max Planck Institute of Biochemistry Am Klopferspitz 18, 82152 Planegg Germany
| | - Christian Meyners
- Department of Chemistry, Technical University of Darmstadt Alarich-Weiss-Straße 4 64293 Darmstadt Germany
| | - Paul Czodrowski
- Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie Otto-Hahn-Straße 6 44227 Dortmund Germany
| | - Vera Krewald
- Department of Chemistry, Technical University of Darmstadt Alarich-Weiss-Straße 4 64293 Darmstadt Germany
| | - Felix Hausch
- Department of Chemistry, Technical University of Darmstadt Alarich-Weiss-Straße 4 64293 Darmstadt Germany
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34
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da Costa KS, Galúcio JM, de Jesus DA, Gomes GC, Lima E Lima AH, Taube PS, Dos Santos AM, Lameira J. Targeting Peptidyl-prolyl Cis-trans Isomerase NIMA-interacting 1: A Structure-based Virtual Screening Approach to Find Novel Inhibitors. Curr Comput Aided Drug Des 2021; 16:605-617. [PMID: 31654518 DOI: 10.2174/1573409915666191025114009] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 09/11/2019] [Accepted: 10/10/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (Pin1) is an enzyme that isomerizes phosphorylated serine or threonine motifs adjacent to proline residues. Pin1 has important roles in several cellular signaling pathways, consequently impacting the development of multiple types of cancers. METHODS Based on the previously reported inhibitory activity of pentacyclic triterpenoids isolated from the gum resin of Boswellia genus against Pin1, we designed a computational experiment using molecular docking, pharmacophore filtering, and structural clustering allied to molecular dynamics (MD) simulations and binding free energy calculations to explore the inhibitory activity of new triterpenoids against Pin1 structure. RESULTS Here, we report different computational evidence that triterpenoids from neem (Azadirachta indica A. Juss), such as 6-deacetylnimbinene, 6-Oacetylnimbandiol, and nimbolide, replicate the binding mode of the Pin1 substrate peptide, interacting with high affinity with the binding site and thus destabilizing the Pin1 structure. CONCLUSIONS Our results are supported by experimental data, and provide interesting structural insights into their molecular mechanism of action, indicating that their structural scaffolds could be used as a start point to develop new inhibitors against Pin1.
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Affiliation(s)
- Kauê Santana da Costa
- Institute of Biodiversity, Federal University of Western Para, Santarem, Para, Brazil
| | - João M Galúcio
- Institute of Biodiversity, Federal University of Western Para, Santarem, Para, Brazil
| | | | - Guelber Cardoso Gomes
- Institute of Pharmaceutical Sciences, Federal University of Para, 66075-110, Belem, Para, Brazil
| | | | - Paulo S Taube
- Institute of Biodiversity, Federal University of Western Para, Santarem, Para, Brazil
| | - Alberto M Dos Santos
- Institute of Biodiversity, Federal University of Western Para, Santarem, Para, Brazil
| | - Jerônimo Lameira
- Institute of Biological Sciences. Federal University of Para, 66075-110, Belem, Para, Brazil
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Gnatzy MT, Geiger TM, Kuehn A, Gutfreund N, Walz M, Kolos JM, Hausch F. Development of NanoBRET-Binding Assays for FKBP-Ligand Profiling in Living Cells. Chembiochem 2021; 22:2257-2261. [PMID: 33887102 PMCID: PMC8360185 DOI: 10.1002/cbic.202100113] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/20/2021] [Indexed: 11/11/2022]
Abstract
FK506-binding proteins (FKBPs) are promising targets for a variety of disorders and infectious diseases. High FKBP occupancy is thought to be necessary for ligands to effectively compete with the endogenous intracellular functions of FKBPs. Here, we report the development of NanoBRET assays for the most prominent cytosolic FKBPs, FKBP12, 12.6, 51 and 52. These assays allowed rapid profiling of FKBP ligands for target engagement and selectivity in living cells. These assays confirmed the selectivity of SAFit-type ligands for FKBP51 over FKBP52 but revealed a substantial offset for the intracellular activity of these ligands compared to bicyclic ligands or natural products. Our results stress the importance to control for intracellular FKBP occupancy and provide the assays to guide further FKBP ligand optimization.
