1
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Scott H, Huang W, Andra K, Mamillapalli S, Gonti S, Day A, Zhang K, Mehzabeen N, Battaile KP, Raju A, Lovell S, Bann JG, Taylor DJ. Structure of the anthrax protective antigen D425A dominant negative mutant reveals a stalled intermediate state of pore maturation. J Mol Biol 2022; 434:167548. [PMID: 35304125 DOI: 10.1016/j.jmb.2022.167548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 03/01/2022] [Accepted: 03/10/2022] [Indexed: 10/18/2022]
Abstract
The tripartite protein complex produced by anthrax bacteria (Bacillus anthracis) is a member of the AB family of β-barrel pore-forming toxins. The protective antigen (PA) component forms an oligomeric prepore that assembles on the host cell surface and serves as a scaffold for binding of lethal and edema factors. Following endocytosis, the acidic environment of the late endosome triggers a pH-induced conformational rearrangement to promote maturation of the PA prepore to a functional, membrane spanning pore that facilitates delivery of lethal and edema factors to the cytosol of the infected host. Here, we show that the dominant-negative D425A mutant of PA stalls anthrax pore maturation in an intermediate state at acidic pH. Our 2.7 Å cryo-EM structure of the intermediate state reveals structural rearrangements that involve constriction of the oligomeric pore combined with an intramolecular dissociation of the pore-forming module. In addition to defining the early stages of anthrax pore maturation, the structure identifies asymmetric conformational changes in the oligomeric pore that are influenced by the precise configuration of adjacent protomers.
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Affiliation(s)
- Harry Scott
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Wei Huang
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Kiran Andra
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA
| | | | - Srinivas Gonti
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA
| | - Alexander Day
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Kaiming Zhang
- Stanford Linear Accelerator Center and the Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Nurjahan Mehzabeen
- Protein Structure Laboratory, University of Kansas, Lawrence, KS 66047, USA
| | - Kevin P Battaile
- IMCA-CAT, APS, Argonne National Laboratory, 9700 South Cass Avenue, Building 435A, Argonne, IL 60439, USA
| | - Anjali Raju
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Scott Lovell
- Protein Structure Laboratory, University of Kansas, Lawrence, KS 66047, USA
| | - James G Bann
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA.
| | - Derek J Taylor
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA; Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106, USA.
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2
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Harshbarger W, Tian S, Wahome N, Balsaraf A, Bhattacharya D, Jiang D, Pandey R, Tungare K, Friedrich K, Mehzabeen N, Biancucci M, Chinchilla-Olszar D, Mallett CP, Huang Y, Wang Z, Bottomley MJ, Malito E, Chandramouli S. Convergent structural features of respiratory syncytial virus neutralizing antibodies and plasticity of the site V epitope on prefusion F. PLoS Pathog 2020; 16:e1008943. [PMID: 33137810 PMCID: PMC7660905 DOI: 10.1371/journal.ppat.1008943] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 11/12/2020] [Accepted: 08/28/2020] [Indexed: 11/21/2022] Open
Abstract
Respiratory syncytial virus (RSV) is a global public health burden for which no licensed vaccine exists. To aid vaccine development via increased understanding of the protective antibody response to RSV prefusion glycoprotein F (PreF), we performed structural and functional studies using the human neutralizing antibody (nAb) RSB1. The crystal structure of PreF complexed with RSB1 reveals a conformational, pre-fusion specific site V epitope with a unique cross-protomer binding mechanism. We identify shared structural features between nAbs RSB1 and CR9501, elucidating for the first time how diverse germlines obtained from different subjects can develop convergent molecular mechanisms for recognition of the same PreF site of vulnerability. Importantly, RSB1-like nAbs were induced upon immunization with PreF in naturally-primed cattle. Together, this work reveals new details underlying the immunogenicity of site V and further supports PreF-based vaccine development efforts. Respiratory syncytial virus (RSV) is a persistent, contagious seasonal pathogen and a serious public health threat. While infants are the most at-risk population, with infections potentially leading to bronchiolitis, adults, especially the elderly, are also burdened by RSV-induced respiratory infections. The only treatment currently available for RSV is passive immunization for high-risk infants. Thus, there is a critical need to develop a vaccine for the vast majority of the vulnerable population for which there is no preventative treatment. The RSV fusion protein in its prefusion form (PreF) is the target of the majority of naturally-induced neutralizing antibodies, and several clinical trials are currently evaluating PreF as a promising vaccine candidate. In this study, we solved the X-ray structure of PreF bound to the Fab fragment of a human neutralizing antibody. The structure reveals plasticity of the epitope, as well as a unique molecular signature for antibodies elicited towards this region of PreF. We also find that similar antibodies are induced upon immunization of naturally-primed cattle with a PreF vaccine antigen, suggesting that this epitope is highly immunogenic. These results will help us better understand the human immune response to RSV infection and vaccination, and guide future vaccine-design efforts.
