1
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Dampalla CS, Kim Y, Zabiegala A, Howard DJ, Nguyen HN, Madden TK, Thurman HA, Cooper A, Liu L, Battaile KP, Lovell S, Chang KO, Groutas WC. Structure-Guided Design of Potent Coronavirus Inhibitors with a 2-Pyrrolidone Scaffold: Biochemical, Crystallographic, and Virological Studies. J Med Chem 2024. [PMID: 38953866 DOI: 10.1021/acs.jmedchem.4c00551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
Zoonotic coronaviruses are known to produce severe infections in humans and have been the cause of significant morbidity and mortality worldwide. SARS-CoV-2 was the largest and latest contributor of fatal cases, even though MERS-CoV has the highest case-fatality ratio among zoonotic coronaviruses. These infections pose a high risk to public health worldwide warranting efforts for the expeditious discovery of antivirals. Hence, we hereby describe a novel series of inhibitors of coronavirus 3CLpro embodying an N-substituted 2-pyrrolidone scaffold envisaged to exploit favorable interactions with the S3-S4 subsites and connected to an invariant Leu-Gln P2-P1 recognition element. Several inhibitors showed nanomolar antiviral activity in enzyme and cell-based assays, with no significant cytotoxicity. High-resolution crystal structures of inhibitors bound to the 3CLpro were determined to probe and identify the molecular determinants associated with binding, to inform the structure-guided optimization of the inhibitors, and to confirm the mechanism of action of the inhibitors.
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Affiliation(s)
- Chamandi S Dampalla
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, United States
| | - Yunjeong Kim
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, United States
| | - Alexandria Zabiegala
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, United States
| | - Dennis J Howard
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, United States
| | - Harry Nhat Nguyen
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, United States
| | - Trent K Madden
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, United States
| | - Hayden A Thurman
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, United States
| | - Anne Cooper
- Protein Structure and X-ray Crystallography Laboratory, The University of Kansas, Lawrence, Kansas 66047, United States
| | - Lijun Liu
- Protein Structure and X-ray Crystallography Laboratory, The University of Kansas, Lawrence, Kansas 66047, United States
| | - Kevin P Battaile
- NYX, New York Structural Biology Center, Upton, New York 11973, United States
| | - Scott Lovell
- Protein Structure and X-ray Crystallography Laboratory, The University of Kansas, Lawrence, Kansas 66047, United States
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, United States
| | - William C Groutas
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, United States
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2
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Rodnin MV, Vasques-Montes V, Kyrychenko A, Oliveira NFB, Kashipathy MM, Battaile KP, Douglas J, Lovell S, Machuqueiro M, Ladokhin AS. Histidine Protonation and Conformational Switching in Diphtheria Toxin Translocation Domain. Toxins (Basel) 2023; 15:410. [PMID: 37505680 PMCID: PMC10467104 DOI: 10.3390/toxins15070410] [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: 05/10/2023] [Revised: 06/06/2023] [Accepted: 06/21/2023] [Indexed: 07/29/2023] Open
Abstract
Protonation of key histidine residues has been long implicated in the acid-mediated cellular action of the diphtheria toxin translocation (T-) domain, responsible for the delivery of the catalytic domain into the cell. Here, we use a combination of computational (constant-pH Molecular Dynamics simulations) and experimental (NMR, circular dichroism, and fluorescence spectroscopy along with the X-ray crystallography) approaches to characterize the initial stages of conformational change happening in solution in the wild-type T-domain and in the H223Q/H257Q double mutant. This replacement suppresses the acid-induced transition, resulting in the retention of a more stable protein structure in solutions at pH 5.5 and, consequently, in reduced membrane-disrupting activity. Here, for the first time, we report the pKa values of the histidine residues of the T-domain, measured by NMR-monitored pH titrations. Most peaks in the histidine side chain spectral region are titrated with pKas ranging from 6.2 to 6.8. However, the two most up-field peaks display little change down to pH 6, which is a limiting pH for this protein in solution at concentrations required for NMR. These peaks are absent in the double mutant, suggesting they belong to H223 and H257. The constant-pH simulations indicate that for the T-domain in solution, the pKa values for histidine residues range from 3.0 to 6.5, with those most difficult to protonate being H251 and H257. Taken together, our experimental and computational data demonstrate that previously suggested cooperative protonation of all six histidines in the T-domain does not occur.
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Affiliation(s)
- Mykola V. Rodnin
- Department of Biochemistry and Molecular Biology, University of Kansas School of Medicine, Kansas City, KS 66160, USA (A.K.)
| | - Victor Vasques-Montes
- Department of Biochemistry and Molecular Biology, University of Kansas School of Medicine, Kansas City, KS 66160, USA (A.K.)
| | - Alexander Kyrychenko
- Department of Biochemistry and Molecular Biology, University of Kansas School of Medicine, Kansas City, KS 66160, USA (A.K.)
- Institute of Chemistry and School of Chemistry, V. N. Karazin Kharkiv National University, 61022 Kharkiv, Ukraine
| | - Nuno F. B. Oliveira
- Institute of Biosystems and Integrative Sciences, University of Lisbon, 1749-016 Lisbon, Portugal (M.M.)
| | - Maithri M. Kashipathy
- Protein Structure and X-ray Crystallography Laboratory, University of Kansas, Lawrence, KS 66047, USA (S.L.)
| | | | - Justin Douglas
- COBRE Bio-NMR Laboratory, University of Kansas, Lawrence, KS 66045, USA;
| | - Scott Lovell
- Protein Structure and X-ray Crystallography Laboratory, University of Kansas, Lawrence, KS 66047, USA (S.L.)
| | - Miguel Machuqueiro
- Institute of Biosystems and Integrative Sciences, University of Lisbon, 1749-016 Lisbon, Portugal (M.M.)
| | - Alexey S. Ladokhin
- Department of Biochemistry and Molecular Biology, University of Kansas School of Medicine, Kansas City, KS 66160, USA (A.K.)
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3
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Goyal P, Deay D, Seibold S, Candido ACL, Lovell S, Battaile KP, Wilson GS, Richter ML, Petillo PA. Structure of Rhizobium sp. 4-9 histamine dehydrogenase and analysis of the electron transfer pathway to an abiological electron acceptor. Arch Biochem Biophys 2023; 742:109612. [PMID: 37146865 DOI: 10.1016/j.abb.2023.109612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/20/2023] [Accepted: 04/24/2023] [Indexed: 05/07/2023]
Abstract
Histamine dehydrogenase from the gram-negative bacterium Rhizobium sp. 4-9 (HaDHR) is a member of a small family of dehydrogenases containing a covalently attached FMN, and the only member so far identified to date that does not exhibit substrate inhibition. In this study, we present the 2.1 Å resolution crystal structure of HaDHR. This new structure allowed for the identification of the internal electron transfer pathway to abiological ferrocene-based mediators. Alanine 437 was identified as the exit point of electrons from the Fe4S4 cluster. The enzyme was modified with a Ser436Cys mutation to facilitate covalent attachment of a ferrocene moiety. When modified with Fc-maleimide, this new construct demonstrated direct electron transfer from the enzyme to a gold electrode in a histamine concentration-dependent manner without the need for any additional electron mediators.