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Affiliation(s)
- Monika T. Gnatzy
- Department Chemistry and Biochemistry Clemens-Schöpf-InstituteTechnical University DarmstadtAlarich-Weiss Straße 464287DarmstadtGermany
| | - Thomas M. Geiger
- Department Chemistry and Biochemistry Clemens-Schöpf-InstituteTechnical University DarmstadtAlarich-Weiss Straße 464287DarmstadtGermany
| | - Angela Kuehn
- Department Chemistry and Biochemistry Clemens-Schöpf-InstituteTechnical University DarmstadtAlarich-Weiss Straße 464287DarmstadtGermany
| | - Niklas Gutfreund
- Institute of Biophysical ChemistryCenter for Biomolecular Magnetic Resonance andCluster of Excellence Macromolecular Complexes (CEF)Goethe University FrankfurtMax-von-Laue-Straße 960438Frankfurt am MainGermany
| | - Michael Walz
- Department Chemistry and Biochemistry Clemens-Schöpf-InstituteTechnical University DarmstadtAlarich-Weiss Straße 464287DarmstadtGermany
| | - Jürgen M. Kolos
- Department Chemistry and Biochemistry Clemens-Schöpf-InstituteTechnical University DarmstadtAlarich-Weiss Straße 464287DarmstadtGermany
| | - Felix Hausch
- Department Chemistry and Biochemistry Clemens-Schöpf-InstituteTechnical University DarmstadtAlarich-Weiss Straße 464287DarmstadtGermany
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Simón Serrano S, Tavecchio M, Grönberg A, Sime W, Jemaà M, Moss S, Gregory MA, Gallay P, Elmér E, Hansson MJ, Massoumi R. Novel Cyclophilin Inhibitor Decreases Cell Proliferation and Tumor Growth in Models of Hepatocellular Carcinoma. Cancers (Basel) 2021; 13:cancers13123041. [PMID: 34207224 PMCID: PMC8234462 DOI: 10.3390/cancers13123041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Cyclophilins, a family of proteins with peptidyl prolyl isomerase activity, have been found to be overexpressed in several cancers, including hepatocellular carcinoma (HCC), and their expression is correlated to a poor prognosis. Cyclophilins play an important role in proliferation and cancer resistance in HCC. In this study, we evaluated the potential capacity of cyclophilin inhibitors as a treatment against HCC. We showed that our selected cyclophilin inhibitor, NV651, was able to decrease cell proliferation in vitro and induce an accumulation of cells in the G2/M phase due to a mitotic block. We could also confirm its capacity to decrease tumor growths in mice and its safety in vitro as well as in vivo. Abstract Hepatocellular carcinoma (HCC), the most common primary liver cancer, is usually diagnosed in its late state. Tyrosine kinase inhibitors such as sorafenib and regorafenib are one of the few treatment options approved for advanced HCC and only prolong the patient’s life expectancy by a few months. Therefore, there is a need for novel effective treatments. Cyclophilins are intracellular proteins that catalyze the cis/trans isomerization of peptide bonds at proline residues. Cyclophilins are known to be overexpressed in HCC, affecting therapy resistance and cell proliferation. In the present study, we explored the potential of cyclophilin inhibitors as new therapeutic options for HCC in vitro and in vivo. Our results showed that the novel cyclophilin inhibitor, NV651, was able to significantly decrease proliferation in a diverse set of HCC cell lines. The exposure of HCC cells to NV651 caused an accumulation of cells during mitosis and consequent accumulation in the G2/M phase of the cell cycle. NV651 reduced tumor growth in vivo using an HCC xenograft model without affecting the body weights of the animals. The safety aspects of NV651 were also confirmed in primary human hepatocytes without any cytotoxic effects. Based on the results obtained in this study, we propose NV651 as a potential treatment strategy for HCC.
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Affiliation(s)
- Sonia Simón Serrano
- Translational Cancer Research, Department of Laboratory Medicine, Lund University, Medicon Village, 223 63 Lund, Sweden; (S.S.S.); (W.S.); (M.J.)
- Abliva AB, Medicon Village, Scheelevägen 2, SE-233 81 Lund, Sweden; (M.T.); (A.G.); (E.E.); (M.J.H.)
| | - Michele Tavecchio
- Abliva AB, Medicon Village, Scheelevägen 2, SE-233 81 Lund, Sweden; (M.T.); (A.G.); (E.E.); (M.J.H.)
- Mitochondrial Medicine, Department of Clinical Sciences, Lund University, BMC A13, SE-221 84 Lund, Sweden
| | - Alvar Grönberg
- Abliva AB, Medicon Village, Scheelevägen 2, SE-233 81 Lund, Sweden; (M.T.); (A.G.); (E.E.); (M.J.H.)
| | - Wondossen Sime
- Translational Cancer Research, Department of Laboratory Medicine, Lund University, Medicon Village, 223 63 Lund, Sweden; (S.S.S.); (W.S.); (M.J.)
| | - Mohamed Jemaà
- Translational Cancer Research, Department of Laboratory Medicine, Lund University, Medicon Village, 223 63 Lund, Sweden; (S.S.S.); (W.S.); (M.J.)
| | - Steven Moss
- Isomerase Therapeutics Ltd., Suite 9, Science Village, Chesterford Research Park, Cambridge CB10 1XL, UK; (S.M.); (M.A.G.)
| | - Matthew Alan Gregory
- Isomerase Therapeutics Ltd., Suite 9, Science Village, Chesterford Research Park, Cambridge CB10 1XL, UK; (S.M.); (M.A.G.)
| | - Philippe Gallay
- Department of Immunology & Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA;
| | - Eskil Elmér
- Abliva AB, Medicon Village, Scheelevägen 2, SE-233 81 Lund, Sweden; (M.T.); (A.G.); (E.E.); (M.J.H.)
