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Zilecka E, Klima M, Stefek M, Dejmek M, Nencka R, Boura E. Structure of SARS-CoV-2 MTase nsp14 with the inhibitor STM957 reveals inhibition mechanism that is shared with a poxviral MTase VP39. J Struct Biol X 2024; 10:100109. [PMID: 39188530 PMCID: PMC11345338 DOI: 10.1016/j.yjsbx.2024.100109] [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: 07/09/2024] [Revised: 07/26/2024] [Accepted: 07/27/2024] [Indexed: 08/28/2024] Open
Abstract
Nsp14 is an RNA methyltransferase (MTase) encoded by all coronaviruses. In fact, many viral families, including DNA viruses, encode MTases that catalyze the methylation of the RNA precap structure, resulting in fully capped viral RNA. This capping is crucial for efficient viral RNA translation, stability, and immune evasion. Our previous research identified nsp14 inhibitors based on the chemical scaffold of its methyl donor - the S-adenosyl methionine (SAM) - featuring a modified adenine base and a substituted arylsulfonamide. However, the binding mode of these inhibitors was based only on docking experiments. To uncover atomic details of nsp14 inhibition we solved the crystal structure of nsp14 bound to STM957. The structure revealed the atomic details of nsp14 inhibition such that the 7-deaza-adenine moiety of STM957 forms specific interactions with Tyr368, Ala353, and Phe367, while the arylsulfonamide moiety engages with Asn388 and Phe506. The large aromatic substituent at the 7-deaza position displaces a network of water molecules near the adenine base. Surprisingly, this was recently observed in the case of an unrelated monkeypox MTase VP39, where the 7-deaza modified SAH analogs also displaced water molecules from the vicinity of the active site.
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Affiliation(s)
- Eva Zilecka
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Martin Klima
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Milan Stefek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Milan Dejmek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Radim Nencka
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
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2
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Poon CCW, Au-Yeung C, Wong KY, Chan Z, Zhou LP, Li G, Wang Y, Zhang Y, Wong MS. Icariin promotes cell adhesion for osteogenesis in bone marrow stromal cells via binding to integrin α5β1. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 133:155887. [PMID: 39067311 DOI: 10.1016/j.phymed.2024.155887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 06/05/2024] [Accepted: 07/14/2024] [Indexed: 07/30/2024]
Abstract
BACKGROUND AND PURPOSE Icariin, an 8-prenylated flavonoid glycoside, is an anabolic agent that could exert rapid estrogenic actions via ligand-independent activation of estrogen receptor alpha (ERα) in osteoblastic cells to promote osteogenesis. However, relatively little is known about its direct cellular target, its protective effects, and cell adhesion activities in bone marrow stromal cells (BMSCs) against microgravity. In the present study, the effects of icariin on osteogenesis and cell adhesion under microgravity were examined with the involvement of integrin receptor α5β1, connexin 43, and CAMs. STUDY DESIGN AND METHODS Icariin was orally administered to 6-month-old ovariectomized (OVX) Sprague-Dawley (SD) rats for 3 months through daily intake of phytoestrogen-free rodent diets containing icariin at 2 different dosages (50 and 500 ppm). BMSCs were harvested for experiments and RNA-sequencing analysis to examine the mechanism of action of icariin and its direct cellular target in stimulating osteogenesis. RESULTS The results revealed that icariin induced the expression of cell adhesion molecules (CAMs) and protected against microgravity-induced disruption of actin cytoskeleton and the loss of osteogenic activities in BMSCs through the activation of connexin-43 (Cx43) and Ras homolog family member A (RhoA) and Rac family small GTPase 1 (Rac1)-mediated signaling pathways. Computerized molecular docking techniques and the competitive solid-phase binding ELISA assay confirmed that icariin could be a direct ligand of integrin alpha 5 beta 1 (α5β1), and it could also increase the protein expression of integrin α5β1 for mechanosensing. CONCLUSION Our findings suggest that icariin could directly activate cell adhesion signaling by binding to integrin α5β1, which opens up new avenues for the development of integrin α5β1 ligand as an agent to protect against unloading-induced bone loss.
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Affiliation(s)
- Christina Chui-Wa Poon
- Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, PR China.; Research Centre for Chinese Medicine Innovation, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, PR China
| | - Chun Au-Yeung
- Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, PR China
| | - Ka-Ying Wong
- Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, PR China
| | - Zoe Chan
- Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, PR China
| | - Li-Ping Zhou
- School of Optometry, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, PR China
| | - Gang Li
- Department of Orthopaedics & Traumatology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, PR China
| | - Yan Wang
- Department of Orthopaedics & Traumatology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, PR China
| | - Yan Zhang
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, PR China
| | - Man-Sau Wong
- Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, PR China.; Research Centre for Chinese Medicine Innovation, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, PR China.; State Key Laboratory of Chinese Medicine and Molecular Pharmacology (Incubation), The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, PR China..
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3
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Man X, Li S, Xu G, Li W, Zhu M, Zhang Z, Liang H, Yang F. Developing a Copper(II) Isopropyl 2-Pyridyl Ketone Thiosemicarbazone Compound Based on the IB Subdomain of Human Serum Albumin-Indomethacin Complex: Inhibiting Tumor Growth by Remodeling the Tumor Microenvironment. J Med Chem 2024; 67:5744-5757. [PMID: 38553427 DOI: 10.1021/acs.jmedchem.3c02378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
To develop a next-generation metal agent and dual-agent multitargeted combination therapy, we developed a copper (Cu) compound based on the properties of the human serum albumin (HSA)-indomethacin (IND) complex to remodel the tumor microenvironment (TME). We optimized a series of Cu(II) isopropyl 2-pyridyl ketone thiosemicarbazone compounds to obtain a Cu(II) compound (C4) with significant cytotoxicity and then constructed an HSA-IND-C4 complex (HSA-IND-C4) delivery system. IND and C4 bind to the hydrophobic cavities of the IB and IIA domains of HSA, respectively. In vivo, the HSA-IND-C4 not only showed enhanced antitumor efficacy relative to C4 and C4 + IND but also improved their targeting ability and decreased their side effects. The antitumor mechanism of C4 + IND involved acting on the different components of the TME. IND inhibited tumor-related inflammation, while C4 not only induced apoptosis and autophagy of cancer cells but also inhibited tumor angiogenesis.
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Affiliation(s)
- Xueyu Man
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources/Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Sciences, Collaborative Innovation Center for Guangxi Ethnic Medicine, Guangxi Normal University, Guilin, Guangxi 541004, China
| | - Shanhe Li
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources/Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Sciences, Collaborative Innovation Center for Guangxi Ethnic Medicine, Guangxi Normal University, Guilin, Guangxi 541004, China
| | - Gang Xu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources/Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Sciences, Collaborative Innovation Center for Guangxi Ethnic Medicine, Guangxi Normal University, Guilin, Guangxi 541004, China
| | - Wenjuan Li
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources/Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Sciences, Collaborative Innovation Center for Guangxi Ethnic Medicine, Guangxi Normal University, Guilin, Guangxi 541004, China
| | - Minghui Zhu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources/Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Sciences, Collaborative Innovation Center for Guangxi Ethnic Medicine, Guangxi Normal University, Guilin, Guangxi 541004, China
| | - Zhenlei Zhang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources/Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Sciences, Collaborative Innovation Center for Guangxi Ethnic Medicine, Guangxi Normal University, Guilin, Guangxi 541004, China
| | - Hong Liang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources/Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Sciences, Collaborative Innovation Center for Guangxi Ethnic Medicine, Guangxi Normal University, Guilin, Guangxi 541004, China
| | - Feng Yang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources/Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Sciences, Collaborative Innovation Center for Guangxi Ethnic Medicine, Guangxi Normal University, Guilin, Guangxi 541004, China
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4
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Gabler T, Dali A, Sebastiani F, Furtmüller PG, Becucci M, Hofbauer S, Smulevich G. Iron insertion into coproporphyrin III-ferrochelatase complex: Evidence for an intermediate distorted catalytic species. Protein Sci 2023; 32:e4788. [PMID: 37743577 PMCID: PMC10578119 DOI: 10.1002/pro.4788] [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: 09/07/2023] [Accepted: 09/20/2023] [Indexed: 09/26/2023]
Abstract
Understanding the reaction mechanism of enzymes at the molecular level is generally a difficult task, since many parameters affect the turnover. Often, due to high reactivity and formation of transient species or intermediates, detailed information on enzymatic catalysis is obtained by means of model substrates. Whenever possible, it is essential to confirm a reaction mechanism based on substrate analogues or model systems by using the physiological substrates. Here we disclose the ferrous iron incorporation mechanism, in solution, and in crystallo, by the coproporphyrin III-coproporphyrin ferrochelatase complex from the firmicute, pathogen, and antibiotic resistant, Listeria monocytogenes. Coproporphyrin ferrochelatase plays an important physiological role as the metalation represents the penultimate reaction step in the prokaryotic coproporphyrin-dependent heme biosynthetic pathway, yielding coproheme (ferric coproporphyrin III). By following the metal titration with resonance Raman spectroscopy and x-ray crystallography, we prove that upon metalation the saddling distortion becomes predominant both in the crystal and in solution. This is a consequence of the readjustment of hydrogen bond interactions of the propionates with the protein scaffold during the enzymatic catalysis. Once the propionates have established the interactions typical of the coproheme complex, the distortion slowly decreases, to reach the almost planar final product.
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Affiliation(s)
- Thomas Gabler
- Department of ChemistryInstitute of Biochemistry, University of Natural Resources and Life SciencesViennaAustria
| | - Andrea Dali
- Dipartimento di Chimica “Ugo Schiff”—DICUSUniversità di FirenzeSesto FiorentinoItaly
| | - Federico Sebastiani
- Dipartimento di Chimica “Ugo Schiff”—DICUSUniversità di FirenzeSesto FiorentinoItaly
| | - Paul Georg Furtmüller
- Department of ChemistryInstitute of Biochemistry, University of Natural Resources and Life SciencesViennaAustria
| | - Maurizio Becucci
- Dipartimento di Chimica “Ugo Schiff”—DICUSUniversità di FirenzeSesto FiorentinoItaly
| | - Stefan Hofbauer
- Department of ChemistryInstitute of Biochemistry, University of Natural Resources and Life SciencesViennaAustria
| | - Giulietta Smulevich
- Dipartimento di Chimica “Ugo Schiff”—DICUSUniversità di FirenzeSesto FiorentinoItaly
- INSTM Research Unit of FirenzeSesto FiorentinoItaly
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5
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Chen H, Lin S, Yang F, Chen Z, Guo L, Yang J, Lin X, Wang L, Duan Y, Wen A, Zhang X, Dai Y, Yin K, Yuan X, Yu C, He Y, He B, Cao Y, Dong H, Li J, Zhao Q, Liu Q, Lu G. Structural and functional basis of low-affinity SAM/SAH-binding in the conserved MTase of the multi-segmented Alongshan virus distantly related to canonical unsegmented flaviviruses. PLoS Pathog 2023; 19:e1011694. [PMID: 37831643 PMCID: PMC10575543 DOI: 10.1371/journal.ppat.1011694] [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: 03/10/2023] [Accepted: 09/18/2023] [Indexed: 10/15/2023] Open
Abstract
Alongshan virus (ALSV), a newly discovered member of unclassified Flaviviridae family, is able to infect humans. ALSV has a multi-segmented genome organization and is evolutionarily distant from canonical mono-segmented flaviviruses. The virus-encoded methyltransferase (MTase) plays an important role in viral replication. Here we show that ALSV MTase readily binds S-adenosyl-L-methionine (SAM) and S-adenosyl-L-homocysteine (SAH) but exhibits significantly lower affinities than canonical flaviviral MTases. Structures of ALSV MTase in the free and SAM/SAH-bound forms reveal that the viral enzyme possesses a unique loop-element lining side-wall of the SAM/SAH-binding pocket. While the equivalent loop in flaviviral MTases half-covers SAM/SAH, contributing multiple hydrogen-bond interactions; the pocket-lining loop of ALSV MTase is of short-length and high-flexibility, devoid of any physical contacts with SAM/SAH. Subsequent mutagenesis data further corroborate such structural difference affecting SAM/SAH-binding. Finally, we also report the structure of ALSV MTase bound with sinefungin, an SAM-analogue MTase inhibitor. These data have delineated the basis for the low-affinity interaction between ALSV MTase and SAM/SAH and should inform on antiviral drug design.