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Affiliation(s)
| | - Sai Tian
- GSK, Rockville, MD, United States of America
| | | | | | | | | | | | | | | | | | | | | | | | - Ying Huang
- GSK, Rockville, MD, United States of America
| | - Zihao Wang
- GSK, Rockville, MD, United States of America
| | | | - Enrico Malito
- GSK, Rockville, MD, United States of America
- * E-mail: (EM); (SC)
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3
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Benson DR, Lovell S, Mehzabeen N, Galeva N, Cooper A, Gao P, Battaile KP, Zhu H. Crystal structures of the naturally fused CS and cytochrome b 5 reductase (b 5R) domains of Ncb5or reveal an expanded CS fold, extensive CS-b 5R interactions and productive binding of the NAD(P) + nicotinamide ring. Acta Crystallogr D Struct Biol 2019; 75:628-638. [PMID: 31282472 DOI: 10.1107/s205979831900754x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 05/23/2019] [Indexed: 01/19/2023]
Abstract
Ncb5or (NADH-cytochrome b5 oxidoreductase), a cytosolic ferric reductase implicated in diabetes and neurological diseases, comprises three distinct domains, cytochrome b5 (b5) and cytochrome b5 reductase (b5R) domains separated by a CHORD-Sgt1 (CS) domain, and a novel 50-residue N-terminal region. Understanding how interdomain interactions in Ncb5or facilitate the shuttling of electrons from NAD(P)H to heme, and how the process compares with the microsomal b5 (Cyb5A) and b5R (Cyb5R3) system, is of interest. A high-resolution structure of the b5 domain (PDB entry 3lf5) has previously been reported, which exhibits substantial differences in comparison to Cyb5A. The structural characterization of a construct comprising the naturally fused CS and b5R domains with bound FAD and NAD+ (PDB entry 6mv1) or NADP+ (PDB entry 6mv2) is now reported. The structures reveal that the linker between the CS and b5R cores is more ordered than predicted, with much of it extending the β-sandwich motif of the CS domain. This limits the flexibility between the two domains, which recognize one another via a short β-sheet motif and a network of conserved side-chain hydrogen bonds, salt bridges and cation-π interactions. Notable differences in FAD-protein interactions in Ncb5or and Cyb5R3 provide insight into the selectivity for docking of their respective b5 redox partners. The structures also afford a structural explanation for the unusual ability of Ncb5or to utilize both NADH and NADPH, and represent the first examples of native, fully oxidized b5R family members in which the nicotinamide ring of NAD(P)+ resides in the active site. Finally, the structures, together with sequence alignments, show that the b5R domain is more closely related to single-domain Cyb5R proteins from plants, fungi and some protists than to Cyb5R3 from animals.
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Affiliation(s)
- David R Benson
- Department of Chemistry, The University of Kansas, 1567 Irving Hill Road, Lawrence, KS 66045, USA
| | - Scott Lovell
- Protein Structure Laboratory, The University of Kansas, 2034 Becker Drive, Lawrence, KS 66047, USA
| | - Nurjahan Mehzabeen
- Protein Structure Laboratory, The University of Kansas, 2034 Becker Drive, Lawrence, KS 66047, USA
| | - Nadezhda Galeva
- Analytical Proteomics Laboratory, The University of Kansas, 2034 Becker Drive, Lawrence, KS 66047, USA
| | - Anne Cooper
- Protein Production Group, The University of Kansas, 2034 Becker Drive, Lawrence, KS 66047, USA
| | - Philip Gao
- Protein Production Group, The University of Kansas, 2034 Becker Drive, Lawrence, KS 66047, USA
| | - Kevin P Battaile
- IMCA-CAT, APS, Argonne National Laboratory, 9700 South Cass Avenue, Building 435A, Argonne, IL 60439, USA
| | - Hao Zhu
- Department of Clinical Laboratory Sciences, The University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
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4
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Galasiti Kankanamalage AC, Weerawarna PM, Rathnayake AD, Kim Y, Mehzabeen N, Battaile KP, Lovell S, Chang KO, Groutas WC. Putative structural rearrangements associated with the interaction of macrocyclic inhibitors with norovirus 3CL protease. Proteins 2019; 87:579-587. [PMID: 30883881 DOI: 10.1002/prot.25682] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 02/12/2019] [Accepted: 03/13/2019] [Indexed: 12/17/2022]
Abstract
Human noroviruses are the primary cause of outbreaks of acute gastroenteritis worldwide. The problem is further compounded by the current lack of norovirus-specific antivirals or vaccines. Noroviruses have a single-stranded, positive sense 7 to 8 kb RNA genome which encodes a polyprotein precursor that is processed by a virus-encoded 3C-like cysteine protease (NV 3CLpro) to generate at least six mature nonstructural proteins. Processing of the polyprotein is essential for virus replication, consequently, NV 3CLpro has emerged as an attractive target for the discovery of norovirus therapeutics and prophylactics. We have recently described the structure-based design of macrocyclic transition state inhibitors of NV 3CLpro. In order to gain insight and understanding into the interaction of macrocyclic inhibitors with the enzyme, as well as probe the effect of ring size on pharmacological activity and cellular permeability, additional macrocyclic inhibitors were synthesized and high resolution cocrystal structures determined. The results of our studies tentatively suggest that the macrocyclic scaffold may hamper optimal binding to the active site by impeding concerted cross-talk between the S2 and S4 subsites.