- Mitochondrial Medicine, Department of Clinical Sciences, Lund University, BMC A13, SE-221 84 Lund, Sweden
| | - Magnus Joakim Hansson
- Abliva AB, Medicon Village, Scheelevägen 2, SE-233 81 Lund, Sweden; (M.T.); (A.G.); (E.E.); (M.J.H.)
- Mitochondrial Medicine, Department of Clinical Sciences, Lund University, BMC A13, SE-221 84 Lund, Sweden
| | - Ramin Massoumi
- Translational Cancer Research, Department of Laboratory Medicine, Lund University, Medicon Village, 223 63 Lund, Sweden; (S.S.S.); (W.S.); (M.J.)
- Correspondence: ; Tel.: +46-46-222-64-30
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Voll AM, Meyners C, Taubert MC, Bajaj T, Heymann T, Merz S, Charalampidou A, Kolos J, Purder PL, Geiger TM, Wessig P, Gassen NC, Bracher A, Hausch F. Makrozyklische FKBP51‐Liganden enthüllen einen transienten Bindungsmodus mit erhöhter Selektivität. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202017352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Andreas M. Voll
- Department Chemistry and Biochemistry Clemens-Schöpf-Institute Technical University Darmstadt Alarich-Weiss Straße 4 64287 Darmstadt Deutschland
| | - Christian Meyners
- Department Chemistry and Biochemistry Clemens-Schöpf-Institute Technical University Darmstadt Alarich-Weiss Straße 4 64287 Darmstadt Deutschland
| | - Martha C. Taubert
- Department Chemistry and Biochemistry Clemens-Schöpf-Institute Technical University Darmstadt Alarich-Weiss Straße 4 64287 Darmstadt Deutschland
| | - Thomas Bajaj
- Research Group Neurohomeostasis Department of Psychiatry and Psychotherapy University of Bonn Venusberg Campus 1 53127 Bonn Deutschland
| | - Tim Heymann
- Department Chemistry and Biochemistry Clemens-Schöpf-Institute Technical University Darmstadt Alarich-Weiss Straße 4 64287 Darmstadt Deutschland
| | - Stephanie Merz
- Department Chemistry and Biochemistry Clemens-Schöpf-Institute Technical University Darmstadt Alarich-Weiss Straße 4 64287 Darmstadt Deutschland
| | - Anna Charalampidou
- Department Chemistry and Biochemistry Clemens-Schöpf-Institute Technical University Darmstadt Alarich-Weiss Straße 4 64287 Darmstadt Deutschland
| | - Jürgen Kolos
- Department Chemistry and Biochemistry Clemens-Schöpf-Institute Technical University Darmstadt Alarich-Weiss Straße 4 64287 Darmstadt Deutschland
| | - Patrick L. Purder
- Department Chemistry and Biochemistry Clemens-Schöpf-Institute Technical University Darmstadt Alarich-Weiss Straße 4 64287 Darmstadt Deutschland
| | - Thomas M. Geiger
- Department Chemistry and Biochemistry Clemens-Schöpf-Institute Technical University Darmstadt Alarich-Weiss Straße 4 64287 Darmstadt Deutschland
| | - Pablo Wessig
- Universität Potsdam Institut für Chemie Karl-Liebknecht-Straße 24–25 14476 Potsdam Deutschland
| | - Nils C. Gassen
- Research Group Neurohomeostasis Department of Psychiatry and Psychotherapy University of Bonn Venusberg Campus 1 53127 Bonn Deutschland
| | - Andreas Bracher
- Max-Planck-Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Deutschland
| | - Felix Hausch
- Department Chemistry and Biochemistry Clemens-Schöpf-Institute Technical University Darmstadt Alarich-Weiss Straße 4 64287 Darmstadt Deutschland
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Voll AM, Meyners C, Taubert MC, Bajaj T, Heymann T, Merz S, Charalampidou A, Kolos J, Purder PL, Geiger TM, Wessig P, Gassen NC, Bracher A, Hausch F. Macrocyclic FKBP51 Ligands Define a Transient Binding Mode with Enhanced Selectivity. Angew Chem Int Ed Engl 2021; 60:13257-13263. [PMID: 33843131 PMCID: PMC8252719 DOI: 10.1002/anie.202017352] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/14/2021] [Indexed: 12/28/2022]
Abstract
Subtype selectivity represents a challenge in many drug discovery campaigns. A typical example is the FK506 binding protein 51 (FKBP51), which has emerged as an attractive drug target. The most advanced FKBP51 ligands of the SAFit class are highly selective vs. FKBP52 but poorly discriminate against the homologs and off-targets FKBP12 and FKBP12.6. During a macrocyclization pilot study, we observed that many of these macrocyclic analogs have unanticipated and unprecedented preference for FKBP51 over FKBP12 and FKBP12.6. Structural studies revealed that these macrocycles bind with a new binding mode featuring a transient conformation, which is disfavored for the small FKBPs. Using a conformation-sensitive assay we show that this binding mode occurs in solution and is characteristic for this new class of compounds. The discovered macrocycles are non-immunosuppressive, engage FKBP51 in cells, and block the cellular effect of FKBP51 on IKKα. Our findings provide a new chemical scaffold for improved FKBP51 ligands and the structural basis for enhanced selectivity.