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Affiliation(s)
- Priyanka Goyal
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA
| | - Dwight Deay
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA
| | - Steve Seibold
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA
| | - A C L Candido
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA
| | - Scott Lovell
- Protein Structure Laboratory, University of Kansas, Lawrence, KS, 66044, USA
| | | | - George S Wilson
- Department of Chemistry, University of Kansas, Lawrence, KS, 66045, USA
| | - Mark L Richter
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA
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4
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Dampalla CS, Miller MJ, Kim Y, Zabiegala A, Nguyen HN, Madden TK, Thurman HA, Machen AJ, Cooper A, Liu L, Battaile KP, Lovell S, Chang KO, Groutas WC. Structure-guided design of direct-acting antivirals that exploit the gem-dimethyl effect and potently inhibit 3CL proteases of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) and middle east respiratory syndrome coronavirus (MERS-CoV). Eur J Med Chem 2023; 254:115376. [PMID: 37080108 PMCID: PMC10105399 DOI: 10.1016/j.ejmech.2023.115376] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/08/2023] [Accepted: 04/11/2023] [Indexed: 04/22/2023]
Abstract
The high morbidity and mortality associated with SARS-CoV-2 infection, the etiological agent of COVID-19, has had a major impact on global public health. Significant progress has been made in the development of an array of vaccines and biologics, however, the emergence of SARS-CoV-2 variants and breakthrough infections are an ongoing major concern. Furthermore, there is an existing paucity of small-molecule host and virus-directed therapeutics and prophylactics that can be used to counter the spread of SARS-CoV-2, and any emerging and re-emerging coronaviruses. We describe herein our efforts to address this urgent need by focusing on the structure-guided design of potent broad-spectrum inhibitors of SARS-CoV-2 3C-like protease (3CLpro or Main protease), an enzyme essential for viral replication. The inhibitors exploit the directional effects associated with the presence of a gem-dimethyl group that allow the inhibitors to optimally interact with the S4 subsite of the enzyme. Several compounds were found to potently inhibit SARS-CoV-2 and MERS-CoV 3CL proteases in biochemical and cell-based assays. Specifically, the EC50 values of aldehyde 1c and its corresponding bisulfite adduct 1d against SARS-CoV-2 were found to be 12 and 10 nM, respectively, and their CC50 values were >50 μM. Furthermore, deuteration of these compounds yielded compounds 2c/2d with EC50 values 11 and 12 nM, respectively. Replacement of the aldehyde warhead with a nitrile (CN) or an α-ketoamide warhead or its corresponding bisulfite adduct yielded compounds 1g, 1eand1f with EC50 values 60, 50 and 70 nM, respectively. High-resolution cocrystal structures have identified the structural determinants associated with the binding of the inhibitors to the active site of the enzyme and, furthermore, have illuminated the mechanism of action of the inhibitors. Overall, the high Safety Index (SI) (SI=CC50/EC50) displayed by these compounds suggests that they are well-suited to conducting further preclinical studies.
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Affiliation(s)
- Chamandi S Dampalla
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, KS, 67260, USA
| | - Matthew J Miller
- Department of Chemistry and Biochemistry, 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
| | - Alexandria Zabiegala
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
| | - Harry Nhat Nguyen
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, KS, 67260, USA
| | - Trent K Madden
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, KS, 67260, USA
| | - Hayden A Thurman
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, KS, 67260, USA
| | - Alexandra J Machen
- Protein Structure and X-ray Crystallography Laboratory, The University of Kansas, Lawrence, KS, 66047, USA
| | - Anne Cooper
- Protein Structure and X-ray Crystallography Laboratory, The University of Kansas, Lawrence, KS, 66047, USA
| | - Lijun Liu
- Protein Structure and X-ray Crystallography Laboratory, The University of Kansas, Lawrence, KS, 66047, USA
| | | | - Scott Lovell
- Protein Structure and X-ray Crystallography 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 and Biochemistry, Wichita State University, Wichita, KS, 67260, USA.
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5
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Rajapaksha N, Soldano A, Yao H, Donnarumma F, Kashipathy MM, Seibold S, Battaile KP, Lovell S, Rivera M. Pseudomonas aeruginosa Dps (PA0962) Functions in H 2O 2 Mediated Oxidative Stress Defense and Exhibits In Vitro DNA Cleaving Activity. Int J Mol Sci 2023; 24:4669. [PMID: 36902100 PMCID: PMC10002758 DOI: 10.3390/ijms24054669] [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: 01/31/2023] [Revised: 02/16/2023] [Accepted: 02/25/2023] [Indexed: 03/04/2023] Open
Abstract
We report the structural, biochemical, and functional characterization of the product of gene PA0962 from Pseudomonas aeruginosa PAO1. The protein, termed Pa Dps, adopts the Dps subunit fold and oligomerizes into a nearly spherical 12-mer quaternary structure at pH 6.0 or in the presence of divalent cations at neutral pH and above. The 12-Mer Pa Dps contains two di-iron centers at the interface of each subunit dimer, coordinated by conserved His, Glu, and Asp residues. In vitro, the di-iron centers catalyze the oxidation of Fe2+ utilizing H2O2 (not O2) as an oxidant, suggesting Pa Dps functions to aid P. aeruginosa to survive H2O2-mediated oxidative stress. In agreement, a P. aeruginosa Δdps mutant is significantly more susceptible to H2O2 than the parent strain. The Pa Dps structure harbors a novel network of Tyr residues at the interface of each subunit dimer between the two di-iron centers, which captures radicals generated during Fe2+ oxidation at the ferroxidase centers and forms di-tyrosine linkages, thus effectively trapping the radicals within the Dps shell. Surprisingly, incubating Pa Dps and DNA revealed unprecedented DNA cleaving activity that is independent of H2O2 or O2 but requires divalent cations and 12-mer Pa Dps.
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Affiliation(s)
- Nimesha Rajapaksha
- Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, LA 70803, USA
| | - Anabel Soldano
- Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, LA 70803, USA
| | - Huili Yao
- Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, LA 70803, USA
| | - Fabrizio Donnarumma
- Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, LA 70803, USA
| | - Maithri M. Kashipathy
- Protein Structure and X-ray Crystallography Laboratory, University of Kansas, 2034 Becker Dr., Lawrence, KS 66047, USA
| | - Steve Seibold
- Protein Structure and X-ray Crystallography Laboratory, University of Kansas, 2034 Becker Dr., Lawrence, KS 66047, USA
| | | | - Scott Lovell
- Protein Structure and X-ray Crystallography Laboratory, University of Kansas, 2034 Becker Dr., Lawrence, KS 66047, USA
| | - Mario Rivera
- Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, LA 70803, USA
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6
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Dampalla C, Nguyen HN, Rathnayake AD, Kim Y, Perera KD, Madden TK, Thurman HA, Machen AJ, Kashipathy MM, Liu L, Battaile KP, Lovell S, Chang KO, Groutas WC. Broad-Spectrum Cyclopropane-Based Inhibitors of Coronavirus 3C-like Proteases: Biochemical, Structural, and Virological Studies. ACS Pharmacol Transl Sci 2023; 6:181-194. [PMID: 36654747 PMCID: PMC9841783 DOI: 10.1021/acsptsci.2c00206] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Indexed: 12/29/2022]
Abstract
The advent of SARS-CoV-2, the causative agent of COVID-19, and its worldwide impact on global health, have provided the impetus for the development of effective countermeasures that can be deployed against the virus, including vaccines, monoclonal antibodies, and direct-acting antivirals (DAAs). Despite these efforts, the current paucity of DAAs has created an urgent need for the creation of an enhanced and diversified portfolio of broadly acting agents with different mechanisms of action that can effectively abrogate viral infection. SARS-CoV-2 3C-like protease (3CLpro), an enzyme essential for viral replication, is a validated target for the discovery of SARS-CoV-2 therapeutics. In this report, we describe the structure-guided utilization of the cyclopropane moiety in the design of highly potent inhibitors of SARS-CoV-2 3CLpro, SARS-CoV-1 3CLpro, and MERS-CoV 3CLpro. High-resolution cocrystal structures were used to identify the structural determinants associated with the binding of the inhibitors to the active site of the enzyme and unravel the mechanism of action. Aldehydes 5c and 11c inhibited SARS-CoV-2 replication with EC50 values of 12 and 11 nM, respectively. Furthermore, the corresponding aldehyde bisulfite adducts 5d and 11d were equipotent with EC50 values of 13 and 12 nM, respectively. The safety index (SI) values for compounds 5c / 11c and 5d / 11d ranged between 7692 and 9090. Importantly, aldehydes 5c / 11c and bisulfite adducts 5d / 11d potently inhibited MERS-CoV 3CLpro with IC50 values of 80 and 120 nM, and 70 and 70 nM, respectively. Likewise, compounds 5c / 11c and 5d / 11d inhibited SARS-CoV-1 with IC50 values of 960 and 350 nM and 790 and 240 nM, respectively. Taken together, these studies suggest that the inhibitors described herein have low cytotoxicity and high potency and are promising candidates for further development as broad-spectrum direct-acting antivirals against highly pathogenic coronaviruses.