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Affiliation(s)
| | | | | | - Yunjeong Kim
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Kansas
| | | | - Kevin P Battaile
- IMCA-CAT, Hauptman-Woodward Medical Research Institute, APS Argonne National Laboratory, Argonne, Illinois
| | - Scott Lovell
- Protein Structure Laboratory, The University of Kansas, Kansas
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Kansas
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5
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Galasiti Kankanamalage AC, Kim Y, Damalanka VC, Rathnayake AD, Fehr AR, Mehzabeen N, Battaile KP, Lovell S, Lushington GH, Perlman S, Chang KO, Groutas WC. Structure-guided design of potent and permeable inhibitors of MERS coronavirus 3CL protease that utilize a piperidine moiety as a novel design element. Eur J Med Chem 2018; 150:334-346. [PMID: 29544147 PMCID: PMC5891363 DOI: 10.1016/j.ejmech.2018.03.004] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 02/28/2018] [Accepted: 03/01/2018] [Indexed: 01/17/2023]
Abstract
There are currently no approved vaccines or small molecule therapeutics available for the prophylaxis or treatment of Middle East Respiratory Syndrome coronavirus (MERS-CoV) infections. MERS-CoV 3CL protease is essential for viral replication; consequently, it is an attractive target that provides a potentially effective means of developing small molecule therapeutics for combatting MERS-CoV. We describe herein the structure-guided design and evaluation of a novel class of inhibitors of MERS-CoV 3CL protease that embody a piperidine moiety as a design element that is well-suited to exploiting favorable subsite binding interactions to attain optimal pharmacological activity and PK properties. The mechanism of action of the compounds and the structural determinants associated with binding were illuminated using X-ray crystallography.
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Affiliation(s)
| | - Yunjeong Kim
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Vishnu C Damalanka
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA
| | - Athri D Rathnayake
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA
| | - Anthony R Fehr
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Nurjahan Mehzabeen
- Protein Structure Laboratory, The University of Kansas, Lawrence, KS 66047, USA
| | - Kevin P Battaile
- IMCA-CAT, Hauptman-Woodward Medical Research Institute, APS Argonne National Laboratory, Argonne, IL 60439, USA
| | - Scott Lovell
- Protein Structure Laboratory, The University of Kansas, Lawrence, KS 66047, USA
| | | | - Stanley Perlman
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.
| | - William C Groutas
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA.
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6
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Damalanka VC, Kim Y, Galasiti Kankanamalage AC, Rathnayake AD, Mehzabeen N, Battaile KP, Lovell S, Nguyen HN, Lushington GH, Chang KO, Groutas WC. Structure-guided design, synthesis and evaluation of oxazolidinone-based inhibitors of norovirus 3CL protease. Eur J Med Chem 2018; 143:881-890. [PMID: 29227928 PMCID: PMC5737831 DOI: 10.1016/j.ejmech.2017.12.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 11/18/2017] [Accepted: 12/04/2017] [Indexed: 11/29/2022]
Abstract
Acute nonbacterial gastroenteritis caused by noroviruses constitutes a global public health concern and a significant economic burden. There are currently no small molecule therapeutics or vaccines for the treatment of norovirus infections. A structure-guided approach was utilized in the design of a series of inhibitors of norovirus 3CL protease that embody an oxazolidinone ring as a novel design element for attaining optimal binding interactions. Low micromolar cell-permeable inhibitors that display anti-norovirus activity have been identified. The mechanism of action, mode of binding, and structural rearrangements associated with the interaction of the inhibitors and the enzyme were elucidated using X-ray crystallography.
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Affiliation(s)
- Vishnu C Damalanka
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA
| | - Yunjeong Kim
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | | | - Athri D Rathnayake
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA
| | - Nurjahan Mehzabeen
- Protein Structure Laboratory, The University of Kansas, Lawrence, KS 66047, USA
| | - Kevin P Battaile
- IMCA-CAT, Hauptman-Woodward Medical Research Institute, APS Argonne National Laboratory, Argonne, IL 60439, USA
| | - Scott Lovell
- Protein Structure Laboratory, The University of Kansas, Lawrence, KS 66047, USA
| | - Harry Nhat Nguyen
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA
| | | | - Kyeong-Ok Chang
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.
| | - William C Groutas
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA.