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Affiliation(s)
- Andreas M. Voll
- Department Chemistry and BiochemistryClemens-Schöpf-InstituteTechnical University DarmstadtAlarich-Weiss Strasse 464287DarmstadtGermany
| | - Christian Meyners
- Department Chemistry and BiochemistryClemens-Schöpf-InstituteTechnical University DarmstadtAlarich-Weiss Strasse 464287DarmstadtGermany
| | - Martha C. Taubert
- Department Chemistry and BiochemistryClemens-Schöpf-InstituteTechnical University DarmstadtAlarich-Weiss Strasse 464287DarmstadtGermany
| | - Thomas Bajaj
- Research Group NeurohomeostasisDepartment of Psychiatry and PsychotherapyUniversity of BonnVenusberg Campus 153127BonnGermany
| | - Tim Heymann
- Department Chemistry and BiochemistryClemens-Schöpf-InstituteTechnical University DarmstadtAlarich-Weiss Strasse 464287DarmstadtGermany
| | - Stephanie Merz
- Department Chemistry and BiochemistryClemens-Schöpf-InstituteTechnical University DarmstadtAlarich-Weiss Strasse 464287DarmstadtGermany
| | - Anna Charalampidou
- Department Chemistry and BiochemistryClemens-Schöpf-InstituteTechnical University DarmstadtAlarich-Weiss Strasse 464287DarmstadtGermany
| | - Jürgen Kolos
- Department Chemistry and BiochemistryClemens-Schöpf-InstituteTechnical University DarmstadtAlarich-Weiss Strasse 464287DarmstadtGermany
| | - Patrick L. Purder
- Department Chemistry and BiochemistryClemens-Schöpf-InstituteTechnical University DarmstadtAlarich-Weiss Strasse 464287DarmstadtGermany
| | - Thomas M. Geiger
- Department Chemistry and BiochemistryClemens-Schöpf-InstituteTechnical University DarmstadtAlarich-Weiss Strasse 464287DarmstadtGermany
| | - Pablo Wessig
- Universität PotsdamInstitut für ChemieKarl-Liebknecht-Strasse 24–2514476PotsdamGermany
| | - Nils C. Gassen
- Research Group NeurohomeostasisDepartment of Psychiatry and PsychotherapyUniversity of BonnVenusberg Campus 153127BonnGermany
| | - Andreas Bracher
- Max-Planck-Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Felix Hausch
- Department Chemistry and BiochemistryClemens-Schöpf-InstituteTechnical University DarmstadtAlarich-Weiss Strasse 464287DarmstadtGermany
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Naegleria fowleri: Protein structures to facilitate drug discovery for the deadly, pathogenic free-living amoeba. PLoS One 2021; 16:e0241738. [PMID: 33760815 PMCID: PMC7990177 DOI: 10.1371/journal.pone.0241738] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/25/2021] [Indexed: 12/19/2022] Open
Abstract
Naegleria fowleri is a pathogenic, thermophilic, free-living amoeba which causes primary amebic meningoencephalitis (PAM). Penetrating the olfactory mucosa, the brain-eating amoeba travels along the olfactory nerves, burrowing through the cribriform plate to its destination: the brain’s frontal lobes. The amoeba thrives in warm, freshwater environments, with peak infection rates in the summer months and has a mortality rate of approximately 97%. A major contributor to the pathogen’s high mortality is the lack of sensitivity of N. fowleri to current drug therapies, even in the face of combination-drug therapy. To enable rational drug discovery and design efforts we have pursued protein production and crystallography-based structure determination efforts for likely drug targets from N. fowleri. The genes were selected if they had homology to drug targets listed in Drug Bank or were nominated by primary investigators engaged in N. fowleri research. In 2017, 178 N. fowleri protein targets were queued to the Seattle Structural Genomics Center of Infectious Disease (SSGCID) pipeline, and to date 89 soluble recombinant proteins and 19 unique target structures have been produced. Many of the new protein structures are potential drug targets and contain structural differences compared to their human homologs, which could allow for the development of pathogen-specific inhibitors. Five of the structures were analyzed in more detail, and four of five show promise that selective inhibitors of the active site could be found. The 19 solved crystal structures build a foundation for future work in combating this devastating disease by encouraging further investigation to stimulate drug discovery for this neglected pathogen.