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Affiliation(s)
- Hua Chen
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Wound Repair and Rehabilitation Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Daping Hospital, Army Medical University, Chongqing, China
| | - Sheng Lin
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Fanli Yang
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zimin Chen
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Liyan Guo
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jing Yang
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xi Lin
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Lingling Wang
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yanping Duan
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ao Wen
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xindan Zhang
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yushan Dai
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Keqing Yin
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xin Yuan
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Chongzhang Yu
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yarong He
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Bin He
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yu Cao
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Disaster Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Haohao Dong
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jian Li
- School of Basic Medical Sciences, Chengdu University, Chengdu, Sichuan, China
| | - Qi Zhao
- College of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Quan Liu
- Center of Infectious diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, State Key Laboratory of Zoonotic Diseases, Changchun, Jilin, China
| | - Guangwen Lu
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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6
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Byl JAW, Mueller R, Bax B, Basarab GS, Chibale K, Osheroff N. A Series of Spiropyrimidinetriones that Enhances DNA Cleavage Mediated by Mycobacterium tuberculosis Gyrase. ACS Infect Dis 2023; 9:706-715. [PMID: 36802491 PMCID: PMC10006343 DOI: 10.1021/acsinfecdis.3c00012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
The rise in drug-resistant tuberculosis has necessitated the search for alternative antibacterial treatments. Spiropyrimidinetriones (SPTs) represent an important new class of compounds that work through gyrase, the cytotoxic target of fluoroquinolone antibacterials. The present study analyzed the effects of a novel series of SPTs on the DNA cleavage activity of Mycobacterium tuberculosis gyrase. H3D-005722 and related SPTs displayed high activity against gyrase and increased levels of enzyme-mediated double-stranded DNA breaks. The activities of these compounds were similar to those of the fluoroquinolones, moxifloxacin, and ciprofloxacin and greater than that of zoliflodacin, the most clinically advanced SPT. All the SPTs overcame the most common mutations in gyrase associated with fluoroquinolone resistance and, in most cases, were more active against the mutant enzymes than wild-type gyrase. Finally, the compounds displayed low activity against human topoisomerase IIα. These findings support the potential of novel SPT analogues as antitubercular drugs.
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Affiliation(s)
- Jo Ann W Byl
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Rudolf Mueller
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Ben Bax
- Medicines Discovery Institute, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - Gregory S Basarab
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Kelly Chibale
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa.,South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
| | - Neil Osheroff
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States.,Medicine (Hematology/Oncology), Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States.,VA Tennessee Valley Healthcare System, Nashville, Tennessee 37212, United States
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7
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Pathak S, Gupta R, Parkar H, Joshi N, Nagotu S, Kale A. The role of Colchicine on actin polymerization dynamics: as a potent anti-angiogenic factor. J Biomol Struct Dyn 2022; 40:11729-11743. [PMID: 34424806 DOI: 10.1080/07391102.2021.1965911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Over the years, cancer research has focused on different strategies to discover drugs and therapies to treat the metastatic stage of cancer. This stage depends upon the type, and the cause of cancer. One of the central facts about any cancer invasion is the formation of new blood vessels that provide nutrients to these uncontrollably dividing cells. This phenomenon is called angiogenesis and is responsible for tumor progression and metastasis. Tumor angiogenesis is a sequential process wherein various angiogenic factors produced by tumor cells bind to receptors of endothelial cells. This stimulates the cytoskeletal protein, especially actin to reorganize themselves and undergo the process of canalization. The driving force for such membrane transformation is spatially and temporally-regulated by polymerization of submembrane actin filaments. So far, Colchicine has been studied for its effectiveness in controlling microtubule reorganization during cell division, but its role is far from understood on actin polymerization. In our current study, we report the effect of Colchicine on actin polymerization dynamics using biophysical analysis like Right light scattering (RLS), Dynamic light scattering (DLS), Circular dichroism (CD) analysis, Scanning electron microscopy (SEM) study. Isothermal titration calorimetry (ITC) and kinetic measurements. Isothermal titration calorimetry (ITC) indicates multiple site binding for colchicine with actin aggregates. We have checked the in vivo effect of colchicine using end3 cells of Saccharomyces cerevisiae. We also report the anti-angiogenesis activity of colchicine via ex-ovo chicken chorioallantoic membrane (CAM) assay. We predict the target site of binding for the drug by docking studies. Based on our findings, we suggest the 'drug-repurposed' function for colchicine as a potential anti-angiogenic candidate.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Samridhi Pathak
- School of Chemical Sciences, UM-DAE Center for excellence in basic sciences, University of Mumbai, Mumbai, Maharashtra, India
| | - Rahul Gupta
- School of Chemical Sciences, UM-DAE Center for excellence in basic sciences, University of Mumbai, Mumbai, Maharashtra, India
| | - Haifa Parkar
- School of Chemical Sciences, UM-DAE Center for excellence in basic sciences, University of Mumbai, Mumbai, Maharashtra, India
| | - Neha Joshi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Shirisha Nagotu
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Avinash Kale
- School of Chemical Sciences, UM-DAE Center for excellence in basic sciences, University of Mumbai, Mumbai, Maharashtra, India
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8
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Beton JG, Cragnolini T, Kaleel M, Mulvaney T, Sweeney A, Topf M. Integrating model simulation tools and
cryo‐electron
microscopy. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Joseph George Beton
- Centre for Structural Systems Biology (CSSB) Leibniz‐Institut für Virologie (LIV) Hamburg Germany
| | - Tristan Cragnolini
- Institute of Structural and Molecular Biology, Birkbeck and University College London London UK
| | - Manaz Kaleel
- Centre for Structural Systems Biology (CSSB) Leibniz‐Institut für Virologie (LIV) Hamburg Germany
| | - Thomas Mulvaney
- Centre for Structural Systems Biology (CSSB) Leibniz‐Institut für Virologie (LIV) Hamburg Germany
| | - Aaron Sweeney
- Centre for Structural Systems Biology (CSSB) Leibniz‐Institut für Virologie (LIV) Hamburg Germany
| | - Maya Topf
- Centre for Structural Systems Biology (CSSB) Leibniz‐Institut für Virologie (LIV) Hamburg Germany
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9
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Vavřina Z, Perlíková P, Milisavljević N, Chevrier F, Smola M, Smith J, Dejmek M, Havlíček V, Buděšínský M, Liboska R, Vaneková L, Brynda J, Boura E, Řezáčová P, Hocek M, Birkuš G. Design, Synthesis, and Biochemical and Biological Evaluation of Novel 7-Deazapurine Cyclic Dinucleotide Analogues as STING Receptor Agonists. J Med Chem 2022; 65:14082-14103. [PMID: 36201304 PMCID: PMC9620234 DOI: 10.1021/acs.jmedchem.2c01305] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Indexed: 11/28/2022]
Abstract
Cyclic dinucleotides (CDNs) are second messengers that activate stimulator of interferon genes (STING). The cGAS-STING pathway plays a promising role in cancer immunotherapy. Here, we describe the synthesis of CDNs containing 7-substituted 7-deazapurine moiety. We used mouse cyclic GMP-AMP synthase and bacterial dinucleotide synthases for the enzymatic synthesis of CDNs. Alternatively, 7-(het)aryl 7-deazapurine CDNs were prepared by Suzuki-Miyaura cross-couplings. New CDNs were tested in biochemical and cell-based assays for their affinity to human STING. Eight CDNs showed better activity than 2'3'-cGAMP, the natural ligand of STING. The effect on cytokine and chemokine induction was also evaluated. The best activities were observed for CDNs bearing large aromatic substituents that point above the CDN molecule. We solved four X-ray structures of complexes of new CDNs with human STING. We observed π-π stacking interactions between the aromatic substituents and Tyr240 that are involved in the stabilization of CDN-STING complexes.
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Affiliation(s)
- Zdeněk Vavřina
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
- Department
of Biochemistry, Faculty of Science, Charles
University, Hlavova 2030/8, Prague 128 00, Czech Republic
| | - Pavla Perlíková
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
- Department
of Organic Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology, Technicka 5, Prague 166 28, Czech Republic
| | - Nemanja Milisavljević
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
- Department
of Organic Chemistry, Faculty of Science, Charles University, Hlavova 2030/8, Prague 128 00, Czech Republic
| | - Florian Chevrier
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
| | - Miroslav Smola
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
| | - Joshua Smith
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
- First
Faculty of Medicine, Charles University, Katerinska 1660/32, Prague 121 08, Czech Republic
| | - Milan Dejmek
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
| | - Vojtěch Havlíček
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
- Department
of Organic Chemistry, Faculty of Science, Charles University, Hlavova 2030/8, Prague 128 00, Czech Republic
| | - Miloš Buděšínský
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
| | - Radek Liboska
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
| | - Lenka Vaneková
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
- Department
of Cell Biology, Faculty of Science, Charles
University, Vinicna 1594/7, Prague 128 43, Czech Republic
| | - Jiří Brynda
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
| | - Evzen Boura
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
| | - Pavlína Řezáčová
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
| | - Michal Hocek
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
| | - Gabriel Birkuš
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
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10
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Feng Y, Zhang F, Huang S, Deng Z, Bai L, Zheng J. Structural visualization of transient interactions between the cis-acting acyltransferase and acyl carrier protein of the salinomycin modular polyketide synthase. ACTA CRYSTALLOGRAPHICA SECTION D STRUCTURAL BIOLOGY 2022; 78:779-791. [DOI: 10.1107/s2059798322004612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 05/02/2022] [Indexed: 11/10/2022]
Abstract
Transient protein–protein interactions between cis-acting acyltransferase (AT) and acyl carrier protein (ACP) domains are critical for the catalysis and processivity of modular polyketide synthases (mPKSs), but are challenging for structural characterization due to the intrinsically weak binding affinity. Here, a stable complex of cis-acting AT and ACP domains from the ninth module of the salinomycin mPKS was obtained using a maleimide cross-linker and the structure of the complex was determined at 2.6 Å resolution. The crystal structure shows that the AT in combination with the ketosynthase (KS)-to-AT linker forms a C-shaped architecture to embrace the ACP. The large hydrolase subdomain of the AT serves as a major binding platform for the ACP, while the small ferredoxin-like subdomain of the AT and the KS-to-AT linker cooperate with each other to constrain binding of the ACP. The importance of interface residues in cis-acting AT–ACP interactions was confirmed by mutagenesis assays. The interaction mode observed in the cis-acting AT–ACP complex is completely different from those observed in trans-acting AT–ACP complexes, where the ACP primarily contacts the small domain of the AT. The complex structure provides detailed mechanistic insights into AT–ACP recognition in cis-AT mPKSs.
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11
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Joosten RP, Nicholls RA, Agirre J. Towards Consistency in Geometry Restraints for Carbohydrates in the Pyranose form: Modern Dictionary Generators Reviewed. Curr Med Chem 2022; 29:1193-1207. [PMID: 34477506 PMCID: PMC7612510 DOI: 10.2174/0929867328666210902140754] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 08/03/2021] [Accepted: 08/07/2021] [Indexed: 11/23/2022]
Abstract
Macromolecular restrained refinement is nowadays the most used method for improving the agreement between an atomic structural model and experimental data. Restraint dictionaries, a key tool behind the success of the method, allow fine-tuning geometric properties such as distances and angles between atoms beyond simplistic expectations. Dictionary generators can provide restraint target estimates derived from different sources, from fully theoretical to experimental and any combination in between. Carbohydrates are stereochemically complex biomolecules and, in their pyranose form, have clear conformational preferences. As such, they pose unique problems to dictionary generators and in the course of this study, require special attention from software developers. Functional differences between restraint generators will be discussed, as well as the process of achieving consistent results with different software designs. The study will conclude a set of practical considerations, as well as recommendations for the generation of new restraint dictionaries, using the improved software alternatives discussed.
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Affiliation(s)
| | | | - Jon Agirre
- Address correspondence to this author at the York Structural Biology Laboratory, Department of Chemistry, University of York, YO10 5DD, England; Tel: +44 (0) 1904 32 8252;, E-mail:
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12
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Novotná B, Holá L, Staś M, Gutten O, Smola M, Zavřel M, Vavřina Z, Buděšínský M, Liboska R, Chevrier F, Dobiaš J, Boura E, Rulíšek L, Birkuš G. Enzymatic Synthesis of 3'-5', 3'-5' Cyclic Dinucleotides, Their Binding Properties to the Stimulator of Interferon Genes Adaptor Protein, and Structure/Activity Correlations. Biochemistry 2021; 60:3714-3727. [PMID: 34788017 DOI: 10.1021/acs.biochem.1c00692] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The 3'-5', 3'-5' cyclic dinucleotides (3'3'CDNs) are bacterial second messengers that can also bind to the stimulator of interferon genes (STING) adaptor protein in vertebrates and activate the host innate immunity. Here, we profiled the substrate specificity of four bacterial dinucleotide synthases from Vibrio cholerae (DncV), Bacillus thuringiensis (btDisA), Escherichia coli (dgcZ), and Thermotoga maritima (tDGC) using a library of 33 nucleoside-5'-triphosphate analogues and then employed these enzymes to synthesize 24 3'3'CDNs. The STING affinity of CDNs was evaluated in cell-based and biochemical assays, and their ability to induce cytokines was determined by employing human peripheral blood mononuclear cells. Interestingly, the prepared heterodimeric 3'3'CDNs bound to the STING much better than their homodimeric counterparts and showed similar or better potency than bacterial 3'3'CDNs. We also rationalized the experimental findings by in-depth STING-CDN structure-activity correlations by dissecting computed interaction free energies into a set of well-defined and intuitive terms. To this aim, we employed state-of-the-art methods of computational chemistry, such as quantum mechanics/molecular mechanics (QM/MM) calculations, and complemented the computed results with the {STING:3'3'c-di-ara-AMP} X-ray crystallographic structure. QM/MM identified three outliers (mostly homodimers) for which we have no clear explanation of their impaired binding with respect to their heterodimeric counterparts, whereas the R2 = 0.7 correlation between the computed ΔG'int_rel and experimental ΔTm's for the remaining ligands has been very encouraging.