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Affiliation(s)
- Chamandi
S. Dampalla
- Department
of Chemistry and Biochemistry, Wichita State
University, Wichita, Kansas 67260, United States
| | - Harry Nhat Nguyen
- Department
of Chemistry and Biochemistry, Wichita State
University, Wichita, Kansas 67260, United States
| | - Athri D. Rathnayake
- Department
of Chemistry and Biochemistry, Wichita State
University, Wichita, Kansas 67260, United States
| | - Yunjeong Kim
- Department
of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, United States
| | - Krishani Dinali Perera
- Department
of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, United States
| | - Trent K. Madden
- Department
of Chemistry and Biochemistry, Wichita State
University, Wichita, Kansas 67260, United States
| | - Hayden A. Thurman
- Department
of Chemistry and Biochemistry, Wichita State
University, Wichita, Kansas 67260, United States
| | - Alexandra J. Machen
- Protein
Structure and X-ray Crystallography Laboratory, The University of Kansas, Lawrence, Kansas 66047, United States
| | - Maithri M. Kashipathy
- Protein
Structure and X-ray Crystallography Laboratory, The University of Kansas, Lawrence, Kansas 66047, United States
| | - Lijun Liu
- Protein
Structure and X-ray Crystallography Laboratory, The University of Kansas, Lawrence, Kansas 66047, United States
| | - Kevin P. Battaile
- NYX,
New York Structural Biology Center, Upton, New York 11973, United States
| | - Scott Lovell
- Protein
Structure and X-ray Crystallography Laboratory, The University of Kansas, Lawrence, Kansas 66047, United States
| | - Kyeong-Ok Chang
- Department
of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, United States
| | - William C. Groutas
- Department
of Chemistry and Biochemistry, Wichita State
University, Wichita, Kansas 67260, United States
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7
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Dampalla CS, Rathnayake AD, Kankanamalage ACG, Kim Y, Perera KD, Nguyen HN, Miller MJ, Madden TK, Picard HR, Thurman HA, Kashipathy MM, Liu L, Battaile KP, Lovell S, Chang KO, Groutas WC. Structure-Guided Design of Potent Spirocyclic Inhibitors of Severe Acute Respiratory Syndrome Coronavirus-2 3C-like Protease. J Med Chem 2022; 65:7818-7832. [PMID: 35638577 PMCID: PMC9172056 DOI: 10.1021/acs.jmedchem.2c00224] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Indexed: 12/22/2022]
Abstract
The worldwide impact of the ongoing COVID-19 pandemic on public health has made imperative the discovery and development of direct-acting antivirals aimed at targeting viral and/or host targets. SARS-CoV-2 3C-like protease (3CLpro) has emerged as a validated target for the discovery of SARS-CoV-2 therapeutics because of the pivotal role it plays in viral replication. We describe herein the structure-guided design of highly potent inhibitors of SARS-CoV-2 3CLpro that incorporate in their structure novel spirocyclic design elements aimed at optimizing potency by accessing new chemical space. Inhibitors of both SARS-CoV-2 3CLpro and MERS-CoV 3CLpro that exhibit nM potency and high safety indices have been identified. The mechanism of action of the inhibitors and the structural determinants associated with binding were established using high-resolution cocrystal structures.
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Affiliation(s)
- Chamandi S. Dampalla
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - Athri D. Rathnayake
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, USA
| | | | - Yunjeong Kim
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
| | - Krishani Dinali Perera
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
| | - Harry Nhat Nguyen
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - Matthew J. Miller
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - Trent K. Madden
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - Hunter R. Picard
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - Hayden A. Thurman
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, USA
| | | | - Lijun Liu
- Protein Structure Laboratory, The University of Kansas, Lawrence, Kansas 66047, USA
| | | | - Scott Lovell
- Protein Structure Laboratory, The University of Kansas, Lawrence, Kansas 66047, USA
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
| | - William C. Groutas
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, USA
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8
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Improving the kinetic parameters of nicotine oxidizing enzymes by homologous structure comparison and rational design. Arch Biochem Biophys 2022; 718:109122. [DOI: 10.1016/j.abb.2022.109122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 12/17/2021] [Accepted: 01/14/2022] [Indexed: 11/17/2022]
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9
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Dampalla CS, Rathnayake AD, Perera KD, Jesri ARM, Nguyen HN, Miller MJ, Thurman HA, Zheng J, Kashipathy MM, Battaile KP, Lovell S, Perlman S, Kim Y, Groutas WC, Chang KO. Structure-Guided Design of Potent Inhibitors of SARS-CoV-2 3CL Protease: Structural, Biochemical, and Cell-Based Studies. J Med Chem 2021; 64:17846-17865. [PMID: 34865476 PMCID: PMC8673480 DOI: 10.1021/acs.jmedchem.1c01037] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Indexed: 12/21/2022]
Abstract
The COVID-19 pandemic is having a major impact on public health worldwide, and there is an urgent need for the creation of an armamentarium of effective therapeutics, including vaccines, biologics, and small-molecule therapeutics, to combat SARS-CoV-2 and emerging variants. Inspection of the virus life cycle reveals multiple viral- and host-based choke points that can be exploited to combat the virus. SARS-CoV-2 3C-like protease (3CLpro), an enzyme essential for viral replication, is an attractive target for therapeutic intervention, and the design of inhibitors of the protease may lead to the emergence of effective SARS-CoV-2-specific antivirals. We describe herein the results of our studies related to the application of X-ray crystallography, the Thorpe-Ingold effect, deuteration, and stereochemistry in the design of highly potent and nontoxic inhibitors of SARS-CoV-2 3CLpro.
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Affiliation(s)
| | - Athri D. Rathnayake
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - Krishani Dinali Perera
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
| | | | - Harry Nhat Nguyen
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - Matthew J. Miller
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - Hayden A. Thurman
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - Jian Zheng
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA
| | | | | | - Scott Lovell
- Protein Structure Laboratory, The University of Kansas, Lawrence, Kansas 66047, USA
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA
| | - Yunjeong Kim
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
| | - William C. Groutas
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
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10
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Dampalla CS, Kim Y, Bickmeier N, Rathnayake AD, Nguyen HN, Zheng J, Kashipathy MM, Baird MA, Battaile KP, Lovell S, Perlman S, Chang KO, Groutas WC. Structure-Guided Design of Conformationally Constrained Cyclohexane Inhibitors of Severe Acute Respiratory Syndrome Coronavirus-2 3CL Protease. J Med Chem 2021; 64:10047-10058. [PMID: 34213885 PMCID: PMC8276672 DOI: 10.1021/acs.jmedchem.1c00319] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Indexed: 12/12/2022]
Abstract
A series of nondeuterated and deuterated dipeptidyl aldehyde and masked aldehyde inhibitors that incorporate in their structure a conformationally constrained cyclohexane moiety was synthesized and found to potently inhibit severe acute respiratory syndrome coronavirus-2 3CL protease in biochemical and cell-based assays. Several of the inhibitors were also found to be nanomolar inhibitors of Middle East respiratory syndrome coronavirus 3CL protease. The corresponding latent aldehyde bisulfite adducts were found to be equipotent to the precursor aldehydes. High-resolution cocrystal structures confirmed the mechanism of action and illuminated the structural determinants involved in binding. The spatial disposition of the compounds disclosed herein provides an effective means of accessing new chemical space and optimizing pharmacological activity. The cellular permeability of the identified inhibitors and lack of cytotoxicity warrant their advancement as potential therapeutics for COVID-19.
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Affiliation(s)
| | - Yunjeong Kim
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
| | - Naemi Bickmeier
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
| | - Athri D. Rathnayake
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - Harry Nhat Nguyen
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - Jian Zheng
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | | | - Matthew A. Baird
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, USA
| | | | - Scott Lovell
- Protein Structure Laboratory, The University of Kansas, Lawrence, Kansas 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, Kansas 66506, USA
| | - William C. Groutas
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, USA
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11
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Weber JJ, Kashipathy MM, Battaile KP, Go E, Desaire H, Kanost MR, Lovell S, Gorman MJ. Structural insight into the novel iron-coordination and domain interactions of transferrin-1 from a model insect, Manduca sexta. Protein Sci 2021; 30:408-422. [PMID: 33197096 PMCID: PMC7784759 DOI: 10.1002/pro.3999] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/11/2020] [Accepted: 11/13/2020] [Indexed: 11/07/2022]
Abstract
Transferrins function in iron sequestration and iron transport by binding iron tightly and reversibly. Vertebrate transferrins coordinate iron through interactions with two tyrosines, an aspartate, a histidine, and a carbonate anion, and conformational changes that occur upon iron binding and release have been described. Much less is known about the structure and functions of insect transferrin-1 (Tsf1), which is present in hemolymph and influences iron homeostasis mostly by unknown mechanisms. Amino acid sequence and biochemical analyses have suggested that iron coordination by Tsf1 differs from that of the vertebrate transferrins. Here we report the first crystal structure (2.05 Å resolution) of an insect transferrin. Manduca sexta (MsTsf1) in the holo form exhibits a bilobal fold similar to that of vertebrate transferrins, but its carboxyl-lobe adopts a novel orientation and contacts with the amino-lobe. The structure revealed coordination of a single Fe3+ ion in the amino-lobe through Tyr90, Tyr204, and two carbonate anions. One carbonate anion is buried near the ferric ion and is coordinated by four residues, whereas the other carbonate anion is solvent exposed and coordinated by Asn121. Notably, these residues are highly conserved in Tsf1 orthologs. Docking analysis suggested that the solvent exposed carbonate position is capable of binding alternative anions. These findings provide a structural basis for understanding Tsf1 function in iron sequestration and transport in insects as well as insight into the similarities and differences in iron homeostasis between insects and humans.