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Jia K, Du H. Mitochondrial Permeability Transition: A Pore Intertwines Brain Aging and Alzheimer's Disease. Cells 2021; 10:649. [PMID: 33804048 PMCID: PMC8001058 DOI: 10.3390/cells10030649] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 03/04/2021] [Accepted: 03/06/2021] [Indexed: 12/15/2022] Open
Abstract
Advanced age is the greatest risk factor for aging-related brain disorders including Alzheimer's disease (AD). However, the detailed mechanisms that mechanistically link aging and AD remain elusive. In recent years, a mitochondrial hypothesis of brain aging and AD has been accentuated. Mitochondrial permeability transition pore (mPTP) is a mitochondrial response to intramitochondrial and intracellular stresses. mPTP overactivation has been implicated in mitochondrial dysfunction in aging and AD brains. This review summarizes the up-to-date progress in the study of mPTP in aging and AD and attempts to establish a link between brain aging and AD from a perspective of mPTP-mediated mitochondrial dysfunction.
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Affiliation(s)
- Kun Jia
- Department of Pharmacology and Toxicology, The University of Kansas, Lawrence, KS 66045, USA;
| | - Heng Du
- Department of Pharmacology and Toxicology, The University of Kansas, Lawrence, KS 66045, USA;
- Higuchi Biosciences Center, The University of Kansas, Lawrence, KS 66045, USA
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Bauder M, Meyners C, Purder PL, Merz S, Sugiarto WO, Voll AM, Heymann T, Hausch F. Structure-Based Design of High-Affinity Macrocyclic FKBP51 Inhibitors. J Med Chem 2021; 64:3320-3349. [PMID: 33666419 DOI: 10.1021/acs.jmedchem.0c02195] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The FK506-binding protein 51 (FKBP51) emerged as a key player in several diseases like stress-related disorders, chronic pain, and obesity. Linear analogues of FK506 called SAFit were shown to be highly selective for FKBP51 over its closest homologue FKBP52, allowing the proof-of-concept studies in animal models. Here, we designed and synthesized the first macrocyclic FKBP51-selective ligands to stabilize the active conformation. All macrocycles retained full FKBP51 affinity and selectivity over FKBP52 and the incorporation of polar functionalities further enhanced affinity. Six high-resolution crystal structures of macrocyclic inhibitors in complex with FKBP51 confirmed the desired selectivity-enabling binding mode. Our results show that macrocyclization is a viable strategy to target the shallow FKBP51 binding site selectively.
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Affiliation(s)
- Michael Bauder
- Department Chemistry and Biochemistry, Clemens-Schöpf-Institute, Technical University Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| | - Christian Meyners
- Department Chemistry and Biochemistry, Clemens-Schöpf-Institute, Technical University Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| | - Patrick L Purder
- Department Chemistry and Biochemistry, Clemens-Schöpf-Institute, Technical University Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| | - Stephanie Merz
- Department Chemistry and Biochemistry, Clemens-Schöpf-Institute, Technical University Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| | - Wisely Oki Sugiarto
- Department Chemistry and Biochemistry, Clemens-Schöpf-Institute, Technical University Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| | - Andreas M Voll
- Department Chemistry and Biochemistry, Clemens-Schöpf-Institute, Technical University Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| | - Tim Heymann
- Department Chemistry and Biochemistry, Clemens-Schöpf-Institute, Technical University Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| | - Felix Hausch
- Department Chemistry and Biochemistry, Clemens-Schöpf-Institute, Technical University Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
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42
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Moyer TB, Parsley NC, Sadecki PW, Schug WJ, Hicks LM. Leveraging orthogonal mass spectrometry based strategies for comprehensive sequencing and characterization of ribosomal antimicrobial peptide natural products. Nat Prod Rep 2021; 38:489-509. [PMID: 32929442 PMCID: PMC7956910 DOI: 10.1039/d0np00046a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: Up to July 2020Ribosomal antimicrobial peptide (AMP) natural products, also known as ribosomally synthesized and post-translationally modified peptides (RiPPs) or host defense peptides, demonstrate potent bioactivities and impressive complexity that complicate molecular and biological characterization. Tandem mass spectrometry (MS) has rapidly accelerated bioactive peptide sequencing efforts, yet standard workflows insufficiently address intrinsic AMP diversity. Herein, orthogonal approaches to accelerate comprehensive and accurate molecular characterization without the need for prior isolation are reviewed. Chemical derivatization, proteolysis (enzymatic and chemical cleavage), multistage MS fragmentation, and separation (liquid chromatography and ion mobility) strategies can provide complementary amino acid composition and post-translational modification data to constrain sequence solutions. Examination of two complex case studies, gomesin and styelin D, highlights the practical implementation of the proposed approaches. Finally, we emphasize the importance of heterogeneous AMP peptidoforms that confer varying biological function, an area that warrants significant further development.