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Affiliation(s)
- Barbora Novotná
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic.,Faculty of Science, Charles University, Albertov 6, Prague 12800, Czech Republic
| | - Lucie Holá
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Monika Staś
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Ondrej Gutten
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Miroslav Smola
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Martin Zavřel
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Zdeněk Vavřina
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic.,Faculty of Science, Charles University, Albertov 6, Prague 12800, Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Radek Liboska
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Florian Chevrier
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Juraj Dobiaš
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Gabriel Birkuš
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic
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13
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Pospich S, Sweeney HL, Houdusse A, Raunser S. High-resolution structures of the actomyosin-V complex in three nucleotide states provide insights into the force generation mechanism. eLife 2021; 10:e73724. [PMID: 34812732 PMCID: PMC8735999 DOI: 10.7554/elife.73724] [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: 09/08/2021] [Accepted: 11/22/2021] [Indexed: 11/13/2022] Open
Abstract
The molecular motor myosin undergoes a series of major structural transitions during its force-producing motor cycle. The underlying mechanism and its coupling to ATP hydrolysis and actin binding are only partially understood, mostly due to sparse structural data on actin-bound states of myosin. Here, we report 26 high-resolution cryo-EM structures of the actomyosin-V complex in the strong-ADP, rigor, and a previously unseen post-rigor transition state that binds the ATP analog AppNHp. The structures reveal a high flexibility of myosin in each state and provide valuable insights into the structural transitions of myosin-V upon ADP release and binding of AppNHp, as well as the actomyosin interface. In addition, they show how myosin is able to specifically alter the structure of F-actin.
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Affiliation(s)
- Sabrina Pospich
- Department of Structural Biochemistry, Max Planck Institute of Molecular PhysiologyDortmundGermany
| | - H Lee Sweeney
- Department of Pharmacology and Therapeutics and the Myology Institute, University of FloridaGainesvilleUnited States
| | - Anne Houdusse
- Structural Motility, Institut Curie, Centre National de la Recherche ScientifiqueParisFrance
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular PhysiologyDortmundGermany
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14
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Abstract
Efforts to improve estrogen receptor-α (ER)-targeted therapies in breast cancer have relied upon a single mechanism, with ligands having a single side chain on the ligand core that extends outward to determine antagonism of breast cancer growth. Here, we describe inhibitors with two ER-targeting moieties, one of which uses an alternate structural mechanism to generate full antagonism, freeing the side chain to independently determine other critical properties of the ligands. By combining two molecular targeting approaches into a single ER ligand, we have generated antiestrogens that function through new mechanisms and structural paradigms to achieve antagonism. These dual-mechanism ER inhibitors (DMERIs) cause alternate, noncanonical structural perturbations of the receptor ligand-binding domain (LBD) to antagonize proliferation in ER-positive breast cancer cells and in allele-specific resistance models. Our structural analyses with DMERIs highlight marked differences from current standard-of-care, single-mechanism antiestrogens. These findings uncover an enhanced flexibility of the ER LBD through which it can access nonconsensus conformational modes in response to DMERI binding, broadly and effectively suppressing ER activity.
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15
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Brzezinski D, Porebski PJ, Kowiel M, Macnar JM, Minor W. Recognizing and validating ligands with CheckMyBlob. Nucleic Acids Res 2021; 49:W86-W92. [PMID: 33905501 PMCID: PMC8262754 DOI: 10.1093/nar/gkab296] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/04/2021] [Accepted: 04/11/2021] [Indexed: 11/15/2022] Open
Abstract
Structure-guided drug design depends on the correct identification of ligands in crystal structures of protein complexes. However, the interpretation of the electron density maps is challenging and often burdened with confirmation bias. Ligand identification can be aided by automatic methods such as CheckMyBlob, a machine learning algorithm that learns to generalize ligand descriptions from sets of moieties deposited in the Protein Data Bank. Here, we present the CheckMyBlob web server, a platform that can identify ligands in unmodeled fragments of electron density maps or validate ligands in existing models. The server processes PDB/mmCIF and MTZ files and returns a ranking of 10 most likely ligands for each detected electron density blob along with interactive 3D visualizations. Additionally, for each prediction/validation, a plugin script is generated that enables users to conduct a detailed analysis of the server results in Coot. The CheckMyBlob web server is available at https://checkmyblob.bioreproducibility.org.
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Affiliation(s)
- Dariusz Brzezinski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA.,Institute of Computing Science, Poznan University of Technology, Poznan, 60-965, Poland.,Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Przemyslaw J Porebski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Marcin Kowiel
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Joanna M Macnar
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA.,College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Warsaw, 02-097, Poland.,Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Warsaw, 02-089, Poland
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
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16
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Nicholls RA, Wojdyr M, Joosten RP, Catapano L, Long F, Fischer M, Emsley P, Murshudov GN. The missing link: covalent linkages in structural models. Acta Crystallogr D Struct Biol 2021; 77:727-745. [PMID: 34076588 PMCID: PMC8171067 DOI: 10.1107/s2059798321003934] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/13/2021] [Indexed: 11/10/2022] Open
Abstract
Covalent linkages between constituent blocks of macromolecules and ligands have been subject to inconsistent treatment during the model-building, refinement and deposition process. This may stem from a number of sources, including difficulties with initially detecting the covalent linkage, identifying the correct chemistry, obtaining an appropriate restraint dictionary and ensuring its correct application. The analysis presented herein assesses the extent of problems involving covalent linkages in the Protein Data Bank (PDB). Not only will this facilitate the remediation of existing models, but also, more importantly, it will inform and thus improve the quality of future linkages. By considering linkages of known type in the CCP4 Monomer Library (CCP4-ML), failure to model a covalent linkage is identified to result in inaccurate (systematically longer) interatomic distances. Scanning the PDB for proximal atom pairs that do not have a corresponding type in the CCP4-ML reveals a large number of commonly occurring types of unannotated potential linkages; in general, these may or may not be covalently linked. Manual consideration of the most commonly occurring cases identifies a number of genuine classes of covalent linkages. The recent expansion of the CCP4-ML is discussed, which has involved the addition of over 16 000 and the replacement of over 11 000 component dictionaries using AceDRG. As part of this effort, the CCP4-ML has also been extended using AceDRG link dictionaries for the aforementioned linkage types identified in this analysis. This will facilitate the identification of such linkage types in future modelling efforts, whilst concurrently easing the process involved in their application. The need for a universal standard for maintaining link records corresponding to covalent linkages, and references to the associated dictionaries used during modelling and refinement, following deposition to the PDB is emphasized. The importance of correctly modelling covalent linkages is demonstrated using a case study, which involves the covalent linkage of an inhibitor to the main protease in various viral species, including SARS-CoV-2. This example demonstrates the importance of properly modelling covalent linkages using a comprehensive restraint dictionary, as opposed to just using a single interatomic distance restraint or failing to model the covalent linkage at all.
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Affiliation(s)
- Robert A. Nicholls
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Marcin Wojdyr
- Global Phasing Limited, Sheraton House, Castle Park, Cambridge CB3 0AX, United Kingdom
| | - Robbie P. Joosten
- Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
- Oncode Institute, The Netherlands
| | - Lucrezia Catapano
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
- Randall Centre for Cell and Molecular Biophysics, Faculty of Life Sciences and Medicine, King’s College London, London SE1 9RT, United Kingdom
| | - Fei Long
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Marcus Fischer
- Chemical Biology and Therapeutics and Structural Biology, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105-3678, USA
| | - Paul Emsley
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Garib N. Murshudov
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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17
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Manna MS, Tamer YT, Gaszek I, Poulides N, Ahmed A, Wang X, Toprak FCR, Woodard DR, Koh AY, Williams NS, Borek D, Atilgan AR, Hulleman JD, Atilgan C, Tambar U, Toprak E. A trimethoprim derivative impedes antibiotic resistance evolution. Nat Commun 2021; 12:2949. [PMID: 34011959 PMCID: PMC8134463 DOI: 10.1038/s41467-021-23191-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 04/06/2021] [Indexed: 01/07/2023] Open
Abstract
The antibiotic trimethoprim (TMP) is used to treat a variety of Escherichia coli infections, but its efficacy is limited by the rapid emergence of TMP-resistant bacteria. Previous laboratory evolution experiments have identified resistance-conferring mutations in the gene encoding the TMP target, bacterial dihydrofolate reductase (DHFR), in particular mutation L28R. Here, we show that 4'-desmethyltrimethoprim (4'-DTMP) inhibits both DHFR and its L28R variant, and selects against the emergence of TMP-resistant bacteria that carry the L28R mutation in laboratory experiments. Furthermore, antibiotic-sensitive E. coli populations acquire antibiotic resistance at a substantially slower rate when grown in the presence of 4'-DTMP than in the presence of TMP. We find that 4'-DTMP impedes evolution of resistance by selecting against resistant genotypes with the L28R mutation and diverting genetic trajectories to other resistance-conferring DHFR mutations with catalytic deficiencies. Our results demonstrate how a detailed characterization of resistance-conferring mutations in a target enzyme can help identify potential drugs against antibiotic-resistant bacteria, which may ultimately increase long-term efficacy of antimicrobial therapies by modulating evolutionary trajectories that lead to resistance.
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Affiliation(s)
- Madhu Sudan Manna
- grid.267313.20000 0000 9482 7121Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX USA ,grid.267313.20000 0000 9482 7121Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Yusuf Talha Tamer
- grid.267313.20000 0000 9482 7121Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Ilona Gaszek
- grid.267313.20000 0000 9482 7121Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Nicole Poulides
- grid.267313.20000 0000 9482 7121Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Ayesha Ahmed
- grid.267313.20000 0000 9482 7121Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Xiaoyu Wang
- grid.267313.20000 0000 9482 7121Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Furkan C. R. Toprak
- grid.264756.40000 0004 4687 2082Texas A&M University, College Station, TX USA
| | - DaNae R. Woodard
- grid.267313.20000 0000 9482 7121Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Andrew Y. Koh
- grid.267313.20000 0000 9482 7121Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX USA ,grid.267313.20000 0000 9482 7121Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Noelle S. Williams
- grid.267313.20000 0000 9482 7121Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Dominika Borek
- grid.267313.20000 0000 9482 7121Department of Molecular Biophysics, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Ali Rana Atilgan
- grid.5334.10000 0004 0637 1566Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - John D. Hulleman
- grid.267313.20000 0000 9482 7121Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, TX USA ,grid.267313.20000 0000 9482 7121Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Canan Atilgan
- grid.5334.10000 0004 0637 1566Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Uttam Tambar
- grid.267313.20000 0000 9482 7121Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Erdal Toprak
- grid.267313.20000 0000 9482 7121Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX USA ,grid.267313.20000 0000 9482 7121Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX USA
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18
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Pei J, Wagner ND, Zou AJ, Chatterjee S, Borek D, Cole AR, Kim PJ, Basler CF, Otwinowski Z, Gross ML, Amarasinghe GK, Leung DW. Structural basis for IFN antagonism by human respiratory syncytial virus nonstructural protein 2. Proc Natl Acad Sci U S A 2021; 118:e2020587118. [PMID: 33649232 PMCID: PMC7958447 DOI: 10.1073/pnas.2020587118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Human respiratory syncytial virus (RSV) nonstructural protein 2 (NS2) inhibits host interferon (IFN) responses stimulated by RSV infection by targeting early steps in the IFN-signaling pathway. But the molecular mechanisms related to how NS2 regulates these processes remain incompletely understood. To address this gap, here we solved the X-ray crystal structure of NS2. This structure revealed a unique fold that is distinct from other known viral IFN antagonists, including RSV NS1. We also show that NS2 directly interacts with an inactive conformation of the RIG-I-like receptors (RLRs) RIG-I and MDA5. NS2 binding prevents RLR ubiquitination, a process critical for prolonged activation of downstream signaling. Structural analysis, including by hydrogen-deuterium exchange coupled to mass spectrometry, revealed that the N terminus of NS2 is essential for binding to the RIG-I caspase activation and recruitment domains. N-terminal mutations significantly diminish RIG-I interactions and result in increased IFNβ messenger RNA levels. Collectively, our studies uncover a previously unappreciated regulatory mechanism by which NS2 further modulates host responses and define an approach for targeting host responses.