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Affiliation(s)
- Jacob J. Weber
- Department of Biochemistry and Molecular BiophysicsKansas State UniversityManhattanKansasUSA
| | - Maithri M. Kashipathy
- Protein Structure Laboratory, Del Shankel Structural Biology CenterUniversity of KansasLawrenceKansasUSA
| | | | - Eden Go
- Department of ChemistryUniversity of KansasLawrenceKansasUSA
| | - Heather Desaire
- Department of ChemistryUniversity of KansasLawrenceKansasUSA
| | - Michael R. Kanost
- Department of Biochemistry and Molecular BiophysicsKansas State UniversityManhattanKansasUSA
| | - Scott Lovell
- Protein Structure Laboratory, Del Shankel Structural Biology CenterUniversity of KansasLawrenceKansasUSA
| | - Maureen J. Gorman
- Department of Biochemistry and Molecular BiophysicsKansas State UniversityManhattanKansasUSA
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12
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Du J, Wrisberg MKV, Gulen B, Stahl M, Pett C, Hedberg C, Lang K, Schneider S, Itzen A. Rab1-AMPylation by Legionella DrrA is allosterically activated by Rab1. Nat Commun 2021; 12:460. [PMID: 33469029 PMCID: PMC7815794 DOI: 10.1038/s41467-020-20702-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 12/16/2020] [Indexed: 01/29/2023] Open
Abstract
Legionella pneumophila infects eukaryotic cells by forming a replicative organelle - the Legionella containing vacuole. During this process, the bacterial protein DrrA/SidM is secreted and manipulates the activity and post-translational modification (PTM) states of the vesicular trafficking regulator Rab1. As a result, Rab1 is modified with an adenosine monophosphate (AMP), and this process is referred to as AMPylation. Here, we use a chemical approach to stabilise low-affinity Rab:DrrA complexes in a site-specific manner to gain insight into the molecular basis of the interaction between the Rab protein and the AMPylation domain of DrrA. The crystal structure of the Rab:DrrA complex reveals a previously unknown non-conventional Rab-binding site (NC-RBS). Biochemical characterisation demonstrates allosteric stimulation of the AMPylation activity of DrrA via Rab binding to the NC-RBS. We speculate that allosteric control of DrrA could in principle prevent random and potentially cytotoxic AMPylation in the host, thereby perhaps ensuring efficient infection by Legionella.
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Affiliation(s)
- Jiqing Du
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, Garching, 85748, Germany.,Center for Experimental Medicine, Institute of Biochemistry and Signal Transduction, Universitätsklinikum Hamburg-Eppendorf (UKE), Hamburg, 20246, Germany
| | - Marie-Kristin von Wrisberg
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, Institute for Advanced Study, Garching, 85748, Germany
| | - Burak Gulen
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, Garching, 85748, Germany.,Center for Experimental Medicine, Institute of Biochemistry and Signal Transduction, Universitätsklinikum Hamburg-Eppendorf (UKE), Hamburg, 20246, Germany
| | - Matthias Stahl
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, Garching, 85748, Germany.,Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Box 1031, 171 21 Solna, Stockholm, Sweden
| | - Christian Pett
- Chemical Biology Center (KBC), Department of Chemistry, Umeå University, Linnaeus väg 10, 90187, Umeå, Sweden
| | - Christian Hedberg
- Chemical Biology Center (KBC), Department of Chemistry, Umeå University, Linnaeus väg 10, 90187, Umeå, Sweden
| | - Kathrin Lang
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, Institute for Advanced Study, Garching, 85748, Germany.
| | - Sabine Schneider
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Ludwig-Maximilians-University Munich, München, 81377, Germany.
| | - Aymelt Itzen
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, Garching, 85748, Germany. .,Center for Experimental Medicine, Institute of Biochemistry and Signal Transduction, Universitätsklinikum Hamburg-Eppendorf (UKE), Hamburg, 20246, Germany. .,Center for Structural Systems Biology (CSSB), University Medical Centre Hamburg-Eppendorf (UKE), Hamburg, Germany.
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13
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The SARS-CoV-2 Conserved Macrodomain Is a Mono-ADP-Ribosylhydrolase. J Virol 2021; 95:JVI.01969-20. [PMID: 33158944 PMCID: PMC7925111 DOI: 10.1128/jvi.01969-20] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 11/02/2020] [Indexed: 11/20/2022] Open
Abstract
SARS-CoV-2 has recently emerged into the human population and has led to a worldwide pandemic of COVID-19 that has caused more than 1.2 million deaths worldwide. With no currently approved treatments, novel therapeutic strategies are desperately needed. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other SARS-related CoVs encode 3 tandem macrodomains within nonstructural protein 3 (nsp3). The first macrodomain, Mac1, is conserved throughout CoVs and binds to and hydrolyzes mono-ADP-ribose (MAR) from target proteins. Mac1 likely counters host-mediated antiviral ADP-ribosylation, a posttranslational modification that is part of the host response to viral infections. Mac1 is essential for pathogenesis in multiple animal models of CoV infection, implicating it as a virulence factor and potential therapeutic target. Here, we report the crystal structure of SARS-CoV-2 Mac1 in complex with ADP-ribose. SARS-CoV-2, SARS-CoV, and Middle East respiratory syndrome coronavirus (MERS-CoV) Mac1 domains exhibit similar structural folds, and all 3 proteins bound to ADP-ribose with affinities in the low micromolar range. Importantly, using ADP-ribose-detecting binding reagents in both a gel-based assay and novel enzyme-linked immunosorbent assays (ELISAs), we demonstrated de-MARylating activity for all 3 CoV Mac1 proteins, with the SARS-CoV-2 Mac1 protein leading to a more rapid loss of substrate than the others. In addition, none of these enzymes could hydrolyze poly-ADP-ribose. We conclude that the SARS-CoV-2 and other CoV Mac1 proteins are MAR-hydrolases with similar functions, indicating that compounds targeting CoV Mac1 proteins may have broad anti-CoV activity. IMPORTANCE SARS-CoV-2 has recently emerged into the human population and has led to a worldwide pandemic of COVID-19 that has caused more than 1.2 million deaths worldwide. With no currently approved treatments, novel therapeutic strategies are desperately needed. All coronaviruses encode a highly conserved macrodomain (Mac1) that binds to and removes ADP-ribose adducts from proteins in a dynamic posttranslational process that is increasingly being recognized as an important factor that regulates viral infection. The macrodomain is essential for CoV pathogenesis and may be a novel therapeutic target. Thus, understanding its biochemistry and enzyme activity are critical first steps for these efforts. Here, we report the crystal structure of SARS-CoV-2 Mac1 in complex with ADP-ribose and describe its ADP-ribose binding and hydrolysis activities in direct comparison to those of SARS-CoV and MERS-CoV Mac1 proteins. These results are an important first step for the design and testing of potential therapies targeting this unique protein domain.