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Affiliation(s)
- Tessa B Moyer
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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43
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Aizpurua JM, Miranda JI, Irastorza A, Torres E, Eceiza M, Sagartzazu-Aizpurua M, Ferrón P, Aldanondo G, Lasa-Fernández H, Marco-Moreno P, Dadie N, López de Munain A, Vallejo-Illarramendi A. Discovery of a novel family of FKBP12 "reshapers" and their use as calcium modulators in skeletal muscle under nitro-oxidative stress. Eur J Med Chem 2021; 213:113160. [PMID: 33493827 DOI: 10.1016/j.ejmech.2021.113160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/23/2020] [Accepted: 01/04/2021] [Indexed: 10/22/2022]
Abstract
The hypothesis of rescuing FKBP12/RyR1 interaction and intracellular calcium homeostasis through molecular "reshaping" of FKBP12 was investigated. To this end, novel 4-arylthioalkyl-1-carboxyalkyl-1,2,3-triazoles were designed and synthesized, and their efficacy was tested in human myotubes. A library of 17 compounds (10a-n) designed to dock the FKBP12/RyR1 hot-spot interface contact residues, was readily prepared from free α-amino acids and arylthioalkynes using CuAAC "click" protocols amenable to one-pot transformations in high overall yields and total configurational integrity. To model nitro-oxidative stress, human myotubes were treated with the peroxynitrite donor SIN1, and evidence was found that some triazoles 10 were able to normalize calcium levels, as well as FKBP12/RyR1 interaction. For example, compound 10 b at 150 nM rescued 46% of FKBP12/RyR1 interaction and up to 70% of resting cytosolic calcium levels in human myotubes under nitro-oxidative stress. All compounds 10 analyzed showed target engagement to FKBP12 and low levels of cytotoxicity in vitro. Compounds 10b, 10c, 10h, and 10iR were identified as potential therapeutic candidates to protect myotubes in muscle disorders with underlying nitro-oxidative stress, FKBP12/RyR1 dysfunction and calcium dysregulation.
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Affiliation(s)
- Jesus M Aizpurua
- Joxe Mari Korta R&D Center, Departamento de Química Orgánica-I, Universidad Del País Vasco UPV/EHU, Avda. Tolosa-72, 20018, San Sebastián, Spain.
| | - José I Miranda
- Joxe Mari Korta R&D Center, Departamento de Química Orgánica-I, Universidad Del País Vasco UPV/EHU, Avda. Tolosa-72, 20018, San Sebastián, Spain
| | - Aitziber Irastorza
- Joxe Mari Korta R&D Center, Departamento de Química Orgánica-I, Universidad Del País Vasco UPV/EHU, Avda. Tolosa-72, 20018, San Sebastián, Spain
| | - Endika Torres
- Joxe Mari Korta R&D Center, Departamento de Química Orgánica-I, Universidad Del País Vasco UPV/EHU, Avda. Tolosa-72, 20018, San Sebastián, Spain
| | - Maite Eceiza
- Joxe Mari Korta R&D Center, Departamento de Química Orgánica-I, Universidad Del País Vasco UPV/EHU, Avda. Tolosa-72, 20018, San Sebastián, Spain
| | - Maialen Sagartzazu-Aizpurua
- Joxe Mari Korta R&D Center, Departamento de Química Orgánica-I, Universidad Del País Vasco UPV/EHU, Avda. Tolosa-72, 20018, San Sebastián, Spain
| | - Pablo Ferrón
- Miramoon Pharma S.L., Avda Tolosa-72, 20018, San Sebastián, Spain
| | - Garazi Aldanondo
- Instituto de Investigación Sanitaria Biodonostia, Grupo de Enfermedades Neuromusculares, Paseo Dr Begiristain s/n, 20014, San Sebastián, Spain; CIBERNED, Instituto de Salud Carlos III, 28031, Madrid, Spain
| | - Haizpea Lasa-Fernández
- Instituto de Investigación Sanitaria Biodonostia, Grupo de Enfermedades Neuromusculares, Paseo Dr Begiristain s/n, 20014, San Sebastián, Spain; CIBERNED, Instituto de Salud Carlos III, 28031, Madrid, Spain; Grupo de Neurosciencias, Departamentos de Pediatría y Neurociencias, Universidad Del País Vasco UPV/EHU, Hospital Donostia, Paseo Dr Begiristain S/n, 20014, San Sebastián, Spain
| | - Pablo Marco-Moreno
- Instituto de Investigación Sanitaria Biodonostia, Grupo de Enfermedades Neuromusculares, Paseo Dr Begiristain s/n, 20014, San Sebastián, Spain; CIBERNED, Instituto de Salud Carlos III, 28031, Madrid, Spain
| | - Naroa Dadie
- Grupo de Neurosciencias, Departamentos de Pediatría y Neurociencias, Universidad Del País Vasco UPV/EHU, Hospital Donostia, Paseo Dr Begiristain S/n, 20014, San Sebastián, Spain
| | - Adolfo López de Munain
- Instituto de Investigación Sanitaria Biodonostia, Grupo de Enfermedades Neuromusculares, Paseo Dr Begiristain s/n, 20014, San Sebastián, Spain; CIBERNED, Instituto de Salud Carlos III, 28031, Madrid, Spain; Grupo de Neurosciencias, Departamentos de Pediatría y Neurociencias, Universidad Del País Vasco UPV/EHU, Hospital Donostia, Paseo Dr Begiristain S/n, 20014, San Sebastián, Spain
| | - Ainara Vallejo-Illarramendi
- Instituto de Investigación Sanitaria Biodonostia, Grupo de Enfermedades Neuromusculares, Paseo Dr Begiristain s/n, 20014, San Sebastián, Spain; CIBERNED, Instituto de Salud Carlos III, 28031, Madrid, Spain; Grupo de Neurosciencias, Departamentos de Pediatría y Neurociencias, Universidad Del País Vasco UPV/EHU, Hospital Donostia, Paseo Dr Begiristain S/n, 20014, San Sebastián, Spain.