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Affiliation(s)
- Jingjing Pei
- John T. Milliken Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO 63110
| | - Nicole D Wagner
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63110
| | - Angela J Zou
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Srirupa Chatterjee
- John T. Milliken Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO 63110
| | - Dominika Borek
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Aidan R Cole
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Preston J Kim
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Christopher F Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303
| | - Zbyszek Otwinowski
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63110
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Daisy W Leung
- John T. Milliken Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO 63110;
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
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19
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Engineering subtilisin proteases that specifically degrade active RAS. Commun Biol 2021; 4:299. [PMID: 33674772 PMCID: PMC7935941 DOI: 10.1038/s42003-021-01818-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 02/10/2021] [Indexed: 12/18/2022] Open
Abstract
We describe the design, kinetic properties, and structures of engineered subtilisin proteases that degrade the active form of RAS by cleaving a conserved sequence in switch 2. RAS is a signaling protein that, when mutated, drives a third of human cancers. To generate high specificity for the RAS target sequence, the active site was modified to be dependent on a cofactor (imidazole or nitrite) and protease sub-sites were engineered to create a linkage between substrate and cofactor binding. Selective proteolysis of active RAS arises from a 2-step process wherein sub-site interactions promote productive binding of the cofactor, enabling cleavage. Proteases engineered in this way specifically cleave active RAS in vitro, deplete the level of RAS in a bacterial reporter system, and also degrade RAS in human cell culture. Although these proteases target active RAS, the underlying design principles are fundamental and will be adaptable to many target proteins.
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20
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Modhiran N, Song H, Liu L, Bletchly C, Brillault L, Amarilla AA, Xu X, Qi J, Chai Y, Cheung STM, Traves R, Setoh YX, Bibby S, Scott CAP, Freney ME, Newton ND, Khromykh AA, Chappell KJ, Muller DA, Stacey KJ, Landsberg MJ, Shi Y, Gao GF, Young PR, Watterson D. A broadly protective antibody that targets the flavivirus NS1 protein. Science 2021; 371:190-194. [PMID: 33414219 DOI: 10.1126/science.abb9425] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 11/30/2020] [Indexed: 12/24/2022]
Abstract
There are no approved flaviviral therapies and the development of vaccines against flaviruses has the potential of being undermined by antibody-dependent enhancement (ADE). The flavivirus nonstructural protein 1 (NS1) is a promising vaccine antigen with low ADE risk but has yet to be explored as a broad-spectrum therapeutic antibody target. Here, we provide the structural basis of NS1 antibody cross-reactivity through cocrystallization of the antibody 1G5.3 with NS1 proteins from dengue and Zika viruses. The 1G5.3 antibody blocks multi-flavivirus NS1-mediated cell permeability in disease-relevant cell lines, and therapeutic application of 1G5.3 reduces viremia and improves survival in dengue, Zika, and West Nile virus murine models. Finally, we demonstrate that 1G5.3 protection is independent of effector function, identifying the 1G5.3 epitope as a key site for broad-spectrum antiviral development.
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Affiliation(s)
- Naphak Modhiran
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Hao Song
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Lidong Liu
- Division of Laboratory Medicine, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Cheryl Bletchly
- Microbiology, Pathology Queensland, Queensland Health, Herston, Queensland, Australia
| | - Lou Brillault
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.,Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Australia
| | - Alberto A Amarilla
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Xiaoying Xu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yan Chai
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Stacey T M Cheung
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Renee Traves
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Yin Xiang Setoh
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Summa Bibby
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Connor A P Scott
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Morgan E Freney
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Natalee D Newton
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Alexander A Khromykh
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Keith J Chappell
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - David A Muller
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Katryn J Stacey
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Michael J Landsberg
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Yi Shi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - George F Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China. .,Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Paul R Young
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.
| | - Daniel Watterson
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.
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21
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Vavřina Z, Gutten O, Smola M, Zavřel M, Aliakbar Tehrani Z, Charvát V, Kožíšek M, Boura E, Birkuš G, Rulíšek L. Protein-Ligand Interactions in the STING Binding Site Probed by Rationally Designed Single-Point Mutations: Experiment and Theory. Biochemistry 2021; 60:607-620. [PMID: 33586948 DOI: 10.1021/acs.biochem.0c00949] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
STING protein (stimulator of interferon genes) plays an important role in the innate immune system. A number of potent compounds regulating its activity have been reported, mostly derivatives of cyclic dinucleotides (CDNs), natural STING agonists. Here, we aim to provide complementary information to large-scale "ligand-profiling" studies by probing the importance of STING-CDN protein-ligand interactions on the protein side. We examined in detail six typical CDNs each in complex with 13 rationally devised mutations in STING: S162A, S162T, Y167F, G230A, R232K, R232H, A233L, A233I, R238K, T263A, T263S, R293Q, and G230A/R293Q. The mutations switch on and off various types of protein-ligand interactions: π-π stacking, hydrogen bonding, ionic pairing, and nonpolar contacts. We correlated experimental data obtained by differential scanning fluorimetry, X-ray crystallography, and isothermal titration calorimetry with theoretical calculations. This enabled us to provide a mechanistic interpretation of the differences in the binding of representative CDNs to STING. We observed that the G230A mutation increased the thermal stability of the protein-ligand complex, indicating an increased level of ligand binding, whereas R238K and Y167F led to a complete loss of stabilization (ligand binding). The effects of the other mutations depended on the type of ligand (CDN) and varied, to some extent. A very good correlation (R2 = 0.6) between the experimental binding affinities and interaction energies computed by quantum chemical methods enabled us to explain the effect of the studied mutations in detail and evaluate specific interactions quantitatively. Our work may inspire development of high-affinity ligands against the common STING haplotypes by targeting the key (sometimes non-intuitive) protein-ligand interactions.
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Affiliation(s)
- Zdeněk Vavřina
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University, Prague 110 00, Czech Republic
| | - Ondrej Gutten
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Miroslav Smola
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Martin Zavřel
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Zahra Aliakbar Tehrani
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic.,Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, Vestec 252 50, Czech Republic
| | - Vilém Charvát
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Milan Kožíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Gabriel Birkuš
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic
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22
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Balobanov V, Lekontseva N, Mikhaylina A, Nikulin A. Use of Fluorescent Nucleotides to Map RNA-Binding Sites on Protein Surface. Methods Mol Biol 2021; 2113:251-262. [PMID: 32006319 DOI: 10.1007/978-1-0716-0278-2_17] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Currently, studies of RNA/protein interactions occupy a prominent place in molecular biology and medicine. The structures of RNA-protein complexes may be determined by X-ray crystallography or NMR for further analyses. These methods are time-consuming and difficult due to the versatility and dynamics of the RNA structure. Furthermore, due to the need to solve the "phase problem" for each dataset in crystallography, crystallographic structures of RNA are still underrepresented. Structure determination of single ribonucleotide-protein complexes is a useful tool to identify the position of single-stranded RNA-binding sites in proteins. We describe here a structural approach that incorporates affinity measurement of a protein for various single ribonucleotides, ranking the RNA/protein complexes according to their stability. This chapter describes how to perform these measurements, including a perspective for the analysis of RNA-binding sites in protein and single-nucleotide crystal soaking.
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Affiliation(s)
- V Balobanov
- Institute of Protein Research Russian Academy of Sciences, Pushchino, Moscow Region, Russia.
| | - N Lekontseva
- Institute of Protein Research Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - A Mikhaylina
- Institute of Protein Research Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - A Nikulin
- Institute of Protein Research Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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23
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Pathak S, Parkar H, Tripathi S, Kale A. Ofloxacin as a Disruptor of Actin Aggresome "Hirano Bodies": A Potential Repurposed Drug for the Treatment of Neurodegenerative Diseases. Front Aging Neurosci 2020; 12:591579. [PMID: 33132905 PMCID: PMC7573105 DOI: 10.3389/fnagi.2020.591579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 09/09/2020] [Indexed: 01/27/2023] Open
Abstract
There is a growing number of aging populations that are more prone to the prevalence of neuropathological disorders. Two major diseases that show a late onset of the symptoms include Alzheimer’s disorder (AD) and Parkinson’s disorder (PD), which are causing an unexpected social and economic impact on the families. A large number of researches in the last decade have focused upon the role of amyloid precursor protein, Aβ-plaque, and intraneuronal neurofibrillary tangles (tau-proteins). However, there is very few understanding of actin-associated paracrystalline structures formed in the hippocampus region of the brain and are called Hirano bodies. These actin-rich inclusion bodies are known to modulate the synaptic plasticity and employ conspicuous effects on long-term potentiation and paired-pulse paradigms. Since the currently known drugs have very little effect in controlling the progression of these diseases, there is a need to develop therapeutic agents, which can have improved efficacy and bioavailability, and can transport across the blood–brain barrier. Moreover, finding novel targets involving compound screening is both laborious and is an expensive process in itself followed by equally tedious Food and Drug Administration (FDA) approval exercise. Finding alternative functions to the already existing FDA-approved molecules for reversing the progression of age-related proteinopathies is of utmost importance. In the current study, we decipher the role of a broad-spectrum general antibiotic (Ofloxacin) on actin polymerization dynamics using various biophysical techniques like right-angle light scattering, dynamic light scattering, circular dichroism spectrometry, isothermal titration calorimetry, scanning electron microscopy, etc. We have also performed in silico docking studies to deduce a plausible mechanism of the drug binding to the actin. We report that actin gets disrupted upon binding to Ofloxacin in a concentration-dependent manner. We have inferred that Ofloxacin, when attached to a drug delivery system, can act as a good candidate for the treatment of neuropathological diseases.
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Affiliation(s)
- Samridhi Pathak
- School of Chemical Sciences, University of Mumbai - Department of Atomic Energy Center for Excellence in Basic Sciences, University of Mumbai, Vidyanagari Campus, Mumbai, India
| | - Haifa Parkar
- School of Chemical Sciences, University of Mumbai - Department of Atomic Energy Center for Excellence in Basic Sciences, University of Mumbai, Vidyanagari Campus, Mumbai, India
| | - Sarita Tripathi
- School of Chemical Sciences, University of Mumbai - Department of Atomic Energy Center for Excellence in Basic Sciences, University of Mumbai, Vidyanagari Campus, Mumbai, India
| | - Avinash Kale
- School of Chemical Sciences, University of Mumbai - Department of Atomic Energy Center for Excellence in Basic Sciences, University of Mumbai, Vidyanagari Campus, Mumbai, India
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24
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Pemberton JG, Kim YJ, Humpolickova J, Eisenreichova A, Sengupta N, Toth DJ, Boura E, Balla T. Defining the subcellular distribution and metabolic channeling of phosphatidylinositol. J Cell Biol 2020; 219:133809. [PMID: 32211894 PMCID: PMC7054996 DOI: 10.1083/jcb.201906130] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 11/08/2019] [Accepted: 12/23/2019] [Indexed: 02/06/2023] Open
Abstract
Phosphatidylinositol (PI) is an essential structural component of eukaryotic membranes that also serves as the common precursor for polyphosphoinositide (PPIn) lipids. Despite the recognized importance of PPIn species for signal transduction and membrane homeostasis, there is still a limited understanding of the relationship between PI availability and the turnover of subcellular PPIn pools. To address these shortcomings, we established a molecular toolbox for investigations of PI distribution within intact cells by exploiting the properties of a bacterial enzyme, PI-specific PLC (PI-PLC). Using these tools, we find a minor presence of PI in membranes of the ER, as well as a general enrichment within the cytosolic leaflets of the Golgi complex, peroxisomes, and outer mitochondrial membrane, but only detect very low steady-state levels of PI within the plasma membrane (PM) and endosomes. Kinetic studies also demonstrate the requirement for sustained PI supply from the ER for the maintenance of monophosphorylated PPIn species within the PM, Golgi complex, and endosomal compartments.