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7
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Shah IS, Lovell S, Mehzabeen N, Battaile KP, Tolbert TJ. Structural characterization of the Man5 glycoform of human IgG3 Fc. Mol Immunol 2017; 92:28-37. [PMID: 29031045 DOI: 10.1016/j.molimm.2017.10.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 09/23/2017] [Accepted: 10/02/2017] [Indexed: 11/15/2022]
Abstract
Immunoglobulin G (IgG) consists of four subclasses in humans: IgG1, IgG2, IgG3 and IgG4, which are highly conserved but have unique differences that result in subclass-specific effector functions. Though IgG1 is the most extensively studied IgG subclass, study of other subclasses is important to understand overall immune function and for development of new therapeutics. When compared to IgG1, IgG3 exhibits a similar binding profile to Fcγ receptors and stronger activation of complement. All IgG subclasses are glycosylated at N297, which is required for Fcγ receptor and C1q complement binding as well as maintaining optimal Fc conformation. We have determined the crystal structure of homogenously glycosylated human IgG3 Fc with a GlcNAc2Man5 (Man5) high mannose glycoform at 1.8Å resolution and compared its structural features with published structures from the other IgG subclasses. Although the overall structure of IgG3 Fc is similar to that of other subclasses, some structural perturbations based on sequence differences were revealed. For instance, the presence of R435 in IgG3 (and H435 in the other IgG subclasses) has been implicated to result in IgG3-specific properties related to binding to protein A, protein G and the neonatal Fc receptor (FcRn). The IgG3 Fc structure helps to explain some of these differences. Additionally, protein-glycan contacts observed in the crystal structure appear to correlate with IgG3 affinity for Fcγ receptors as shown by binding studies with IgG3 Fc glycoforms. Finally, this IgG3 Fc structure provides a template for further studies aimed at engineering the Fc for specific gain of function.
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Affiliation(s)
- Ishan S Shah
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, USA
| | - Scott Lovell
- Protein Structure Laboratory, Del Shankel Structural Biology Center, University of Kansas, Lawrence, KS, USA
| | - Nurjahan Mehzabeen
- Protein Structure Laboratory, Del Shankel Structural Biology Center, University of Kansas, Lawrence, KS, USA
| | - Kevin P Battaile
- IMCA-CAT, Hauptman-Woodward Medical Research Institute, Argonne, IL, USA
| | - Thomas J Tolbert
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, USA.
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8
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Barta ML, Shearer JP, Arizmendi O, Tremblay JM, Mehzabeen N, Zheng Q, Battaile KP, Lovell S, Tzipori S, Picking WD, Shoemaker CB, Picking WL. Single-domain antibodies pinpoint potential targets within Shigella invasion plasmid antigen D of the needle tip complex for inhibition of type III secretion. J Biol Chem 2017; 292:16677-16687. [PMID: 28842484 DOI: 10.1074/jbc.m117.802231] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 08/14/2017] [Indexed: 12/18/2022] Open
Abstract
Numerous Gram-negative pathogens infect eukaryotes and use the type III secretion system (T3SS) to deliver effector proteins into host cells. One important T3SS feature is an extracellular needle with an associated tip complex responsible for assembly of a pore-forming translocon in the host cell membrane. Shigella spp. cause shigellosis, also called bacillary dysentery, and invade colonic epithelial cells via the T3SS. The tip complex of Shigella flexneri contains invasion plasmid antigen D (IpaD), which initially regulates secretion and provides a physical platform for the translocon pore. The tip complex represents a promising therapeutic target for many important T3SS-containing pathogens. Here, in an effort to further elucidate its function, we created a panel of single-VH domain antibodies (VHHs) that recognize distinct epitopes within IpaD. These VHHs recognized the in situ tip complex and modulated the infectious properties of Shigella Moreover, structural elucidation of several IpaD-VHH complexes provided critical insights into tip complex formation and function. Of note, one VHH heterodimer could reduce Shigella hemolytic activity by >80%. Our observations along with previous findings support the hypothesis that the hydrophobic translocator (IpaB in Shigella) likely binds to a region within the tip protein that is structurally conserved across all T3SS-possessing pathogens, suggesting potential therapeutic avenues for managing infections by these pathogens.