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44
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Park HS, Kang YK. Puckering transition of the proline residue along the pseudorotational path: revisited. NEW J CHEM 2021. [DOI: 10.1039/d1nj01361k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Puckering transitions of the proline residue for Ac-Pro-X with trans and cis prolyl peptide bonds were explored along the pseudorotation phase angle using DFT methods in the gas phase and in water.
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Affiliation(s)
- Hae Sook Park
- Department of Nursing
- Cheju Halla University
- Cheju 63092
- Republic of Korea
| | - Young Kee Kang
- Department of Chemistry
- Chungbuk National University
- Cheongju
- Republic of Korea
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45
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Wakchaure PD, Ganguly B. Tuning the electronic effects in designing ligands for the inhibition of rotamase activity of FK506 binding protein. Theor Chem Acc 2021. [DOI: 10.1007/s00214-020-02717-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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46
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Panel M, Ahmed-Belkacem A, Ruiz I, Guichou JF, Pawlotsky JM, Ghaleh B, Morin D. A Phenyl-Pyrrolidine Derivative Reveals a Dual Inhibition Mechanism of Myocardial Mitochondrial Permeability Transition Pore, Which Is Limited by Its Myocardial Distribution. J Pharmacol Exp Ther 2020; 376:348-357. [DOI: 10.1124/jpet.120.000359] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/08/2020] [Indexed: 12/15/2022] Open
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47
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Caminati G, Procacci P. Mounting evidence of FKBP12 implication in neurodegeneration. Neural Regen Res 2020; 15:2195-2202. [PMID: 32594030 PMCID: PMC7749462 DOI: 10.4103/1673-5374.284980] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 02/18/2020] [Accepted: 03/24/2020] [Indexed: 12/25/2022] Open
Abstract
Intrinsically disordered proteins, such as tau or α-synuclein, have long been associated with a dysfunctional role in neurodegenerative diseases. In Alzheimer's and Parkinson's' diseases, these proteins, sharing a common chemical-physical pattern with alternating hydrophobic and hydrophilic domains rich in prolines, abnormally aggregate in tangles in the brain leading to progressive loss of neurons. In this review, we present an overview linking the studies on the implication of the peptidyl-prolyl isomerase domain of immunophilins, and notably FKBP12, to a variety of neurodegenerative diseases, focusing on the molecular origin of such a role. The involvement of FKBP12 dysregulation in the aberrant aggregation of disordered proteins pinpoints this protein as a possible therapeutic target and, at the same time, as a predictive biomarker for early diagnosis in neurodegeneration, calling for the development of reliable, fast and cost-effective detection methods in body fluids for community-based screening campaigns.
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Affiliation(s)
- Gabriella Caminati
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
- Center for Colloid and Surface Science (CSGI), University of Florence, Sesto Fiorentino, Italy
| | - Piero Procacci
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
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48
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Geisler M, Hegedűs T. A twist in the ABC: regulation of ABC transporter trafficking and transport by FK506-binding proteins. FEBS Lett 2020; 594:3986-4000. [PMID: 33125703 DOI: 10.1002/1873-3468.13983] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/02/2020] [Accepted: 10/15/2020] [Indexed: 01/07/2023]
Abstract
Post-transcriptional regulation of ATP-binding cassette (ABC) proteins has been so far shown to encompass protein phosphorylation, maturation, and ubiquitination. Yet, recent accumulating evidence implicates FK506-binding proteins (FKBPs), a type of peptidylprolyl cis-trans isomerase (PPIase) proteins, in ABC transporter regulation. In this perspective article, we summarize current knowledge on ABC transporter regulation by FKBPs, which seems to be conserved over kingdoms and ABC subfamilies. We uncover striking functional similarities but also differences between regulatory FKBP-ABC modules in plants and mammals. We dissect a PPIase- and HSP90-dependent and independent impact of FKBPs on ABC biogenesis and transport activity. We propose and discuss a putative new mode of transient ABC transporter regulation by cis-trans isomerization of X-prolyl bonds.