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14
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Rodnin MV, Kashipathy MM, Kyrychenko A, Battaile KP, Lovell S, Ladokhin AS. Structure of the Diphtheria Toxin at Acidic pH: Implications for the Conformational Switching of the Translocation Domain. Toxins (Basel) 2020; 12:toxins12110704. [PMID: 33171806 PMCID: PMC7695028 DOI: 10.3390/toxins12110704] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/29/2020] [Accepted: 11/05/2020] [Indexed: 12/28/2022] Open
Abstract
Diphtheria toxin, an exotoxin secreted by Corynebacterium that causes disease in humans by inhibiting protein synthesis, enters the cell via receptor-mediated endocytosis. The subsequent endosomal acidification triggers a series of conformational changes, resulting in the refolding and membrane insertion of the translocation (T-)domain and ultimately leading to the translocation of the catalytic domain into the cytoplasm. Here, we use X-ray crystallography along with circular dichroism and fluorescence spectroscopy to gain insight into the mechanism of the early stages of pH-dependent conformational transition. For the first time, we present the high-resolution structure of the diphtheria toxin at a mildly acidic pH (5–6) and compare it to the structure at neutral pH (7). We demonstrate that neither catalytic nor receptor-binding domains change their structure upon this acidification, while the T-domain undergoes a conformational change that results in the unfolding of the TH2–3 helices. Surprisingly, the TH1 helix maintains its conformation in the crystal of the full-length toxin even at pH 5. This contrasts with the evidence from the new and previously published data, obtained by spectroscopic measurements and molecular dynamics computer simulations, which indicate the refolding of TH1 upon the acidification of the isolated T-domain. The overall results imply that the membrane interactions of the T-domain are critical in ensuring the proper conformational changes required for the preparation of the diphtheria toxin for the cellular entry.
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Affiliation(s)
- Mykola V. Rodnin
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA; (M.V.R.); (A.K.)
| | - Maithri M. Kashipathy
- Protein Structure Laboratory, Shankel Structural Biology Center, University of Kansas, Lawrence, KS 66047, USA; (M.M.K.); (S.L.)
| | - Alexander Kyrychenko
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA; (M.V.R.); (A.K.)
- Institute of Chemistry and School of Chemistry, V. N. Karazin Kharkiv National University, 61022 Kharkiv, Ukraine
| | - Kevin P. Battaile
- NYX beamline, New York Structural Biology Center, Upton, NY 11973, USA;
| | - Scott Lovell
- Protein Structure Laboratory, Shankel Structural Biology Center, University of Kansas, Lawrence, KS 66047, USA; (M.M.K.); (S.L.)
| | - Alexey S. Ladokhin
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA; (M.V.R.); (A.K.)
- Correspondence: ; Tel.: +1-913-588-0489; Fax: +1-913-588-7440
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15
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Alhammad YMO, Kashipathy MM, Roy A, Gagné JP, McDonald P, Gao P, Nonfoux L, Battaile KP, Johnson DK, Holmstrom ED, Poirier GG, Lovell S, Fehr AR. The SARS-CoV-2 conserved macrodomain is a mono-ADP-ribosylhydrolase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.05.11.089375. [PMID: 32511412 PMCID: PMC7263559 DOI: 10.1101/2020.05.11.089375] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
UNLABELLED Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other SARS-like-CoVs encode 3 tandem macrodomains within non-structural protein 3 (nsp3). The first macrodomain, Mac1, is conserved throughout CoVs, and binds to and hydrolyzes mono-ADP-ribose (MAR) from target proteins. Mac1 likely counters host-mediated anti-viral ADP-ribosylation, a posttranslational modification that is part of the host response to viral infections. Mac1 is essential for pathogenesis in multiple animal models of CoV infection, implicating it as a virulence factor and potential therapeutic target. Here we report the crystal structure of SARS-CoV-2 Mac1 in complex with ADP-ribose. SARS-CoV-2, SARS-CoV and MERS-CoV Mac1 exhibit similar structural folds and all 3 proteins bound to ADP-ribose with low μM affinities. Importantly, using ADP-ribose detecting binding reagents in both a gel-based assay and novel ELISA assays, we demonstrated de-MARylating activity for all 3 CoV Mac1 proteins, with the SARS-CoV-2 Mac1 protein leading to a more rapid loss of substrate compared to the others. In addition, none of these enzymes could hydrolyze poly-ADP-ribose. We conclude that the SARS-CoV-2 and other CoV Mac1 proteins are MAR-hydrolases with similar functions, indicating that compounds targeting CoV Mac1 proteins may have broad anti-CoV activity. IMPORTANCE SARS-CoV-2 has recently emerged into the human population and has led to a worldwide pandemic of COVID-19 that has caused greater than 900 thousand deaths worldwide. With, no currently approved treatments, novel therapeutic strategies are desperately needed. All coronaviruses encode for a highly conserved macrodomain (Mac1) that binds to and removes ADP-ribose adducts from proteins in a dynamic post-translational process increasingly recognized as an important factor that regulates viral infection. The macrodomain is essential for CoV pathogenesis and may be a novel therapeutic target. Thus, understanding its biochemistry and enzyme activity are critical first steps for these efforts. Here we report the crystal structure of SARS-CoV-2 Mac1 in complex with ADP-ribose, and describe its ADP-ribose binding and hydrolysis activities in direct comparison to SARS-CoV and MERS-CoV Mac1 proteins. These results are an important first step for the design and testing of potential therapies targeting this unique protein domain.
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16
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Rathnayake AD, Kim Y, Dampalla CS, Nguyen HN, Jesri ARM, Kashipathy MM, Lushington GH, Battaile KP, Lovell S, Chang KO, Groutas WC. Structure-Guided Optimization of Dipeptidyl Inhibitors of Norovirus 3CL Protease. J Med Chem 2020; 63:11945-11963. [PMID: 32945669 DOI: 10.1021/acs.jmedchem.0c01252] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Acute gastroenteritis caused by noroviruses has a major impact on public health worldwide in terms of morbidity, mortality, and economic burden. The disease impacts most severely immunocompromised patients, the elderly, and children. The current lack of approved vaccines and small-molecule therapeutics for the treatment and prophylaxis of norovirus infections underscores the need for the development of norovirus-specific drugs. The studies described herein entail the use of the gem-dimethyl moiety as a means of improving the pharmacological activity and physicochemical properties of a dipeptidyl series of transition state inhibitors of norovirus 3CL protease, an enzyme essential for viral replication. Several compounds were found to be potent inhibitors of the enzyme in biochemical and cell-based assays. The pharmacological activity and cellular permeability of the inhibitors were found to be sensitive to the location of the gem-dimethyl group.
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Affiliation(s)
- Athri D Rathnayake
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, United States
| | - Yunjeong Kim
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, United States
| | - Chamandi S Dampalla
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, United States
| | - Harry Nhat Nguyen
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, United States
| | - Abdul-Rahman M Jesri
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, United States
| | - Maithri M Kashipathy
- Protein Structure Laboratory, The University of Kansas, Lawrence, Kansas 66047, United States
| | | | - Kevin P Battaile
- NYX, New York Structural Biology Center, Upton, New York 11973, United States
| | - Scott Lovell
- Protein Structure Laboratory, The University of Kansas, Lawrence, Kansas 66047, United States
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine & 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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17
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Rathnayake AD, Zheng J, Kim Y, Perera KD, Mackin S, Meyerholz DK, Kashipathy MM, Battaile KP, Lovell S, Perlman S, Groutas WC, Chang KO. 3C-like protease inhibitors block coronavirus replication in vitro and improve survival in MERS-CoV-infected mice. Sci Transl Med 2020; 12:scitranslmed.abc5332. [PMID: 32747425 PMCID: PMC7574915 DOI: 10.1126/scitranslmed.abc5332] [Citation(s) in RCA: 155] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/31/2020] [Indexed: 12/15/2022]
Abstract
Coronavirus 3C-like proteases (3CLpro) are attractive therapeutic targets because they play a vital role in coronavirus replication. Rathnayake et al. now report a series of optimized coronavirus 3CLpro inhibitors that blocked replication of the human coronaviruses MERS-CoV and SARS-CoV-2 in cultured cells. Administration of a lead compound to a MERS-CoV mouse model demonstrated proof-of-concept efficacy. These findings suggest that this lead compound should be investigated further as a potential therapeutic for human coronavirus infection. Pathogenic coronaviruses are a major threat to global public health, as exemplified by severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and the newly emerged SARS-CoV-2, the causative agent of coronavirus disease 2019 (COVID-19). We describe herein the structure-guided optimization of a series of inhibitors of the coronavirus 3C-like protease (3CLpro), an enzyme essential for viral replication. The optimized compounds were effective against several human coronaviruses including MERS-CoV, SARS-CoV, and SARS-CoV-2 in an enzyme assay and in cell-based assays using Huh-7 and Vero E6 cell lines. Two selected compounds showed antiviral effects against SARS-CoV-2 in cultured primary human airway epithelial cells. In a mouse model of MERS-CoV infection, administration of a lead compound 1 day after virus infection increased survival from 0 to 100% and reduced lung viral titers and lung histopathology. These results suggest that this series of compounds has the potential to be developed further as antiviral drugs against human coronaviruses.