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Affiliation(s)
- Michael L Barta
- From the Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047
| | - Jonathan P Shearer
- Department of Infectious Diseases and Global Health, Tufts Clinical and Translational Science Institute, North Grafton, Massachusetts 02111
| | - Olivia Arizmendi
- From the Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047
| | - Jacqueline M Tremblay
- Department of Infectious Diseases and Global Health, Tufts Clinical and Translational Science Institute, North Grafton, Massachusetts 02111
| | - Nurjahan Mehzabeen
- Protein Structure Laboratory, Del Shankel Structural Biology Center, University of Kansas, Lawrence, Kansas 66047, and
| | - Qi Zheng
- From the Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047
| | - Kevin P Battaile
- IMCA-CAT, Hauptman-Woodward Medical Research Institute, Argonne, Illinois 60439
| | - Scott Lovell
- Protein Structure Laboratory, Del Shankel Structural Biology Center, University of Kansas, Lawrence, Kansas 66047, and
| | - Saul Tzipori
- Department of Infectious Diseases and Global Health, Tufts Clinical and Translational Science Institute, North Grafton, Massachusetts 02111
| | - William D Picking
- From the Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047
| | - Charles B Shoemaker
- Department of Infectious Diseases and Global Health, Tufts Clinical and Translational Science Institute, North Grafton, Massachusetts 02111
| | - Wendy L Picking
- From the Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047,
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9
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Yu H, Dranchak P, Li Z, MacArthur R, Munson MS, Mehzabeen N, Baird NJ, Battalie KP, Ross D, Lovell S, Carlow CKS, Suga H, Inglese J. Macrocycle peptides delineate locked-open inhibition mechanism for microorganism phosphoglycerate mutases. Nat Commun 2017; 8:14932. [PMID: 28368002 PMCID: PMC5382265 DOI: 10.1038/ncomms14932] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 02/13/2017] [Indexed: 11/22/2022] Open
Abstract
Glycolytic interconversion of phosphoglycerate isomers is catalysed in numerous pathogenic microorganisms by a cofactor-independent mutase (iPGM) structurally distinct from the mammalian cofactor-dependent (dPGM) isozyme. The iPGM active site dynamically assembles through substrate-triggered movement of phosphatase and transferase domains creating a solvent inaccessible cavity. Here we identify alternate ligand binding regions using nematode iPGM to select and enrich lariat-like ligands from an mRNA-display macrocyclic peptide library containing >1012 members. Functional analysis of the ligands, named ipglycermides, demonstrates sub-nanomolar inhibition of iPGM with complete selectivity over dPGM. The crystal structure of an iPGM macrocyclic peptide complex illuminated an allosteric, locked-open inhibition mechanism placing the cyclic peptide at the bi-domain interface. This binding mode aligns the pendant lariat cysteine thiolate for coordination with the iPGM transition metal ion cluster. The extended charged, hydrophilic binding surface interaction rationalizes the persistent challenges these enzymes have presented to small-molecule screening efforts highlighting the important roles of macrocyclic peptides in expanding chemical diversity for ligand discovery.
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Affiliation(s)
- Hao Yu
- Department of Chemistry, Graduate School of Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Patricia Dranchak
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, USA
| | - Zhiru Li
- Division of Genome Biology, New England Biolabs, Ipswich, Massachusetts 01938, USA
| | - Ryan MacArthur
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, USA
| | - Matthew S. Munson
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Nurjahan Mehzabeen
- Proton Structure Laboratory, Structural Biology Center, University of Kansas, Lawrence, Kansas 66047, USA
| | - Nathan J. Baird
- National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Kevin P. Battalie
- IMCA-CAT Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - David Ross
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Scott Lovell
- Proton Structure Laboratory, Structural Biology Center, University of Kansas, Lawrence, Kansas 66047, USA
| | | | - Hiroaki Suga
- Department of Chemistry, Graduate School of Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - James Inglese
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, USA
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10
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Damalanka VC, Kim Y, Galasiti Kankanamalage AC, Lushington GH, Mehzabeen N, Battaile KP, Lovell S, Chang KO, Groutas WC. Design, synthesis, and evaluation of a novel series of macrocyclic inhibitors of norovirus 3CL protease. Eur J Med Chem 2017; 127:41-61. [PMID: 28038326 PMCID: PMC5296247 DOI: 10.1016/j.ejmech.2016.12.033] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 12/01/2016] [Accepted: 12/16/2016] [Indexed: 02/01/2023]
Abstract
Norovirus infections have a major impact on public health worldwide, yet there is a current dearth of norovirus-specific therapeutics and prophylactics. This report describes the discovery of a novel class of macrocyclic inhibitors of norovirus 3C-like protease, a cysteine protease that is essential for virus replication. SAR, structural, and biochemical studies were carried out to ascertain the effect of structure on pharmacological activity and permeability. Insights gained from these studies have laid a solid foundation for capitalizing on the therapeutic potential of the series of inhibitors described herein.
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Affiliation(s)
- Vishnu C Damalanka
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA
| | - Yunjeong Kim
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | | | | | - Nurjahan Mehzabeen
- Protein Structure Laboratory, The University of Kansas, Lawrence, KS 66047, USA
| | - Kevin P Battaile
- IMCA-CAT, Hauptman-Woodward Medical Research Institute, APS Argonne National Laboratory, Argonne, IL 60439, USA
| | - Scott Lovell
- Protein Structure Laboratory, The University of Kansas, Lawrence, KS 66047, USA
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.
| | - William C Groutas
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA.