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Affiliation(s)
- Markus Geisler
- Department of Biology, University of Fribourg, Switzerland
| | - Tamás Hegedűs
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
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49
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Favretto F, Flores D, Baker JD, Strohäker T, Andreas LB, Blair LJ, Becker S, Zweckstetter M. Catalysis of proline isomerization and molecular chaperone activity in a tug-of-war. Nat Commun 2020; 11:6046. [PMID: 33247146 PMCID: PMC7695863 DOI: 10.1038/s41467-020-19844-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/20/2020] [Indexed: 02/03/2023] Open
Abstract
Catalysis of cis/trans isomerization of prolines is important for the activity and misfolding of intrinsically disordered proteins. Catalysis is achieved by peptidylprolyl isomerases, a superfamily of molecular chaperones. Here, we provide atomic insight into a tug-of-war between cis/trans isomerization and molecular chaperone activity. Catalysis of proline isomerization by cyclophilin A lowers the energy barrier for α-synuclein misfolding, while isomerase-binding to a separate, disease-associated protein region opposes aggregation. We further show that cis/trans isomerization outpowers the holding activity of cyclophilin A. Removal of the proline isomerization barrier through posttranslational truncation of α-synuclein reverses the action of the proline isomerase and turns it into a potent molecular chaperone that inhibits protein misfolding. The data reveal a conserved mechanism of dual functionality in cis/trans isomerases and define its molecular determinants acting on intrinsically disordered proteins. Cyclophilin A (CypA) is a peptidylprolyl isomerase that also has chaperone activity and interacts with the intrinsically disordered protein α-Synuclein (aSyn). Here, the authors combine NMR measurements and biochemical experiments to characterise the interplay between the catalysis of proline isomerization and molecular chaperone activity of CypA and find that both activities have opposing effects on aSyn and further show that the that cis/trans isomerization outpowers the holding activity of CypA.
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Affiliation(s)
- Filippo Favretto
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075, Göttingen, Germany
| | - David Flores
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075, Göttingen, Germany
| | - Jeremy D Baker
- Department of Molecular Medicine, Morsani College of Medicine, USF Health Byrd Alzheimer's Institute, University of South Florida, Tampa, FL, 33613, USA
| | - Timo Strohäker
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075, Göttingen, Germany
| | - Loren B Andreas
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany
| | - Laura J Blair
- Department of Molecular Medicine, Morsani College of Medicine, USF Health Byrd Alzheimer's Institute, University of South Florida, Tampa, FL, 33613, USA
| | - Stefan Becker
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075, Göttingen, Germany. .,Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany.
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50
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Atack TC, Raymond DD, Blomquist CA, Pasaje CF, McCarren PR, Moroco J, Befekadu HB, Robinson FP, Pal D, Esherick LY, Ianari A, Niles JC, Sellers WR. Targeted Covalent Inhibition of Plasmodium FK506 Binding Protein 35. ACS Med Chem Lett 2020; 11:2131-2138. [PMID: 33209191 PMCID: PMC7667655 DOI: 10.1021/acsmedchemlett.0c00272] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 09/01/2020] [Indexed: 01/04/2023] Open
Abstract
![]()
FK506-binding
protein 35, FKBP35, has been implicated as an essential
malarial enzyme. Rapamycin and FK506 exhibit antiplasmodium activity
in cultured parasites. However, due to the highly conserved nature
of the binding pockets of FKBPs and the immunosuppressive properties
of these drugs, there is a need for compounds that selectively inhibit
FKBP35 and lack the undesired side effects. In contrast to human FKBPs,
FKBP35 contains a cysteine, C106, adjacent to the rapamycin binding
pocket, providing an opportunity to develop targeted covalent inhibitors
of Plasmodium FKBP35. Here, we synthesize inhibitors
of FKBP35, show that they directly bind FKBP35 in a model cellular
setting, selectively covalently modify C106, and exhibit antiplasmodium
activity in blood-stage cultured parasites.
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Affiliation(s)
- Thomas C. Atack
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Donald D. Raymond
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Christa A. Blomquist
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Charisse Flerida Pasaje
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Patrick R. McCarren
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Jamie Moroco
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Henock B. Befekadu
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Foxy P. Robinson
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Debjani Pal
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Lisl Y. Esherick
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Alessandra Ianari
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Jacquin C. Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - William R. Sellers
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
- Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts 02115, United States
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