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Affiliation(s)
- Athri D Rathnayake
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA
| | - Jian Zheng
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA
| | - Yunjeong Kim
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Krishani Dinali Perera
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Samantha Mackin
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA
| | - David K Meyerholz
- Department of Pathology, University of Iowa, Iowa City, IA 52242, USA
| | | | | | - Scott Lovell
- Protein Structure Laboratory, University of Kansas, Lawrence, KS 66045, USA
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA.
| | - William C Groutas
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA.
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.
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18
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Reese HR, Shanahan CC, Proulx C, Menegatti S. Peptide science: A "rule model" for new generations of peptidomimetics. Acta Biomater 2020; 102:35-74. [PMID: 31698048 DOI: 10.1016/j.actbio.2019.10.045] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 10/17/2019] [Accepted: 10/30/2019] [Indexed: 02/07/2023]
Abstract
Peptides have been heavily investigated for their biocompatible and bioactive properties. Though a wide array of functionalities can be introduced by varying the amino acid sequence or by structural constraints, properties such as proteolytic stability, catalytic activity, and phase behavior in solution are difficult or impossible to impart upon naturally occurring α-L-peptides. To this end, sequence-controlled peptidomimetics exhibit new folds, morphologies, and chemical modifications that create new structures and functions. The study of these new classes of polymers, especially α-peptoids, has been highly influenced by the analysis, computational, and design techniques developed for peptides. This review examines techniques to determine primary, secondary, and tertiary structure of peptides, and how they have been adapted to investigate peptoid structure. Computational models developed for peptides have been modified to predict the morphologies of peptoids and have increased in accuracy in recent years. The combination of in vitro and in silico techniques have led to secondary and tertiary structure design principles that mirror those for peptides. We then examine several important developments in peptoid applications inspired by peptides such as pharmaceuticals, catalysis, and protein-binding. A brief survey of alternative backbone structures and research investigating these peptidomimetics shows how the advancement of peptide and peptoid science has influenced the growth of numerous fields of study. As peptide, peptoid, and other peptidomimetic studies continue to advance, we will expect to see higher throughput structural analyses, greater computational accuracy and functionality, and wider application space that can improve human health, solve environmental challenges, and meet industrial needs. STATEMENT OF SIGNIFICANCE: Many historical, chemical, and functional relations draw a thread connecting peptides to their recent cognates, the "peptidomimetics". This review presents a comprehensive survey of this field by highlighting the width and relevance of these familial connections. In the first section, we examine the experimental and computational techniques originally developed for peptides and their morphing into a broader analytical and predictive toolbox. The second section presents an excursus of the structures and properties of prominent peptidomimetics, and how the expansion of the chemical and structural diversity has returned new exciting properties. The third section presents an overview of technological applications and new families of peptidomimetics. As the field grows, new compounds emerge with clear potential in medicine and advanced manufacturing.
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19
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Lan L, Xing M, Kashipathy M, Douglas J, Gao P, Battaile K, Hanzlik R, Lovell S, Xu L. Crystal and solution structures of human oncoprotein Musashi-2 N-terminal RNA recognition motif 1. Proteins 2019; 88:573-583. [PMID: 31603583 PMCID: PMC7079100 DOI: 10.1002/prot.25836] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 09/16/2019] [Accepted: 09/28/2019] [Indexed: 01/03/2023]
Abstract
Musashi‐2 (MSI2) belongs to Musashi family of RNA binding proteins (RBP). Like Musashi‐1 (MSI1), it is overexpressed in a variety of cancers and is a promising therapeutic target. Both MSI proteins contain two N‐terminal RNA recognition motifs and play roles in posttranscriptional regulation of target mRNAs. Previously, we have identified several inhibitors of MSI1, all of which bind to MSI2 as well. In order to design MSI2‐specific inhibitors and compare the differences of binding mode of the inhibitors, we set out to solve the structure of MSI2‐RRM1, the key motif that is responsible for the binding. Here, we report the crystal structure and the first NMR solution structure of MSI2‐RRM1, and compare these to the structures of MSI1‐RBD1 and other RBPs. A high degree of structural similarity was observed between the crystal and solution NMR structures. MSI2‐RRM1 shows a highly similar overall folding topology to MSI1‐RBD1 and other RBPs. The structural information of MSI2‐RRM1 will be helpful for understanding MSI2‐RNA interaction and for guiding rational drug design of MSI2‐specific inhibitors.
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Affiliation(s)
- Lan Lan
- Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas
| | - Minli Xing
- Bio-NMR Core Facility, NIH COBRE in Protein Structure and Function, The University of Kansas, Lawrence, Kansas
| | - Maithri Kashipathy
- Protein Structure Laboratory, NIH COBRE in Protein Structure and Function, The University of Kansas, Lawrence, Kansas
| | - Justin Douglas
- Bio-NMR Core Facility, NIH COBRE in Protein Structure and Function, The University of Kansas, Lawrence, Kansas
| | - Philip Gao
- Protein Production Group, NIH COBRE in Protein Structure and Function, The University of Kansas, Lawrence, Kansas
| | - Kevin Battaile
- IMCA-CAT, Hauptman Woodward Medical Research Institute, Argonne, Illinois
| | - Robert Hanzlik
- Department of Medicinal Chemistry, The University of Kansas, Lawrence, Kansas
| | - Scott Lovell
- Protein Structure Laboratory, NIH COBRE in Protein Structure and Function, The University of Kansas, Lawrence, Kansas
| | - Liang Xu
- Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas.,Department of Radiation Oncology, The University of Kansas Cancer Center, Kansas City, Kansas
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20
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Wang S, Gegenfurtner FA, Crevenna AH, Ziegenhain C, Kliesmete Z, Enard W, Müller R, Vollmar AM, Schneider S, Zahler S. Chivosazole A Modulates Protein-Protein Interactions of Actin. JOURNAL OF NATURAL PRODUCTS 2019; 82:1961-1970. [PMID: 31260301 DOI: 10.1021/acs.jnatprod.9b00335] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Actin is a protein of central importance for many cellular key processes. It is regulated by local interactions with a large number of actin binding proteins (ABPs). Various compounds are known to either increase or decrease the polymerization dynamics of actin. However, no actin binding compound has been developed for clinical applications yet because of selectivity issues. We provide a crystal structure of the natural product chivosazole A (ChivoA) bound to actin and show that-in addition to inhibiting nucleation, polymerization, and severing of F-actin filaments-it selectively modulates binding of ABPs to G-actin: Although unphysiological actin dimers are induced by ChivoA, interaction with gelsolin, profilin, cofilin, and thymosin-β4 is inhibited. Moreover, ChivoA causes transcriptional effects differing from latrunculin B, an actin binder with a different binding site. Our data show that ChivoA and related compounds could serve as scaffolds for the development of actin binding molecules selectively targeting specific actin functions.