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11
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Galasiti Kankanamalage AC, Kim Y, Rathnayake AD, Damalanka VC, Weerawarna PM, Doyle ST, Alsoudi AF, Dissanayake DMP, Lushington GH, Mehzabeen N, Battaile KP, Lovell S, Chang KO, Groutas WC. Structure-based exploration and exploitation of the S 4 subsite of norovirus 3CL protease in the design of potent and permeable inhibitors. Eur J Med Chem 2016; 126:502-516. [PMID: 27914364 DOI: 10.1016/j.ejmech.2016.11.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 11/10/2016] [Accepted: 11/12/2016] [Indexed: 12/17/2022]
Abstract
Human noroviruses are the primary cause of epidemic and sporadic acute gastroenteritis. The worldwide high morbidity and mortality associated with norovirus infections, particularly among the elderly, immunocompromised patients and children, constitute a serious public health concern. There are currently no approved human vaccines or norovirus-specific small-molecule therapeutics or prophylactics. Norovirus 3CL protease has recently emerged as a potential therapeutic target for the development of anti-norovirus agents. We hypothesized that the S4 subsite of the enzyme may provide an effective means of designing potent and cell permeable inhibitors of the enzyme. We report herein the structure-guided exploration and exploitation of the S4 subsite of norovirus 3CL protease in the design and synthesis of effective inhibitors of the protease.
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Affiliation(s)
| | - Yunjeong Kim
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Athri D Rathnayake
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA
| | - Vishnu C Damalanka
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA
| | | | - Sean T Doyle
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA
| | - Amer F Alsoudi
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA
| | | | | | - Nurjahan Mehzabeen
- Protein Structure Laboratory, The University of Kansas, Lawrence, KS 66047, USA
| | - Kevin P Battaile
- IMCA-CAT, Hauptman-Woodward Medical Research Institute, APS Argonne National Laboratory, Argonne, IL 60439, USA
| | - Scott Lovell
- Protein Structure Laboratory, The University of Kansas, Lawrence, KS 66047, USA
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.
| | - William C Groutas
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA.
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12
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Nikolaienko RM, Hammel M, Dubreuil V, Zalmai R, Hall DR, Mehzabeen N, Karuppan SJ, Harroch S, Stella SL, Bouyain S. Structural Basis for Interactions Between Contactin Family Members and Protein-tyrosine Phosphatase Receptor Type G in Neural Tissues. J Biol Chem 2016; 291:21335-21349. [PMID: 27539848 DOI: 10.1074/jbc.m116.742163] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/10/2016] [Indexed: 01/06/2023] Open
Abstract
Protein-tyrosine phosphatase receptor type G (RPTPγ/PTPRG) interacts in vitro with contactin-3-6 (CNTN3-6), a group of glycophosphatidylinositol-anchored cell adhesion molecules involved in the wiring of the nervous system. In addition to PTPRG, CNTNs associate with multiple transmembrane proteins and signal inside the cell via cis-binding partners to alleviate the absence of an intracellular region. Here, we use comprehensive biochemical and structural analyses to demonstrate that PTPRG·CNTN3-6 complexes share similar binding affinities and a conserved arrangement. Furthermore, as a first step to identifying PTPRG·CNTN complexes in vivo, we found that PTPRG and CNTN3 associate in the outer segments of mouse rod photoreceptor cells. In particular, PTPRG and CNTN3 form cis-complexes at the surface of photoreceptors yet interact in trans when expressed on the surfaces of apposing cells. Further structural analyses suggest that all CNTN ectodomains adopt a bent conformation and might lie parallel to the cell surface to accommodate these cis and trans binding modes. Taken together, these studies identify a PTPRG·CNTN complex in vivo and provide novel insights into PTPRG- and CNTN-mediated signaling.
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Affiliation(s)
- Roman M Nikolaienko
- From the Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri 64110
| | - Michal Hammel
- the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Véronique Dubreuil
- the Départment de Neuroscience, Institut Pasteur de Paris, 25-28 Rue du Dr. Roux, 75624 Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR 7216, CNRS, Paris, France, and
| | - Rana Zalmai
- From the Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri 64110
| | - David R Hall
- From the Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri 64110
| | - Nurjahan Mehzabeen
- From the Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri 64110
| | - Sebastian J Karuppan
- From the Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri 64110
| | - Sheila Harroch
- Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR 7216, CNRS, Paris, France, and
| | - Salvatore L Stella
- the Department of Basic Medical Science, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri 64108
| | - Samuel Bouyain
- From the Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri 64110,
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13
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Weerawarna PM, Kim Y, Galasiti Kankanamalage AC, Damalanka VC, Lushington GH, Alliston KR, Mehzabeen N, Battaile KP, Lovell S, Chang KO, Groutas WC. Structure-based design and synthesis of triazole-based macrocyclic inhibitors of norovirus protease: Structural, biochemical, spectroscopic, and antiviral studies. Eur J Med Chem 2016; 119:300-18. [PMID: 27235842 PMCID: PMC4916972 DOI: 10.1016/j.ejmech.2016.04.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 04/04/2016] [Accepted: 04/06/2016] [Indexed: 01/14/2023]
Abstract
Outbreaks of acute gastroenteritis caused by noroviruses constitute a public health concern worldwide. To date, there are no approved drugs or vaccines for the management and prophylaxis of norovirus infections. A potentially effective strategy for the development of norovirus therapeutics entails the discovery of inhibitors of norovirus 3CL protease, an enzyme essential for noroviral replication. We describe herein the structure-based design of the first class of permeable, triazole-based macrocyclic inhibitors of norovirus 3C-like protease, as well as pertinent X-ray crystallographic, biochemical, spectroscopic, and antiviral studies. Novel triazole-based macrocyclic inhibitors of norovirus 3CL protease were synthesized. The interplay of conformation and activity was probed using NMR and X-ray crystallography. Bound inhibitors assume a β-strand conformation according to X-ray crystal structure. Loss of critical hydrogen bonding interactions was revealed by X-ray crystallography.