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Affiliation(s)
- Joshua G Pemberton
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Yeun Ju Kim
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Jana Humpolickova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Andrea Eisenreichova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Nivedita Sengupta
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Daniel J Toth
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Tamas Balla
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
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25
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Pathak S, Deori N, Sharma A, Nagotu S, Kale A. In vitro, in vivo and in silico rationale for the muscle loss due to therapeutic drugs used in the treatment of Mycobacterium tuberculosis infection. J Biomol Struct Dyn 2020; 40:44-60. [PMID: 32795137 DOI: 10.1080/07391102.2020.1806928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Tuberculosis globally affects millions of people every year and is responsible for high rates of mortality and morbidity in tropical countries like India. The treatment of tuberculosis involves using the first line of drugs especially Isoniazid, Pyrazinamide, Streptomycin, Ethambutol and Rifampicin for treatment under the DOTS (Directly Observed Treatment Shots) regime which can last up to minimum of six months. These drugs although widely used against Mycobacterium tuberculosis has given rise to multi drug resistant (MDR) tuberculosis strain. It has been observed widely that prolonged drug treatment for tuberculosis patient has rendered several side effects that include increasing muscle wasting and malnutrition. In our study, we have investigated the role of these major tuberculosis drugs namely Rifampicin, Streptomycin, Isoniazid, Pyrazinamide, and Ethambutol on actin polymerization which are famously known to be a central player in the sarcomere region of the muscle in human body. For in vitro studies, we have used biophysical approaches such as 90° scattering assay (RLS), size exclusion chromatography (SEC), Dynamic light scattering (DLS), Circular dichroism spectroscopy (CD), Scanning electron microscopy (SEM), Transmission electron microscopy (TEM), kinetic analysis to understand the time taken to break down effect of above mentioned drugs on actin disruption. In vivo analysis was carried out on yeast Δend3 mutants which are rich in F-actin filaments in order to understand the effect of the aforementioned drugs in rendering the muscle wasting phenomenon in tuberculosis. Furthermore, we also carried out in silico analysis to understand the probable modes of binding of these drugs on actin filaments.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Samridhi Pathak
- School of Chemical Sciences, UM-DAE Center for excellence in basic sciences, University of Mumbai, Mumbai, India
| | - Nayan Deori
- Organelle Biology and Cellular Ageing Lab (OBCAL), Department of Biosciences and Bioengineering (BSBE), Indian Institute of Technology Guwahati (IITG), Guwahati, India
| | - Aditi Sharma
- School of Biotechnology and Bioinformatics, D. Y. Patil Deemed to be University, Navi Mumbai, India
| | - Shirisha Nagotu
- Organelle Biology and Cellular Ageing Lab (OBCAL), Department of Biosciences and Bioengineering (BSBE), Indian Institute of Technology Guwahati (IITG), Guwahati, India
| | - Avinash Kale
- School of Chemical Sciences, UM-DAE Center for excellence in basic sciences, University of Mumbai, Mumbai, India
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26
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Levenfors JJ, Nord C, Bjerketorp J, Ståhlberg J, Larsson R, Guss B, Öberg B, Broberg A. Antibacterial pyrrolidinyl and piperidinyl substituted 2,4-diacetylphloroglucinols from Pseudomonas protegens UP46. J Antibiot (Tokyo) 2020; 73:739-747. [PMID: 32439988 DOI: 10.1038/s41429-020-0318-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/24/2020] [Accepted: 04/28/2020] [Indexed: 12/12/2022]
Abstract
In the search for new antibiotic compounds, fractionation of Pseudomonas protegens UP46 culture extracts afforded several known Pseudomonas compounds, including 2,4-diacetylphloroglucinol (DAPG), as well as two new antibacterial alkaloids, 6-(pyrrolidin-2-yl)DAPG (1) and 6-(piperidin-2-yl)DAPG (2). The structures of 1 and 2 were determined by nuclear magnetic resonance spectroscopy and mass spectrometry. Compounds 1 and 2 were found to have antibacterial activity against the Gram-positive bacteria Staphylococcus aureus and Bacillus cereus, with minimal inhibitory concentration (MIC) 2 and 4 μg ml-1, respectively, for 1, and 2 μg ml-1 for both pathogens for 2. The MICs for 1 and 2, against all tested Gram-negative bacteria, were >32 μg ml-1. The half maximal inhibitory concentrations against HepG2 cells for compounds 1 and 2 were 11 and 18 μg ml-1, respectively, which suggested 1 and 2 be too toxic for further evaluation as possible new antibacterial drugs. Stable isotope labelling experiments showed the pyrrolidinyl group of 1 to originate from ornithine and the piperidinyl group of 2 to originate from lysine. The P. protegens acetyl transferase (PpATase) is involved in the biosynthesis of monoacetylphloroglucinol and DAPG. No optical rotation was detected for 1 or 2, and a possible reason for this was investigated by studying if the PpATase may catalyse a stereo-non-specific introduction of the pyrrolidinyl/piperidinyl group in 1 and 2, but unless the PpATase can be subjected to major conformational changes, the enzyme cannot be involved in this reaction. The PpATase is, however, likely to catalyse the formation of 2,4,6-triacetylphloroglucinol from DAPG.
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Affiliation(s)
- Jolanta J Levenfors
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07, Uppsala, Sweden.,Ultupharma AB, Södra Rudbecksgatan 13, SE-752 36, Uppsala, Sweden
| | - Christina Nord
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07, Uppsala, Sweden
| | - Joakim Bjerketorp
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07, Uppsala, Sweden.,Ultupharma AB, Södra Rudbecksgatan 13, SE-752 36, Uppsala, Sweden
| | - Jerry Ståhlberg
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07, Uppsala, Sweden
| | - Rolf Larsson
- Department of Medical Sciences, Uppsala University, SE-751 85, Uppsala, Sweden
| | - Bengt Guss
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, P.O. Box 7036, SE-750 07, Uppsala, Sweden
| | - Bo Öberg
- Ultupharma AB, Södra Rudbecksgatan 13, SE-752 36, Uppsala, Sweden.,Department of Medicinal Chemistry, Uppsala University, P.O. Box 574, SE-751 23, Uppsala, Sweden
| | - Anders Broberg
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07, Uppsala, Sweden.
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27
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Lekontseva N, Mikhailina A, Fando M, Kravchenko O, Balobanov V, Tishchenko S, Nikulin A. Crystal structures and RNA-binding properties of Lsm proteins from archaea Sulfolobus acidocaldarius and Methanococcus vannielii: Similarity and difference of the U-binding mode. Biochimie 2020; 175:1-12. [PMID: 32422160 DOI: 10.1016/j.biochi.2020.05.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/30/2020] [Accepted: 05/01/2020] [Indexed: 12/13/2022]
Abstract
Sm and Sm-like (Lsm) proteins are considered as an evolutionary conserved family involved in RNA metabolism in organisms from bacteria and archaea to human. Currently, the function of Sm-like archaeal proteins (SmAP) is not well understood. Here, we report the crystal structures of SmAP proteins from Sulfolobus acidocaldarius and Methanococcus vannielii and a comparative analysis of their RNA-binding sites. Our data show that these SmAPs have only a uridine-specific RNA-binding site, unlike their bacterial homolog Hfq, which has three different RNA-binding sites. Moreover, variations in the amino acid composition of the U-binding sites of the two SmAPs lead to a difference in protein affinity for oligo(U) RNA. Surface plasmon resonance data and nucleotide-binding analysis confirm the high affinity of SmAPs for uridine nucleotides and oligo(U) RNA and the reduced affinity for adenines, guanines, cytidines and corresponding oligo-RNAs. In addition, we demonstrate that MvaSmAP1 and SacSmAP2 are capable of melting an RNA hairpin and, apparently, promote its interaction with complementary RNA.
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Affiliation(s)
- N Lekontseva
- Institute of Protein Research Russian Academy of Sciences, Institutskaya 4, Moscow Region, Pushchino, 142290, Russia
| | - A Mikhailina
- Institute of Protein Research Russian Academy of Sciences, Institutskaya 4, Moscow Region, Pushchino, 142290, Russia
| | - M Fando
- Institute of Protein Research Russian Academy of Sciences, Institutskaya 4, Moscow Region, Pushchino, 142290, Russia
| | - O Kravchenko
- Institute of Protein Research Russian Academy of Sciences, Institutskaya 4, Moscow Region, Pushchino, 142290, Russia
| | - V Balobanov
- Institute of Protein Research Russian Academy of Sciences, Institutskaya 4, Moscow Region, Pushchino, 142290, Russia
| | - S Tishchenko
- Institute of Protein Research Russian Academy of Sciences, Institutskaya 4, Moscow Region, Pushchino, 142290, Russia
| | - A Nikulin
- Institute of Protein Research Russian Academy of Sciences, Institutskaya 4, Moscow Region, Pushchino, 142290, Russia.
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28
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Casañal A, Lohkamp B, Emsley P. Current developments in Coot for macromolecular model building of Electron Cryo-microscopy and Crystallographic Data. Protein Sci 2020; 29:1069-1078. [PMID: 31730249 PMCID: PMC7096722 DOI: 10.1002/pro.3791] [Citation(s) in RCA: 380] [Impact Index Per Article: 95.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 11/13/2019] [Accepted: 11/14/2019] [Indexed: 12/20/2022]
Abstract
Coot is a tool widely used for model building, refinement, and validation of macromolecular structures. It has been extensively used for crystallography and, more recently, improvements have been introduced to aid in cryo‐EM model building and refinement, as cryo‐EM structures with resolution ranging 2.5–4 A are now routinely available. Model building into these maps can be time‐consuming and requires experience in both biochemistry and building into low‐resolution maps. To simplify and expedite the model building task, and minimize the needed expertise, new tools are being added in Coot. Some examples include morphing, Geman‐McClure restraints, full‐chain refinement, and Fourier‐model based residue‐type‐specific Ramachandran restraints. Here, we present the current state‐of‐the‐art in Coot usage.
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Affiliation(s)
- Ana Casañal
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Bernhard Lohkamp
- Division of Molecular Structural Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Paul Emsley
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
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29
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Zheng Z, Cheng Q, Chan EWC, Chen S. Genetic and Biochemical Characterization of VMB-1, a Novel Metallo-β-Lactamase Encoded by a Conjugative, Broad-Host Range IncC Plasmid from Vibrio spp. ACTA ACUST UNITED AC 2020; 4:e1900221. [PMID: 32293144 DOI: 10.1002/adbi.201900221] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/21/2019] [Indexed: 11/12/2022]
Abstract
The increasing incidence of phenotypic resistance to carbapenems in recent years is mainly attributed to acquisition of mobile carbapenemase-encoding genetic elements by major bacterial pathogens. Here, a novel carbapenemase known as Vibrio metallo-β-lactamase 1 (VMB-1), which is encoded by a gene (blaVMB-1 ) located in an integron-bearing, highly transmissible IncC type plasmid, namely pVB1796, is identified and characterized, both genetically and functionally. Recovered from a foodborne Vibrio alginolyticus strain that exhibits resistance to all known β-lactam antibiotics, pVB1796 is found to possess a hybrid backbone that exhibits unique features of both type 1 and type 2 IncC elements. VMB-1 exhibits 94% sequence homology with several recently reported but poorly characterized metallo-β-lactamases (MBLs) produced by the marine organisms Alteromonadaceae, Glaciecola, and Thalassomonas actiniarum. Sequence alignment analysis shows that VMB-1 shares a structurally identical active site with subclass B1 MBLs. Importantly, pVB1796 is found to be efficiently transferred from Vibrio to other Gram-negative bacterial pathogens, including Salmonella typhimurium, Klebsiella pneumoniae, and Acinetobacter baumanni, via conjugation. These findings suggest that blaVMB-1 -bearing plasmids have the potential to be disseminated to other Gram-negative bacterial pathogens in the near future and render carbapenems useless in treatment of multidrug resistant infections.
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Affiliation(s)
- Zhiwei Zheng
- Shenzhen Key Laboratory for Food Biological Safety Control, Food Safety and Technology Research Centre, The Hong Kong PolyU Shenzhen Research Institute, Shenzhen, 518052, P. R. China.,Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, 999077, Hong Kong
| | - Qipeng Cheng
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, 999077, Hong Kong.,State Key Lab of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, 999077, Hong Kong
| | - Edward Wai-Chi Chan
- State Key Lab of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, 999077, Hong Kong
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, 999077, Hong Kong
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30
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Lountos GT, Zhao XZ, Kiselev E, Tropea JE, Needle D, Pommier Y, Burke TR, Waugh DS. Identification of a ligand binding hot spot and structural motifs replicating aspects of tyrosyl-DNA phosphodiesterase I (TDP1) phosphoryl recognition by crystallographic fragment cocktail screening. Nucleic Acids Res 2019; 47:10134-10150. [PMID: 31199869 DOI: 10.1093/nar/gkz515] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 05/20/2019] [Accepted: 06/11/2019] [Indexed: 02/02/2023] Open
Abstract
Tyrosyl DNA-phosphodiesterase I (TDP1) repairs type IB topoisomerase (TOP1) cleavage complexes generated by TOP1 inhibitors commonly used as anticancer agents. TDP1 also removes DNA 3' end blocking lesions generated by chain-terminating nucleosides and alkylating agents, and base oxidation both in the nuclear and mitochondrial genomes. Combination therapy with TDP1 inhibitors is proposed to synergize with topoisomerase targeting drugs to enhance selectivity against cancer cells exhibiting deficiencies in parallel DNA repair pathways. A crystallographic fragment screening campaign against the catalytic domain of TDP1 was conducted to identify new lead compounds. Crystal structures revealed two fragments that bind to the TDP1 active site and exhibit inhibitory activity against TDP1. These fragments occupy a similar position in the TDP1 active site as seen in prior crystal structures of TDP1 with bound vanadate, a transition state mimic. Using structural insights into fragment binding, several fragment derivatives have been prepared and evaluated in biochemical assays. These results demonstrate that fragment-based methods can be a highly feasible approach toward the discovery of small-molecule chemical scaffolds to target TDP1, and for the first time, we provide co-crystal structures of small molecule inhibitors bound to TDP1, which could serve for the rational development of medicinal TDP1 inhibitors.