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Affiliation(s)
- Shuaijun Wang
- Department of Pharmacy , Ludwig-Maximilians-University , 81377 Munich , Germany
| | | | - Alvaro H Crevenna
- Biomolecular Self-Organization Laboratory , ITQB-Universidade Nova de Lisboa , 2780-157 Oeiras , Portugal
| | - Christoph Ziegenhain
- Department of Biology II , Ludwig-Maximilians-University , 82152 Planegg-Martinsried , Germany
| | - Zane Kliesmete
- Department of Biology II , Ludwig-Maximilians-University , 82152 Planegg-Martinsried , Germany
| | - Wolfgang Enard
- Department of Biology II , Ludwig-Maximilians-University , 82152 Planegg-Martinsried , Germany
| | - Rolf Müller
- Department of Pharmacy , Saarland University , 66125 Saarbrücken , Germany
- Department of Microbial Natural Products , Helmholtz Institute for Pharmaceutical Research Saarland and Helmholtz Centre for Infection Research , 66123 Saarbrücken , Germany
| | - Angelika M Vollmar
- Department of Pharmacy , Ludwig-Maximilians-University , 81377 Munich , Germany
| | - Sabine Schneider
- Department of Chemistry , Technical University Munich , 85748 Garching , Germany
| | - Stefan Zahler
- Department of Pharmacy , Ludwig-Maximilians-University , 81377 Munich , Germany
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21
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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 CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:628-638. [PMID: 31282472 DOI: 10.1107/s205979831900754x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [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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22
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Crystal Structure of VapBC-1 from Nontypeable Haemophilus influenzae and the Effect of PIN Domain Mutations on Survival during Infection. J Bacteriol 2019; 201:JB.00026-19. [PMID: 30936373 DOI: 10.1128/jb.00026-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 03/29/2019] [Indexed: 12/15/2022] Open
Abstract
Toxin-antitoxin (TA) gene pairs have been identified in nearly all bacterial genomes sequenced to date and are thought to facilitate persistence and antibiotic tolerance. TA loci are classified into various types based upon the characteristics of their antitoxins, with those in type II expressing proteic antitoxins. Many toxins from type II modules are ribonucleases that maintain a PilT N-terminal (PIN) domain containing conserved amino acids considered essential for activity. The vapBC (virulence-associated protein) TA system is the largest subfamily in this class and has been linked to pathogenesis of nontypeable Haemophilus influenzae (NTHi). In this study, the crystal structure of the VapBC-1 complex from NTHi was determined to 2.20 Å resolution. Based on this structure, aspartate-to-asparagine and glutamate-to-glutamine mutations of four conserved residues in the PIN domain of the VapC-1 toxin were constructed and the effects of the mutations on protein-protein interactions, growth of Escherichia coli, and pathogenesis ex vivo were tested. Finally, a novel model system was designed and utilized that consists of an NTHi ΔvapBC-1 strain complemented in cis with the TA module containing a mutated or wild-type toxin at an ectopic site on the chromosome. This enabled the analysis of the effect of PIN domain toxin mutants in tandem with their wild-type antitoxin under the control of the vapBC-1 native promoter and in single copy. This is the first report of a system facilitating the study of TA mutant operons in the background of NTHi during infections of primary human tissues ex vivo IMPORTANCE Herein the crystal structure of the VapBC-1 complex from nontypeable Haemophilus influenzae (NTHi) is described. Our results show that some of the mutations in the PIN domain of the VapC-1 toxin were associated with decreased toxicity in E. coli, but the mutants retained the ability to homodimerize and to heterodimerize with the wild-type cognate antitoxin, VapB-1. A new system was designed and constructed to quantify the effects of these mutations on NTHi survival during infections of primary human tissues ex vivo Any mutation to a conserved amino acid in the PIN domain significantly decreased the number of survivors compared to that of the in cis wild-type toxin under the same conditions.
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23
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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] [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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24
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Karkehabadi S, Hansson H, Mikkelsen NE, Kim S, Kaper T, Sandgren M, Gudmundsson M. Structural studies of a glycoside hydrolase family 3 β-glucosidase from the model fungus Neurospora crassa. Acta Crystallogr F Struct Biol Commun 2018; 74:787-796. [PMID: 30511673 PMCID: PMC6277957 DOI: 10.1107/s2053230x18015662] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 11/05/2018] [Indexed: 11/29/2022] Open
Abstract
The glycoside hydrolase family 3 (GH3) β-glucosidases are a structurally diverse family of enzymes. Cel3A from Neurospora crassa (NcCel3A) belongs to a subfamily of key enzymes that are crucial for industrial biomass degradation. β-Glucosidases hydrolyse the β-1,4 bond at the nonreducing end of cellodextrins. The hydrolysis of cellobiose is of special importance as its accumulation inhibits other cellulases acting on crystalline cellulose. Here, the crystal structure of the biologically relevant dimeric form of NcCel3A is reported. The structure has been refined to 2.25 Å resolution, with an Rcryst and Rfree of 0.18 and 0.22, respectively. NcCel3A is an extensively N-glycosylated glycoprotein that shares 46% sequence identity with Hypocrea jecorina Cel3A, the structure of which has recently been published, and 61% sequence identity with the thermophilic β-glucosidase from Rasamsonia emersonii. NcCel3A is a three-domain protein with a number of extended loops that deepen the active-site cleft of the enzyme. These structures characterize this subfamily of GH3 β-glucosidases and account for the high cellobiose specificity of this subfamily.
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Affiliation(s)
- Saeid Karkehabadi
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07 Uppsala, Sweden
| | - Henrik Hansson
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07 Uppsala, Sweden
| | - Nils Egil Mikkelsen
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07 Uppsala, Sweden
| | - Steve Kim
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, CA 94304, USA
| | - Thijs Kaper
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, CA 94304, USA
| | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07 Uppsala, Sweden
| | - Mikael Gudmundsson
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07 Uppsala, Sweden
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25
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Shabalin IG, Porebski PJ, Minor W. Refining the macromolecular model - achieving the best agreement with the data from X-ray diffraction experiment. CRYSTALLOGR REV 2018; 24:236-262. [PMID: 30416256 DOI: 10.1080/0889311x.2018.1521805] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Refinement of macromolecular X-ray crystal structures involves using complex software with hundreds of different settings. The complexity of underlying concepts and the sheer amount sof instructions may make it difficult for less experienced crystallographers to achieve optimal results in their refinements. This tutorial review offers guidelines for choosing the best settings for the reciprocal-space refinement of macromolecular models and provides practical tips for manual model correction. To help aspiring crystallographers navigate the process, some of the most practically important concepts of protein structure refinement are described. Among the topics covered are the use and purpose of R-free, geometrical restraints, restraints on atomic displacement parameters (ADPs), refinement weights, various parametrizations of ADPs (full anisotropic refinement and TLS), and omit maps. We also give practical tips for manual model correction in Coot, modelling of side-chains with poor or missing density, and ligand identification, fitting, and refinement.
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Affiliation(s)
- Ivan G Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, United States.,Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA, 22908, United States
| | - Przemyslaw J Porebski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, United States.,Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA, 22908, United States
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, United States.,Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA, 22908, United States
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26
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Wijerathne H, Yao H, Wang Y, Lovell S, Battaile KP, Rivera M. Bfd, a New Class of [2Fe-2S] Protein That Functions in Bacterial Iron Homeostasis, Requires a Structural Anion Binding Site. Biochemistry 2018; 57:5533-5543. [PMID: 30183257 DOI: 10.1021/acs.biochem.8b00823] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Mobilization of iron from bacterioferritin (BfrB) requires specific interactions with a [2Fe-2S] ferredoxin (Bfd). Blocking the BfrB:Bfd interaction results in irreversible iron accumulation in BfrB and iron deficiency in the cytosol [Eshelman, K., et al. (2017) Metallomics 9, 646-659]. The only known Bfd structure, which was obtained in complex with BfrB (Protein Data Bank entry 4E6K ), indicated a new fold and suggested that the stability of Bfd is aided by an anion binding site consisting of R26, R29, and K46. We investigated the Bfd fold using site-directed mutagenesis, X-ray crystallography, and biochemistry in solution. The X-ray structure, which is nearly identical to that of Bfd in the BfrB:Bfd complex, shows that the [2Fe-2S] cluster preorganizes residues at the BfrB:Bfd interface into a structure complementary to the Bfd binding site on BfrB. Studies in solution showed rapid loss of the [2Fe-2S] cluster at a low ionic strength but higher stability with an increasing ionic strength, thus supporting a structural anion binding site. Structures of the R26E and R26E/K46Y mutants are nearly identical to that of Bfd, except for a new network of hydrogen bonds stabilizing the region encompassing the former anion binding site. The stability of the R26E and R26E/K46Y mutants, which is weakly and completely independent of solution ionic strength, respectively, corroborates that Bfd requires an anion binding site. The mutations, which caused only small changes to the strength of the BfrB:Bfd interaction and mobilization of iron from BfrB, indicate that the anion binding site in Bfd serves primarily a structural role.