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Affiliation(s)
| | - Yunjeong Kim
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | | | - Vishnu C Damalanka
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA
| | | | - Kevin R Alliston
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA
| | - Nurjahan Mehzabeen
- Protein Structure Laboratory, The University of Kansas, Lawrence, KS 66047, USA
| | - Kevin P Battaile
- IMCA-CAT, Hauptman-Woodward Medical Research Institute, APS Argonne National Laboratory, Argonne, IL 60439, USA
| | - Scott Lovell
- Protein Structure Laboratory, The University of Kansas, Lawrence, KS 66047, USA
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.
| | - William C Groutas
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA.
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14
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O'Neil P, Lovell S, Mehzabeen N, Battaile K, Biswas I. Crystal structure of histone-like protein from Streptococcus mutans refined to 1.9 Å resolution. Acta Crystallogr F Struct Biol Commun 2016; 72:257-62. [PMID: 27050257 DOI: 10.1107/s2053230x1600217x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 02/04/2016] [Indexed: 12/18/2022]
Abstract
Nucleoid-associated proteins (NAPs) in prokaryotes play an important architectural role in DNA bending, supercoiling and DNA compaction. In addition to architectural roles, some NAPs also play regulatory roles in DNA replication and repair, and act as global transcriptional regulators in many bacteria. Bacteria encode multiple NAPs and some of them are even essential for survival. Streptococcus mutans, a dental pathogen, encodes one such essential NAP called histone-like protein (HLP). Here, the three-dimensional structure of S. mutans HLP has been determined to 1.9 Å resolution. The HLP structure is a dimer and shares a high degree of similarity with other bacterial NAPs, including HU. Since HLPs are essential for the survival of pathogenic streptococci, this structure determination is potentially beneficial for future drug development against these pathogens.
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Affiliation(s)
- Pierce O'Neil
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
| | - Scott Lovell
- Protein Structure Laboratory, Del Shankel Structural Biology Center, University of Kansas, Kansas City, KS 66047, USA
| | - Nurjahan Mehzabeen
- Protein Structure Laboratory, Del Shankel Structural Biology Center, University of Kansas, Kansas City, KS 66047, USA
| | - Kevin Battaile
- IMCA-CAT, Hauptman-Woodward Medical Research Institute, APS, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Indranil Biswas
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
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15
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Damalanka VC, Kim Y, Alliston KR, Weerawarna PM, Galasiti Kankanamalage AC, Lushington GH, Mehzabeen N, Battaile KP, Lovell S, Chang KO, Groutas WC. Oxadiazole-Based Cell Permeable Macrocyclic Transition State Inhibitors of Norovirus 3CL Protease. J Med Chem 2016; 59:1899-913. [PMID: 26823007 DOI: 10.1021/acs.jmedchem.5b01464] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Human noroviruses are the primary causative agents of acute gastroenteritis and a pressing public health burden worldwide. There are currently no vaccines or small molecule therapeutics available for the treatment or prophylaxis of norovirus infections. Norovirus 3CL protease plays a vital role in viral replication by generating structural and nonstructural proteins via the cleavage of the viral polyprotein. Thus, molecules that inhibit the viral protease may have potential therapeutic value. We describe herein the structure-based design, synthesis, and in vitro and cell-based evaluation of the first class of oxadiazole-based, permeable macrocyclic inhibitors of norovirus 3CL protease.