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Affiliation(s)
- George T Lountos
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Xue Zhi Zhao
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Evgeny Kiselev
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Joseph E Tropea
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Danielle Needle
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Yves Pommier
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Terrence R Burke
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - David S Waugh
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
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31
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Novotná B, Vaneková L, Zavřel M, Buděšínský M, Dejmek M, Smola M, Gutten O, Tehrani ZA, Pimková Polidarová M, Brázdová A, Liboska R, Štěpánek I, Vavřina Z, Jandušík T, Nencka R, Rulíšek L, Bouřa E, Brynda J, Páv O, Birkuš G. Enzymatic Preparation of 2'-5',3'-5'-Cyclic Dinucleotides, Their Binding Properties to Stimulator of Interferon Genes Adaptor Protein, and Structure/Activity Correlations. J Med Chem 2019; 62:10676-10690. [PMID: 31715099 DOI: 10.1021/acs.jmedchem.9b01062] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cyclic dinucleotides are second messengers in the cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway, which plays an important role in recognizing tumor cells and viral or bacterial infections. They bind to the STING adaptor protein and trigger expression of cytokines via TANK binding kinase 1 (TBK1)/interferon regulatory factor 3 (IRF3) and inhibitor of nuclear factor-κB (IκB) kinase (IKK)/nuclear factor-κB (NFκB) signaling cascades. In this work, we describe an enzymatic preparation of 2'-5',3'-5'-cyclic dinucleotides (2'3'CDNs) with use of cyclic GMP-AMP synthases (cGAS) from human, mouse, and chicken. We profile substrate specificity of these enzymes by employing a small library of nucleotide-5'-triphosphate (NTP) analogues and use them to prepare 33 2'3'CDNs. We also determine affinity of these CDNs to five different STING haplotypes in cell-based and biochemical assays and describe properties needed for their optimal activity toward all STING haplotypes. Next, we study their effect on cytokine and chemokine induction by human peripheral blood mononuclear cells (PBMCs) and evaluate their cytotoxic effect on monocytes. Additionally, we report X-ray crystal structures of two new CDNs bound to STING protein and discuss structure-activity relationship by using quantum and molecular mechanical (QM/MM) computational modeling.
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Affiliation(s)
- Barbora Novotná
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic.,Faculty of Science , Charles University , Prague 110 00 , Czech Republic
| | - Lenka Vaneková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic.,Faculty of Science , Charles University , Prague 110 00 , Czech Republic
| | - Martin Zavřel
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Milan Dejmek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Miroslav Smola
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Ondrej Gutten
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Zahra Aliakbar Tehrani
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Markéta Pimková Polidarová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic.,Faculty of Science , Charles University , Prague 110 00 , Czech Republic
| | - Andrea Brázdová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Radek Liboska
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Ivan Štěpánek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Zdeněk Vavřina
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic.,Faculty of Science , Charles University , Prague 110 00 , Czech Republic
| | - Tomáš Jandušík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic.,Faculty of Food and Biochemical Technology , University of Chemistry and Technology , Prague 166 28 , Czech Republic
| | - Radim Nencka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Evžen Bouřa
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Ondřej Páv
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Gabriel Birkuš
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
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32
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Zhang Z, Yu P, Gou Y, Zhang J, Li S, Cai M, Sun H, Yang F, Liang H. Novel Brain-Tumor-Inhibiting Copper(II) Compound Based on a Human Serum Albumin (HSA)-Cell Penetrating Peptide Conjugate. J Med Chem 2019; 62:10630-10644. [DOI: 10.1021/acs.jmedchem.9b00939] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Zhenlei Zhang
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, Guilin, Guangxi 541004, P. R. China
| | - Ping Yu
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, Guilin, Guangxi 541004, P. R. China
| | - Yi Gou
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, Guilin, Guangxi 541004, P. R. China
| | - Juzheng Zhang
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, Guilin, Guangxi 541004, P. R. China
| | - Shanhe Li
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, Guilin, Guangxi 541004, P. R. China
| | - Meiling Cai
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, Guilin, Guangxi 541004, P. R. China
| | - Hongbin Sun
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, China Pharmaceutical University, Nanjing, Jiangsu 210009, P. R. China
| | - Feng Yang
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, Guilin, Guangxi 541004, P. R. China
| | - Hong Liang
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, Guilin, Guangxi 541004, P. R. China
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33
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Kowiel M, Brzezinski D, Porebski PJ, Shabalin IG, Jaskolski M, Minor W. Automatic recognition of ligands in electron density by machine learning. Bioinformatics 2019; 35:452-461. [PMID: 30016407 DOI: 10.1093/bioinformatics/bty626] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 07/12/2018] [Indexed: 11/13/2022] Open
Abstract
Motivation The correct identification of ligands in crystal structures of protein complexes is the cornerstone of structure-guided drug design. However, cognitive bias can sometimes mislead investigators into modeling fictitious compounds without solid support from the electron density maps. Ligand identification can be aided by automatic methods, but existing approaches are based on time-consuming iterative fitting. Results Here we report a new machine learning algorithm called CheckMyBlob that identifies ligands from experimental electron density maps. In benchmark tests on portfolios of up to 219 931 ligand binding sites containing the 200 most popular ligands found in the Protein Data Bank, CheckMyBlob markedly outperforms the existing automatic methods for ligand identification, in some cases doubling the recognition rates, while requiring significantly less time. Our work shows that machine learning can improve the automation of structure modeling and significantly accelerate the drug screening process of macromolecule-ligand complexes. Availability and implementation Code and data are available on GitHub at https://github.com/dabrze/CheckMyBlob. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Marcin Kowiel
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Dariusz Brzezinski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.,Institute of Computing Science, Poznan University of Technology, Poznan, Poland
| | - Przemyslaw J Porebski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.,Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, VA, USA
| | - Ivan G Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.,Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, VA, USA
| | - Mariusz Jaskolski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.,Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.,Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, VA, USA
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34
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Moreno-Chicano T, Ebrahim A, Axford D, Appleby MV, Beale JH, Chaplin AK, Duyvesteyn HME, Ghiladi RA, Owada S, Sherrell DA, Strange RW, Sugimoto H, Tono K, Worrall JAR, Owen RL, Hough MA. High-throughput structures of protein-ligand complexes at room temperature using serial femtosecond crystallography. IUCRJ 2019; 6:1074-1085. [PMID: 31709063 PMCID: PMC6830213 DOI: 10.1107/s2052252519011655] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 08/21/2019] [Indexed: 05/09/2023]
Abstract
High-throughput X-ray crystal structures of protein-ligand complexes are critical to pharmaceutical drug development. However, cryocooling of crystals and X-ray radiation damage may distort the observed ligand binding. Serial femtosecond crystallography (SFX) using X-ray free-electron lasers (XFELs) can produce radiation-damage-free room-temperature structures. Ligand-binding studies using SFX have received only modest attention, partly owing to limited beamtime availability and the large quantity of sample that is required per structure determination. Here, a high-throughput approach to determine room-temperature damage-free structures with excellent sample and time efficiency is demonstrated, allowing complexes to be characterized rapidly and without prohibitive sample requirements. This yields high-quality difference density maps allowing unambiguous ligand placement. Crucially, it is demonstrated that ligands similar in size or smaller than those used in fragment-based drug design may be clearly identified in data sets obtained from <1000 diffraction images. This efficiency in both sample and XFEL beamtime opens the door to true high-throughput screening of protein-ligand complexes using SFX.
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Affiliation(s)
- Tadeo Moreno-Chicano
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Ali Ebrahim
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Danny Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Martin V. Appleby
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - John H. Beale
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Amanda K. Chaplin
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Helen M. E. Duyvesteyn
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Division of Structural Biology (STRUBI), University of Oxford, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN, England
| | - Reza A. Ghiladi
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA
| | - Shigeki Owada
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Darren A. Sherrell
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Richard W. Strange
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | | | - Kensuke Tono
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Jonathan A. R. Worrall
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Robin L. Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Michael A. Hough
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
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35
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Cheng Y, He B, Yang J, Ye F, Lin S, Yang F, Chen Z, Chen Z, Cao Y, Lu G. Crystal structure of the S1 subunit N-terminal domain from DcCoV UAE-HKU23 spike protein. Virology 2019; 535:74-82. [PMID: 31279241 PMCID: PMC7112003 DOI: 10.1016/j.virol.2019.06.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 06/18/2019] [Accepted: 06/26/2019] [Indexed: 02/05/2023]
Abstract
The DcCoV UAE-HKU23 coronavirus is a newly-found betacoronavirus (betaCoV) that can infect human cells. The viral spike protein plays pivotal roles in mediating receptor-recognition and membrane-fusion, and is therefore a key factor involved in viral pathogenesis and inter-species transmission. Here we reported the structural and functional characterization of the spike N-terminal domain (NTD) from DcCoV UAE-HKU23 (HKU23-NTD). Via mucin-binding assays, we showed that HKU23-NTD is able to bind sugars. We further solved the structure of HKU23-NTD, performed structure-guided mutagenesis and successfully located the potential sugar-binding pockets in the structure. Furthermore, via comparison of available betaCoV NTD structures, we demonstrated that betaCoV NTDs contain a conserved β-sandwich core, but exhibit variant folds in the peripheral elements located in the top-ceiling region and on the lateral side. While showing different compositions and structures, these peripheral elements are topologically equivalent β-sandwich-core insertions, highlighting a divergent evolution process for betaCoVs to form different lineages.
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Affiliation(s)
- Yanwei Cheng
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, 610041, China,Disaster Medicine Center, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Bin He
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, 610041, China,Disaster Medicine Center, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Jing Yang
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, 610041, China
| | - Fei Ye
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, 610041, China
| | - Sheng Lin
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, 610041, China
| | - Fanli Yang
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, 610041, China
| | - Zimin Chen
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, 610041, China
| | - Zhujun Chen
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, 610041, China
| | - Yu Cao
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, 610041, China,Disaster Medicine Center, Sichuan University, Chengdu, Sichuan, 610041, China,Corresponding author. West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, 610041, China
| | - Guangwen Lu
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, 610041, China,Corresponding author
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36
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Smola M, Birkus G, Boura E. No magnesium is needed for binding of the stimulator of interferon genes to cyclic dinucleotides. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2019; 75:593-598. [PMID: 31475926 DOI: 10.1107/s2053230x19010999] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 08/06/2019] [Indexed: 02/08/2023]
Abstract
Stimulator of interferon genes (STING) binds cyclic dinucleotides (CDNs), which induce a large conformational change of the protein. The structural basis of activation of STING by CDNs is rather well understood. Unliganded STING forms an open dimer that undergoes a large conformational change (∼10 Å) to a closed conformation upon the binding of a CDN molecule. This event activates downstream effectors of STING and subsequently leads to activation of the type 1 interferon response. However, a previously solved structure of STING with 3',3'-c-di-GMP shows Mg atoms mediating the interaction of STING with this CDN. Here, it is shown that no Mg atoms are needed for this interaction; in fact, magnesium can in some cases obstruct the binding of a CDN to STING.
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Affiliation(s)
- Miroslav Smola
- Gilead Sciences Research Centre at IOCB Prague, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 166 10 Prague, Czech Republic
| | - Gabriel Birkus
- Gilead Sciences Research Centre at IOCB Prague, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 166 10 Prague, Czech Republic
| | - Evzen Boura
- Gilead Sciences Research Centre at IOCB Prague, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 166 10 Prague, Czech Republic
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37
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Crystal structure of PA0833 periplasmic domain from Pseudomonas aeruginosa reveals an unexpected enlarged peptidoglycan binding pocket. Biochem Biophys Res Commun 2019; 511:875-881. [PMID: 30850161 DOI: 10.1016/j.bbrc.2019.02.104] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 02/20/2019] [Indexed: 02/05/2023]
Abstract
PA0833 of Pseudomonas aeruginosa is recently identified as an OmpA C-like protein that is able to interact with bacterial peptidoglycan (PGN). In this study, we reported the biochemical and structural characterization of the PGN-binding periplasmic-domain of PA0833 (PA0833-PD). Via mutagenesis, key residues responsible for engaging PGN were identified, which also enables us to localize the PGN-binding pocket in a 2.0 Å crystal structure solved in this study. In contrast to its homologous proteins (as represented by AbOmpA-PD of Acinetobacter baumannii) that interact with PGN by directly engaging the DAP (diaminopimelate) moiety, PA0833-PD exhibits an enlarged PGN-binding pocket due to residue insertions and the formation of an extra α-helix in one lateral side of the pocket. Accordingly, single DAP molecule does not show detectable interactions with PA0833-PD in solution, highlighting that other PGN-components, in addition to DAP, are also required to restore the full binding capacity observed between PA0833 and PGN.
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38
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Chen Z, Ye F, Lin S, Yang F, Cheng Y, Cao Y, Chen Z, Lu G. Crystal structure of Usutu virus envelope protein in the pre-fusion state. Virol J 2018; 15:183. [PMID: 30477514 PMCID: PMC6260896 DOI: 10.1186/s12985-018-1092-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 11/08/2018] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Usutu virus (USUV) is a mosquito-born flavivirus that can infect multiple avian and mammalian species. The viral surface envelope (E) protein functions to initiate the viral infection by recognizing cellular receptors and mediating the subsequent membrane fusion, and is therefore a key virulence factor involved in the pathogenesis of USUV. The structural features of USUV-E, however, remains un-investigated thus far. FINDINGS Using the crystallographic method, we determined the structure of USUV-E in the pre-fusion state at 2.0 angstrom. As expected, the overall fold of USUV-E, with three β-barrel domains (DI, DII, and DIII), resembles those of other flaviviral E proteins. In comparison to other pre-fusion E structures, however, USUV-E exhibits an apparently enlarged inter-domain angle between DI and DII, leading to a more extended conformation. Using our structure and other reported pre-fusion E structures, the DI-DII domain-angle difference was analyzed in a pairwise manner. The result shows a much higher degree of variations for USUV-E, indicating the potential for remarkable DI-DII domain angle plasticity among flaviviruses. CONCLUSION We report the crystal structure of USUV-E and show that its pre-fusion structure has an enlarged DI-DII domain-angle which has not been observed in other reported flaviviral E-structures.
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Affiliation(s)
- Zimin Chen
- 0000 0004 1770 1022grid.412901.fWest China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan China
| | - Fei Ye
- 0000 0004 1770 1022grid.412901.fWest China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan China
| | - Sheng Lin
- 0000 0004 1770 1022grid.412901.fWest China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan China
| | - Fanli Yang
- 0000 0004 1770 1022grid.412901.fWest China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan China
| | - Yanwei Cheng
- 0000 0004 1770 1022grid.412901.fWest China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan China
| | - Yu Cao
- 0000 0004 1770 1022grid.412901.fWest China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan China ,0000 0001 0807 1581grid.13291.38Disaster Medicine Center, Sichuan University, Chengdu, 610041 Sichuan China
| | - Zhujun Chen
- 0000 0004 1770 1022grid.412901.fWest China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan China
| | - Guangwen Lu
- 0000 0004 1770 1022grid.412901.fWest China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan China
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Mboge MY, Chen Z, Wolff A, Mathias JV, Tu C, Brown KD, Bozdag M, Carta F, Supuran CT, McKenna R, Frost SC. Selective inhibition of carbonic anhydrase IX over carbonic anhydrase XII in breast cancer cells using benzene sulfonamides: Disconnect between activity and growth inhibition. PLoS One 2018; 13:e0207417. [PMID: 30452451 PMCID: PMC6242694 DOI: 10.1371/journal.pone.0207417] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 10/30/2018] [Indexed: 12/11/2022] Open
Abstract
Carbonic anhydrases (CAs) have been linked to tumor progression, particularly membrane-bound CA isoform IX (CA IX). The role of CA IX in the context of breast cancer is to regulate the pH of the tumor microenvironment. In contrast to CA IX, expression of CA XII, specifically in breast cancer, is associated with better outcome despite performing the same catalytic function. In this study, we have structurally modeled the orientation of bound ureido-substituted benzene sulfonamides (USBs) within the active site of CA XII, in comparison to CA IX and cytosolic off-target CA II, to understand isoform specific inhibition. This has identified specific residues within the CA active site, which differ between isoforms that are important for inhibitor binding and isoform specificity. The ability of these sulfonamides to block CA IX activity in breast cancer cells is less effective than their ability to block activity of the recombinant protein (by one to two orders of magnitude depending on the inhibitor). The same is true for CA XII activity but now they are two to three orders of magnitude less effective. Thus, there is significantly greater specificity for CA IX activity over CA XII. While the inhibitors block cell growth, without inducing cell death, this again occurs at two orders of magnitude above the Ki values for inhibition of CA IX and CA XII activity in their respective cell types. Surprisingly, the USBs inhibited cell growth even in cells where CA IX and CA XII expression was ablated. Despite the potential for these sulfonamides as chemotherapeutic agents, these data suggest that we reconsider the role of CA activity on growth potentiation.
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Affiliation(s)
- Mam Y. Mboge
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, United States of America
| | - Zhijuan Chen
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, United States of America
| | - Alyssa Wolff
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, United States of America
| | - John V. Mathias
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, United States of America
| | - Chingkuang Tu
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, United States of America
| | - Kevin D. Brown
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, United States of America
| | - Murat Bozdag
- University of Florence, NEUROFARBA Department, Sezione di Farmaceutica e Nutraceutica, Sesto Fiorentino (Florence), Italy
| | - Fabrizio Carta
- University of Florence, NEUROFARBA Department, Sezione di Farmaceutica e Nutraceutica, Sesto Fiorentino (Florence), Italy
| | - Claudiu T. Supuran
- University of Florence, NEUROFARBA Department, Sezione di Farmaceutica e Nutraceutica, Sesto Fiorentino (Florence), Italy
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, United States of America
| | - Susan C. Frost
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, United States of America
- * E-mail:
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Wang J, Gou Y, Zhang Z, Yu P, Qi J, Qin Q, Sun H, Wu X, Liang H, Yang F. Developing an Anticancer Copper(II) Multitarget Pro-Drug Based on the His146 Residue in the IB Subdomain of Modified Human Serum Albumin. Mol Pharm 2018; 15:2180-2193. [PMID: 29722993 DOI: 10.1021/acs.molpharmaceut.8b00045] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Designing a multitarget anticancer drug with improved delivery and therapeutic efficiency in vivo presents a great challenge. Thus, we proposed to design an anticancer multitarget metal pro-drug derived from thiosemicarbazone based on the His146 residue in the IB subdomain of palmitic acid (PA)-modified human serum albumin (HSA-PA). The structure-activity relationship of six Cu(II) compounds with 6-methyl-2-formylpyridine-4N-substituted thiosemicarbazones were investigated, and then the multitarget capability of 4b was confirmed in cancer cell DNA and proteins. The structure of the HSA-PA-4b complex (HSA-PA-4b) revealed that 4b is bound to the IB subdomain of modified HSA, and that His146 replaces the nitrate ligand in 4b, coordinating with Cu2+, whereas PA is complexed with the IIA subdomain by its carboxyl forming hydrogen bonds with Lys199 and His242. In vivo data showed that 4b and the HSA-PA-4b complex inhibit lung tumor growth, and the targeting ability and therapeutic efficacy of the PA-modified HSA complex was stronger than 4b alone.
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Affiliation(s)
- Jun Wang
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources , Guangxi Normal University , Guilin , Guangxi 541003 , China
| | - Yi Gou
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources , Guangxi Normal University , Guilin , Guangxi 541003 , China.,School of Pharmacy , Nantong University , Nantong , Jiangsu 226000 , China
| | - Zhenlei Zhang
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources , Guangxi Normal University , Guilin , Guangxi 541003 , China
| | - Ping Yu
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources , Guangxi Normal University , Guilin , Guangxi 541003 , China
| | - Jinxu Qi
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources , Guangxi Normal University , Guilin , Guangxi 541003 , China
| | - Qipin Qin
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources , Guangxi Normal University , Guilin , Guangxi 541003 , China
| | - Hongbin Sun
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources , Guangxi Normal University , Guilin , Guangxi 541003 , China
| | - Xiaoyang Wu
- Ben May Department for Cancer Research , University of Chicago , Chicago , Illinois 60637 , United States
| | - Hong Liang
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources , Guangxi Normal University , Guilin , Guangxi 541003 , China
| | - Feng Yang
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources , Guangxi Normal University , Guilin , Guangxi 541003 , China
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41
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Shang Z, Song H, Shi Y, Qi J, Gao GF. Crystal Structure of the Capsid Protein from Zika Virus. J Mol Biol 2018; 430:948-962. [DOI: 10.1016/j.jmb.2018.02.006] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 01/31/2018] [Accepted: 02/09/2018] [Indexed: 12/27/2022]
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Mahon BP, Ambadapadi S, Yaron JR, Lomelino CL, Pinard MA, Keinan S, Kurnikov I, Macaulay C, Zhang L, Reeves W, McFadden G, Tibbetts S, McKenna R, Lucas AR. Crystal Structure of Cleaved Serp-1, a Myxomavirus-Derived Immune Modulating Serpin: Structural Design of Serpin Reactive Center Loop Peptides with Improved Therapeutic Function. Biochemistry 2018; 57:1096-1107. [PMID: 29227673 DOI: 10.1021/acs.biochem.7b01171] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Myxomavirus-derived protein Serp-1 has potent anti-inflammatory activity in models of vasculitis, lupus, viral sepsis, and transplant. Serp-1 has also been tested successfully in a Phase IIa clinical trial in unstable angina, representing a "first-in-class" therapeutic. Recently, peptides derived from the reactive center loop (RCL) have been developed as stand-alone therapeutics for reducing vasculitis and improving survival in MHV68-infected mice. However, both Serp-1 and the RCL peptides lose activity in MHV68-infected mice after antibiotic suppression of intestinal microbiota. Here, we utilize a structure-guided approach to design and test a series of next-generation RCL peptides with improved therapeutic potential that is not reduced when the peptides are combined with antibiotic treatments. The crystal structure of cleaved Serp-1 was determined to 2.5 Å resolution and reveals a classical serpin structure with potential for serpin-derived RCL peptides to bind and inhibit mammalian serpins, plasminogen activator inhibitor 1 (PAI-1), anti-thrombin III (ATIII), and α-1 antitrypsin (A1AT), and target proteases. Using in silico modeling of the Serp-1 RCL peptide, S-7, we designed several modified RCL peptides that were predicted to have stronger interactions with human serpins because of the larger number of stabilizing hydrogen bonds. Two of these peptides (MPS7-8 and -9) displayed extended activity, improving survival where activity was previously lost in antibiotic-treated MHV68-infected mice (P < 0.0001). Mass spectrometry and kinetic assays suggest interaction of the peptides with ATIII, A1AT, and target proteases in mouse and human plasma. In summary, we present the next step toward the development of a promising new class of anti-inflammatory serpin-based therapeutics.
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Affiliation(s)
- Brian P Mahon
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States.,Department of Biochemistry and Molecular Biology, University of Florida College of Medicine , Gainesville, Florida 32610-0277, United States
| | - Sriram Ambadapadi
- Department of Medicine, Divisions of Cardiovascular Medicine and Rheumatology, University of Florida , Gainesville, Florida 32610-0277, United States
| | | | - Carrie L Lomelino
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine , Gainesville, Florida 32610-0277, United States
| | - Melissa A Pinard
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine , Gainesville, Florida 32610-0277, United States
| | - Shahar Keinan
- Cloud Pharmaceuticals , 6 Davis Drive, Research Triangle Park, North Carolina 27709, United States
| | - Igor Kurnikov
- Cloud Pharmaceuticals , 6 Davis Drive, Research Triangle Park, North Carolina 27709, United States
| | | | | | - Westley Reeves
- Department of Medicine, Divisions of Cardiovascular Medicine and Rheumatology, University of Florida , Gainesville, Florida 32610-0277, United States
| | | | | | - Robert McKenna
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine , Gainesville, Florida 32610-0277, United States
| | - Alexandra R Lucas
- Department of Medicine, Divisions of Cardiovascular Medicine and Rheumatology, University of Florida , Gainesville, Florida 32610-0277, United States.,Saint Joseph's Hospital, Dignity Health , Phoenix, Arizona 85013, United States
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The mechanism of NDM-1-catalyzed carbapenem hydrolysis is distinct from that of penicillin or cephalosporin hydrolysis. Nat Commun 2017; 8:2242. [PMID: 29269938 PMCID: PMC5740130 DOI: 10.1038/s41467-017-02339-w] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 11/22/2017] [Indexed: 02/08/2023] Open
Abstract
New Delhi metallo-β-lactamases (NDMs), the recent additions to metallo-β-lactamases (MBLs), pose a serious public health threat due to its highly efficient hydrolysis of β-lactam antibiotics and rapid worldwide dissemination. The MBL-hydrolyzing mechanism for carbapenems is less studied than that of penicillins and cephalosporins. Here, we report crystal structures of NDM-1 in complex with hydrolyzed imipenem and meropenem, at resolutions of 1.80–2.32 Å, together with NMR spectra monitoring meropenem hydrolysis. Three enzyme-intermediate/product derivatives, EI1, EI2, and EP, are trapped in these crystals. Our structural data reveal double-bond tautomerization from Δ2 to Δ1, absence of a bridging water molecule and an exclusive β-diastereomeric product, all suggesting that the hydrolytic intermediates are protonated by a bulky water molecule incoming from the β-face. These results strongly suggest a distinct mechanism of NDM-1-catalyzed carbapenem hydrolysis from that of penicillin or cephalosporin hydrolysis, which may provide a novel rationale for design of mechanism-based inhibitors. New Delhi metallo-β-lactamases (NDMs) hydrolyze almost all β-lactam antibiotics and pose a major public health threat. Here, the authors study the mechanism of NDM-1 catalyzed carbapenem hydrolysis and present the crystal structures of the enzyme-intermediate and product complexes, which is important for drug design.