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Affiliation(s)
- Vishnu C Damalanka
- Department of Chemistry, Wichita State University , Wichita, Kansas 67260, United States
| | - Yunjeong Kim
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University , Manhattan, Kansas 66506, United States
| | - Kevin R Alliston
- Department of Chemistry, Wichita State University , Wichita, Kansas 67260, United States
| | - Pathum M Weerawarna
- Department of Chemistry, Wichita State University , Wichita, Kansas 67260, United States
| | | | | | - Nurjahan Mehzabeen
- Protein Structure Laboratory, The University of Kansas , Lawrence, Kansas 66047, United States
| | - Kevin P Battaile
- IMCA-CAT, Hauptman-Woodward Medical Research Institute, APS Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Scott Lovell
- Protein Structure Laboratory, The University of Kansas , Lawrence, Kansas 66047, United States
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University , Manhattan, Kansas 66506, United States
| | - William C Groutas
- Department of Chemistry, Wichita State University , Wichita, Kansas 67260, United States
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16
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Galasiti Kankanamalage AC, Kim Y, Weerawarna PM, Uy RAZ, Damalanka VC, Mandadapu SR, Alliston KR, Mehzabeen N, Battaile KP, Lovell S, Chang KO, Groutas WC. Structure-guided design and optimization of dipeptidyl inhibitors of norovirus 3CL protease. Structure-activity relationships and biochemical, X-ray crystallographic, cell-based, and in vivo studies. J Med Chem 2015; 58:3144-55. [PMID: 25761614 DOI: 10.1021/jm5019934] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Norovirus infection constitutes the primary cause of acute viral gastroenteritis. There are currently no vaccines or norovirus-specific antiviral therapeutics available for the management of norovirus infection. Norovirus 3C-like protease is essential for viral replication, consequently, inhibition of this enzyme is a fruitful avenue of investigation that may lead to the emergence of antinorovirus therapeutics. We describe herein the optimization of dipeptidyl inhibitors of norovirus 3C-like protease using iterative SAR, X-ray crystallographic, and enzyme and cell-based studies. We also demonstrate herein in vivo efficacy of an inhibitor using the murine model of norovirus infection.
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Affiliation(s)
| | | | - Pathum M Weerawarna
- †Department of Chemistry, Wichita State University, 1845 North Fairmount Avenue, Wichita, Kansas 67260, United States
| | - Roxanne Adeline Z Uy
- †Department of Chemistry, Wichita State University, 1845 North Fairmount Avenue, Wichita, Kansas 67260, United States
| | - Vishnu C Damalanka
- †Department of Chemistry, Wichita State University, 1845 North Fairmount Avenue, Wichita, Kansas 67260, United States
| | - Sivakoteswara Rao Mandadapu
- †Department of Chemistry, Wichita State University, 1845 North Fairmount Avenue, Wichita, Kansas 67260, United States
| | - Kevin R Alliston
- †Department of Chemistry, Wichita State University, 1845 North Fairmount Avenue, Wichita, Kansas 67260, United States
| | - Nurjahan Mehzabeen
- §Protein Structure Laboratory,The University of Kansas, Lawrence, Kansas 66047, United States
| | - Kevin P Battaile
- ∥IMCA-CAT, Hauptman-Woodward Medical Research Institute, APS Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Scott Lovell
- §Protein Structure Laboratory,The University of Kansas, Lawrence, Kansas 66047, United States
| | | | - William C Groutas
- †Department of Chemistry, Wichita State University, 1845 North Fairmount Avenue, Wichita, Kansas 67260, United States
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17
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Singh CR, Lovell S, Mehzabeen N, Chowdhury WQ, Geanes ES, Battaile KP, Roelofs J. 1.15 Å resolution structure of the proteasome-assembly chaperone Nas2 PDZ domain. Acta Crystallogr F Struct Biol Commun 2014; 70:418-23. [PMID: 24699731 PMCID: PMC3976055 DOI: 10.1107/s2053230x14003884] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 02/19/2014] [Indexed: 01/18/2023] Open
Abstract
The 26S proteasome is a 2.5 MDa protease dedicated to the degradation of ubiquitinated proteins in eukaryotes. The assembly of this complex containing 66 polypeptides is assisted by at least nine proteasome-specific chaperones. One of these, Nas2, binds to the proteasomal AAA-ATPase subunit Rpt5. The PDZ domain of Nas2 binds to the C-terminal tail of Rpt5; however, it does not require the C-terminus of Rpt5 for binding. Here, the 1.15 Å resolution structure of the PDZ domain of Nas2 is reported. This structure will provide a basis for further insights regarding the structure and function of Nas2 in proteasome assembly.
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Affiliation(s)
- Chingakham R. Singh
- Division of Biology, Kansas State University, 338 Ackert Hall, Manhattan, KS 66506, USA
| | - Scott Lovell
- Protein Structure Laboratory, University of Kansas, Del Shankel Structural Biology Center, Lawrence, KS 66047, USA
| | - Nurjahan Mehzabeen
- Protein Structure Laboratory, University of Kansas, Del Shankel Structural Biology Center, Lawrence, KS 66047, USA
| | - Wasimul Q. Chowdhury
- Division of Biology, Kansas State University, 338 Ackert Hall, Manhattan, KS 66506, USA
| | - Eric S. Geanes
- Division of Biology, Kansas State University, 338 Ackert Hall, Manhattan, KS 66506, USA
| | - Kevin P. Battaile
- IMCA-CAT Hauptman–Woodward Medical Research Institute, 9700 South Cass Avenue, Building 435A, Argonne, IL 60439, USA
| | - Jeroen Roelofs
- Division of Biology, Kansas State University, 338 Ackert Hall, Manhattan, KS 66506, USA
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