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Chalupska D, Eisenreichova A, Różycki B, Rezabkova L, Humpolickova J, Klima M, Boura E. Structural analysis of phosphatidylinositol 4-kinase IIIβ (PI4KB) - 14-3-3 protein complex reveals internal flexibility and explains 14-3-3 mediated protection from degradation in vitro. J Struct Biol 2017; 200:36-44. [PMID: 28864297 DOI: 10.1016/j.jsb.2017.08.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 08/26/2017] [Accepted: 08/28/2017] [Indexed: 12/31/2022]
Abstract
Phosphatidylinositol 4-kinase IIIβ (PI4KB) is responsible for the synthesis of the Golgi and trans-Golgi network (TGN) pool of phosphatidylinositol 4-phospahte (PI4P). PI4P is the defining lipid hallmark of Golgi and TGN and also serves as a signaling lipid and as a precursor for higher phosphoinositides. In addition, PI4KB is hijacked by many single stranded plus RNA (+RNA) viruses to generate PI4P-rich membranes that serve as viral replication organelles. Given the importance of this enzyme in cells, it has to be regulated. 14-3-3 proteins bind PI4KB upon its phosphorylation by protein kinase D, however, the structural basis of PI4KB recognition by 14-3-3 proteins is unknown. Here, we characterized the PI4KB:14-3-3 protein complex biophysically and structurally. We discovered that the PI4KB:14-3-3 protein complex is tight and is formed with 2:2 stoichiometry. Surprisingly, the enzymatic activity of PI4KB is not directly modulated by 14-3-3 proteins. However, 14-3-3 proteins protect PI4KB from proteolytic degradation in vitro. Our structural analysis revealed that the PI4KB:14-3-3 protein complex is flexible but mostly within the disordered regions connecting the 14-3-3 binding site of the PI4KB with the rest of the PI4KB enzyme. It also predicted no direct modulation of PI4KB enzymatic activity by 14-3-3 proteins and that 14-3-3 binding will not interfere with PI4KB recruitment to the membrane by the ACBD3 protein. In addition, the structural analysis explains the observed protection from degradation; it revealed that several disordered regions of PI4KB become protected from proteolytical degradation upon 14-3-3 binding. All the structural predictions were subsequently biochemically validated.
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Affiliation(s)
- Dominika Chalupska
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo nam. 2., 166 10 Prague 6, Czech Republic
| | - Andrea Eisenreichova
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo nam. 2., 166 10 Prague 6, Czech Republic
| | - Bartosz Różycki
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Lenka Rezabkova
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232, Villigen PSI, Switzerland
| | - Jana Humpolickova
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo nam. 2., 166 10 Prague 6, Czech Republic
| | - Martin Klima
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo nam. 2., 166 10 Prague 6, Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo nam. 2., 166 10 Prague 6, Czech Republic.
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45
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Marsian J, Fox H, Bahar MW, Kotecha A, Fry EE, Stuart DI, Macadam AJ, Rowlands DJ, Lomonossoff GP. Plant-made polio type 3 stabilized VLPs-a candidate synthetic polio vaccine. Nat Commun 2017; 8:245. [PMID: 28811473 PMCID: PMC5557999 DOI: 10.1038/s41467-017-00090-w] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 05/31/2017] [Indexed: 11/24/2022] Open
Abstract
Poliovirus (PV) is the causative agent of poliomyelitis, a crippling human disease known since antiquity. PV occurs in two distinct antigenic forms, D and C, of which only the D form elicits a robust neutralizing response. Developing a synthetically produced stabilized virus-like particle (sVLP)-based vaccine with D antigenicity, without the drawbacks of current vaccines, will be a major step towards the final eradication of poliovirus. Such a sVLP would retain the native antigenic conformation and the repetitive structure of the original virus particle, but lack infectious genomic material. In this study, we report the production of synthetically stabilized PV VLPs in plants. Mice carrying the gene for the human PV receptor are protected from wild-type PV when immunized with the plant-made PV sVLPs. Structural analysis of the stabilized mutant at 3.6 Å resolution by cryo-electron microscopy and single-particle reconstruction reveals a structure almost indistinguishable from wild-type PV3.Despite the success of current vaccination against poliomyelitis, safe, cheap and effective vaccines remain sought for continuing eradication effort. Here the authors use plants to express stabilized virus-like particles of type 3 poliovirus that can induce a protective immune response in mice transgenic for the human poliovirus receptor.
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Affiliation(s)
- Johanna Marsian
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Helen Fox
- The National Institute for Biological Standards and Control, Potters Bar, EN6 3QG, UK
| | - Mohammad W Bahar
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, OX3 7BN, UK
| | - Abhay Kotecha
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, OX3 7BN, UK
| | - Elizabeth E Fry
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, OX3 7BN, UK
| | - David I Stuart
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, OX3 7BN, UK
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Andrew J Macadam
- The National Institute for Biological Standards and Control, Potters Bar, EN6 3QG, UK
| | - David J Rowlands
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
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46
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Unliganded and substrate bound structures of the cellooligosaccharide active lytic polysaccharide monooxygenase LsAA9A at low pH. Carbohydr Res 2017; 448:187-190. [DOI: 10.1016/j.carres.2017.03.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/10/2017] [Accepted: 03/10/2017] [Indexed: 11/20/2022]
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47
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Nemchinova M, Balobanov V, Nikonova E, Lekontseva N, Mikhaylina A, Tishchenko S, Nikulin A. An Experimental Tool to Estimate the Probability of a Nucleotide Presence in the Crystal Structures of the Nucleotide-Protein Complexes. Protein J 2017; 36:157-165. [PMID: 28317076 DOI: 10.1007/s10930-017-9709-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A correlation between the ligand-protein affinity and the identification of the ligand in the experimental electron density maps obtained by X-ray crystallography has been tested for a number of RNA-binding proteins. Bacterial translation regulators ProQ, TRAP, Rop, and Hfq together with their archaeal homologues SmAP have been used. The equilibrium dissociation constants for the N-methyl-anthraniloyl-labelled adenosine and guanosine monophosphates titrated by the proteins have been determined by the fluorescent anisotropy measurements. The estimated stability of the nucleotide-protein complexes has been matched with a presence of the nucleotides in the structures of the proposed nucleotide-protein complexes. It has been shown that the ribonucleotides can be definitely identified in the experimental electron density maps at equilibrium dissociation constant <10 μM. At KD of 20-40 μM, long incubation of the protein crystals in the nucleotide solution is required to obtain the structures of the complexes. The complexes with KD value higher than 50 μM are not stable enough to survive in crystallization conditions.
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Affiliation(s)
- Maria Nemchinova
- Institute of Protein Research RAS, Pushchino, Russian Federation
| | - Vitaly Balobanov
- Institute of Protein Research RAS, Pushchino, Russian Federation
| | | | | | - Alisa Mikhaylina
- Institute of Protein Research RAS, Pushchino, Russian Federation
| | | | - Alexey Nikulin
- Institute of Protein Research RAS, Pushchino, Russian Federation.
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48
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Han X, Qi J, Song H, Wang Q, Zhang Y, Wu Y, Lu G, Yuen KY, Shi Y, Gao GF. Structure of the S1 subunit C-terminal domain from bat-derived coronavirus HKU5 spike protein. Virology 2017; 507:101-109. [PMID: 28432925 PMCID: PMC7111649 DOI: 10.1016/j.virol.2017.04.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 04/10/2017] [Accepted: 04/15/2017] [Indexed: 02/05/2023]
Abstract
Accumulating evidence indicates that MERS-CoV originated from bat coronaviruses (BatCoVs). Previously, we demonstrated that both MERS-CoV and BatCoV HKU4 use CD26 as a receptor, but how the BatCoVs evolved to bind CD26 is an intriguing question. Here, we solved the crystal structure of the S1 subunit C-terminal domain of HKU5 (HKU5-CTD), another BatCoV that is phylogenetically related to MERS-CoV but cannot bind to CD26. We observed that the conserved core subdomain and those of other betacoronaviruses (betaCoVs) have a similar topology of the external subdomain, indicating the same ancestor of lineage C betaCoVs. However, two deletions in two respective loops located in HKU5-CTD result in conformational variations in CD26-binding interface and are responsible for the non-binding of HKU5-CTD to CD26. Combined with sequence variation in the HKU5-CTD receptor binding interface, we propose the necessity for surveilling the mutation in BatCoV HKU5 spike protein in case of bat-to-human interspecies transmission.
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Affiliation(s)
- Xue Han
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hao Song
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Qihui Wang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen 518112, China
| | - Yanfang Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Wu
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen 518112, China; School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Guangwen Lu
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan 610041, China
| | - Kwok-Yung Yuen
- State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, Pokfulam 999077, Hong Kong Special Administration Region; Department of Microbiology, The University of Hong Kong, Pokfulam 999077, Hong Kong Special Administration Region; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China
| | - Yi Shi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen 518112, China; Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences, Beijing 100101, China.
| | - George F Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen 518112, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China; Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences, Beijing 100101, China; National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China.
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Abstract
PGAM5 is a mitochondrial membrane protein that functions as an atypical Ser/Thr phosphatase and is a regulator of oxidative stress response, necroptosis, and autophagy. Here we present several crystal structures of PGAM5 including the activating N-terminal regulatory sequences, providing a model for structural plasticity, dimerization of the catalytic domain, and the assembly into an enzymatically active dodecameric form. Oligomeric states observed in structures were supported by hydrogen exchange mass spectrometry, size-exclusion chromatography, and analytical ultracentrifugation experiments in solution. We report that the catalytically important N-terminal WDPNWD motif acts as a structural integrator assembling PGAM5 into a dodecamer, allosterically activating the phosphatase by promoting an ordering of the catalytic loop. Additionally the observed active site plasticity enabled visualization of essential conformational rearrangements of catalytic elements. The comprehensive biophysical characterization offers detailed structural models of this key mitochondrial phosphatase that has been associated with the development of diverse diseases. PGAM5 catalytic domain shares phosphoglycerate mutase fold and forms stable dimer WDPNWD motif allosterically activates the fully active dodecameric form Crystal structures reveal conformational plasticity of the PGAM5 active site
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50
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Mboge MY, Mahon BP, Lamas N, Socorro L, Carta F, Supuran CT, Frost SC, McKenna R. Structure activity study of carbonic anhydrase IX: Selective inhibition with ureido-substituted benzenesulfonamides. Eur J Med Chem 2017; 132:184-191. [PMID: 28363153 PMCID: PMC5946058 DOI: 10.1016/j.ejmech.2017.03.026] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 03/14/2017] [Accepted: 03/15/2017] [Indexed: 11/27/2022]
Abstract
Ureido-substituted benzenesulfonamides (USBs) show great promise as selective and potent inhibitors for human carbonic anhydrase hCA IX and XII, with one such compound (SLC-0111/U-F) currently in clinical trials (clinical trials.gov, NCT02215850). In this study, the crystal structures of both hCA II (off-target) and an hCA IX-mimic (target) in complex with selected USBs (U-CH3, U-F, and U-NO2), at resolutions of 1.9 Å or better, are presented, and demonstrate differences in the binding modes within the two isoforms. The presence of residue Phe 131 in hCA II causes steric hindrance (U-CH3, 1765 nM; U-F, 960 nM; U-NO2, 15 nM) whereas in hCA IX (U-CH3, 7 nM; U-F, 45 nM; U-NO2, 1 nM) and hCA XII (U-CH3, 6 nM; U-F, 4 nM; U-NO2, 6 nM), 131 is a Val and Ala, respectively, allows for more favorable binding. Our results provide insight into the mechanism of USB selective inhibition and useful information for structural design and drug development, including synthesis of hybrid USB compounds with improved physiochemical properties.
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Affiliation(s)
- Mam Y Mboge
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Box 100245, Gainesville, FL 32610, USA
| | - Brian P Mahon
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Box 100245, Gainesville, FL 32610, USA
| | - Nicole Lamas
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Box 100245, Gainesville, FL 32610, USA
| | - Lillien Socorro
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Box 100245, Gainesville, FL 32610, USA
| | - Fabrizio Carta
- University of Florence, NEUROFARBA Department, Sezione di Farmaceutica e Nutraceutica, Via Ugo Schiff 6, 50019 Sesto Fiorentino (Florence), Italy
| | - Claudiu T Supuran
- University of Florence, NEUROFARBA Department, Sezione di Farmaceutica e Nutraceutica, Via Ugo Schiff 6, 50019 Sesto Fiorentino (Florence), Italy
| | - Susan C Frost
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Box 100245, Gainesville, FL 32610, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Box 100245, Gainesville, FL 32610, USA.
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