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Affiliation(s)
- Harshani Wijerathne
- Department of Chemistry , University of Kansas , Multidisciplinary Research Building, 2030 Becker Drive , Lawrence , Kansas 66047 , United States
| | - Huili Yao
- Department of Chemistry , Louisiana State University , 229A Choppin Hall , Baton Rouge , Louisiana 70803 , United States
| | - Yan Wang
- Department of Chemistry , University of Kansas , Multidisciplinary Research Building, 2030 Becker Drive , Lawrence , Kansas 66047 , United States
| | - Scott Lovell
- Protein Structure Laboratory, Del Shankel Structural Biology Center , University of Kansas , 2034 Becker Drive , Lawrence , Kansas 66047 , United States
| | - Kevin P Battaile
- IMCA-CAT , Hauptman Woodward Medical Research Institute , 9700 South Cass Avenue, Building 435A , Argonne , Illinois 60439 , United States
| | - Mario Rivera
- Department of Chemistry , Louisiana State University , 229A Choppin Hall , Baton Rouge , Louisiana 70803 , United States
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27
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Barta ML, Tachiyama S, Muthuramalingam M, Arizmendi O, Villanueva CE, Ramyar KX, Geisbrecht BV, Lovell S, Battaile KP, Picking WL, Picking WD. Using disruptive insertional mutagenesis to identify the in situ structure-function landscape of the Shigella translocator protein IpaB. Protein Sci 2018; 27:1392-1406. [PMID: 29672980 DOI: 10.1002/pro.3428] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 04/12/2018] [Accepted: 04/16/2018] [Indexed: 11/11/2022]
Abstract
Bacterial type III secretion systems (T3SS) are used to inject proteins into mammalian cells to subvert cellular functions. The Shigella T3SS apparatus (T3SA) is comprised of a basal body, cytoplasmic sorting platform and exposed needle with needle "tip complex" (TC). TC maturation occurs when the translocator protein IpaB is recruited to the needle tip where both IpaD and IpaB control secretion induction. IpaB insertion into the host membrane is the first step of translocon pore formation and secretion induction. We employed disruptive insertional mutagenesis, using bacteriophage T4 lysozyme (T4L), within predicted IpaB loops to show how topological features affect TC functions (secretion control, translocon formation and effector secretion). Insertions within the N-terminal half of IpaB were most likely to result in a loss of steady-state secretion control, however, all but the two that were not recognized by the T3SA retained nearly wild-type hemolysis (translocon formation) and invasiveness levels (effector secretion). In contrast, all but one insertion in the C-terminal half of IpaB maintained secretion control but were impaired for hemolysis and invasion. These nature of the data suggest the latter mutants are defective in a post-secretion event, most likely due to impaired interactions with the second translocator protein IpaC. Intriguingly, only two insertion mutants displayed readily detectable T4L on the bacterial surface. The data create a picture in which the makeup and structure of a functional T3SA TC is highly amenable to physical perturbation, indicating that the tertiary structure of IpaB within the TC is more plastic than previously realized.
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Affiliation(s)
- Michael L Barta
- Higuchi Biosciences Center, University of Kansas, Lawrence, Kansas, 66047
| | - Shoichi Tachiyama
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, 66045
| | | | - Olivia Arizmendi
- Higuchi Biosciences Center, University of Kansas, Lawrence, Kansas, 66047
| | - Cecilia E Villanueva
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, 66045
| | - Kasra X Ramyar
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, 66506
| | - Brian V Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, 66506
| | - Scott Lovell
- Protein Structure Laboratory, Del Shankel Structural Biology Center, University of Kansas, Lawrence, KS, 66045
| | - Kevin P Battaile
- IMCA-CAT, Hauptman-Woodward Medical Research Institute, Argonne, Illinois, 60439
| | - Wendy L Picking
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas, 66047
| | - William D Picking
- Higuchi Biosciences Center, University of Kansas, Lawrence, Kansas, 66047.,Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas, 66047
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28
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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: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [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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29
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Abstract
X-Ray diffraction data at atomic resolution, i.e., beyond 1.2 Å, provide the most detailed and reliable information we have about the structure of macromolecules, which is especially important for validating new discoveries and resolving subtle issues of molecular mechanisms. Refinement at atomic resolution allows reliable interpretation of static disorder and solvent structure, as well as modeling of anisotropic atomic vibrations and even of H atoms. Stereochemical restraints can be relaxed or removed, providing unbiased information about macromolecular stereochemistry, which in turn can be used to define improved conformation-dependent libraries, and the surplus of data allows estimation of least-squares uncertainties in the derived parameters. At ultrahigh resolution it is possible to study charge density distribution by multipolar refinement of electrons in non-spherical orbitals.
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30
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Klaeger S, Heinzlmeir S, Wilhelm M, Polzer H, Vick B, Koenig PA, Reinecke M, Ruprecht B, Petzoldt S, Meng C, Zecha J, Reiter K, Qiao H, Helm D, Koch H, Schoof M, Canevari G, Casale E, Depaolini SR, Feuchtinger A, Wu Z, Schmidt T, Rueckert L, Becker W, Huenges J, Garz AK, Gohlke BO, Zolg DP, Kayser G, Vooder T, Preissner R, Hahne H, Tõnisson N, Kramer K, Götze K, Bassermann F, Schlegl J, Ehrlich HC, Aiche S, Walch A, Greif PA, Schneider S, Felder ER, Ruland J, Médard G, Jeremias I, Spiekermann K, Kuster B. The target landscape of clinical kinase drugs. Science 2018; 358:358/6367/eaan4368. [PMID: 29191878 DOI: 10.1126/science.aan4368] [Citation(s) in RCA: 512] [Impact Index Per Article: 85.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 09/20/2017] [Indexed: 02/06/2023]
Abstract
Kinase inhibitors are important cancer therapeutics. Polypharmacology is commonly observed, requiring thorough target deconvolution to understand drug mechanism of action. Using chemical proteomics, we analyzed the target spectrum of 243 clinically evaluated kinase drugs. The data revealed previously unknown targets for established drugs, offered a perspective on the "druggable" kinome, highlighted (non)kinase off-targets, and suggested potential therapeutic applications. Integration of phosphoproteomic data refined drug-affected pathways, identified response markers, and strengthened rationale for combination treatments. We exemplify translational value by discovering SIK2 (salt-inducible kinase 2) inhibitors that modulate cytokine production in primary cells, by identifying drugs against the lung cancer survival marker MELK (maternal embryonic leucine zipper kinase), and by repurposing cabozantinib to treat FLT3-ITD-positive acute myeloid leukemia. This resource, available via the ProteomicsDB database, should facilitate basic, clinical, and drug discovery research and aid clinical decision-making.
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Affiliation(s)
- Susan Klaeger
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stephanie Heinzlmeir
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Harald Polzer
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Internal Medicine III, University Hospital, Ludwig-Maximilians-Universität (LMU) München, Munich, Germany
| | - Binje Vick
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, German Center for Environmental Health (HMGU), Munich, Germany
| | | | - Maria Reinecke
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Benjamin Ruprecht
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Svenja Petzoldt
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Chen Meng
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Jana Zecha
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Katrin Reiter
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Internal Medicine III, University Hospital, Ludwig-Maximilians-Universität (LMU) München, Munich, Germany
| | - Huichao Qiao
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Dominic Helm
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Heiner Koch
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Melanie Schoof
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | | | - Elena Casale
- Oncology, Nerviano Medical Sciences Srl, Milan, Italy
| | | | - Annette Feuchtinger
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Zhixiang Wu
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Tobias Schmidt
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | | | | | | | - Anne-Kathrin Garz
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Medicine III, Klinikum rechts der Isar, TUM, Munich, Germany
| | - Bjoern-Oliver Gohlke
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Structural Bioinformatics Group, Charité-Universitätsmedizin, Berlin, Germany
| | - Daniel Paul Zolg
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Gian Kayser
- Institute of Surgical Pathology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tonu Vooder
- Center of Thoracic Surgery, Krefeld, Germany.,Estonian Genome Center, University of Tartu, Tartu, Estonia.,Tartu University Hospital, Tartu, Estonia
| | - Robert Preissner
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Structural Bioinformatics Group, Charité-Universitätsmedizin, Berlin, Germany
| | - Hannes Hahne
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Neeme Tõnisson
- Estonian Genome Center, University of Tartu, Tartu, Estonia.,Tartu University Hospital, Tartu, Estonia
| | - Karl Kramer
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Katharina Götze
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Medicine III, Klinikum rechts der Isar, TUM, Munich, Germany
| | - Florian Bassermann
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Medicine III, Klinikum rechts der Isar, TUM, Munich, Germany
| | | | | | | | - Axel Walch
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Philipp A Greif
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Internal Medicine III, University Hospital, Ludwig-Maximilians-Universität (LMU) München, Munich, Germany
| | - Sabine Schneider
- Department of Chemistry, TUM, Garching, Germany.,Center For Integrated Protein Science Munich (CIPSM), Munich, Germany
| | | | - Juergen Ruland
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institut für Klinische Chemie und Pathobiochemie, TUM, Munich, Germany
| | - Guillaume Médard
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Irmela Jeremias
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, German Center for Environmental Health (HMGU), Munich, Germany.,Department of Pediatrics, Dr von Hauner Children's Hospital, LMU, Munich, Germany
| | - Karsten Spiekermann
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Internal Medicine III, University Hospital, Ludwig-Maximilians-Universität (LMU) München, Munich, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany. .,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Center For Integrated Protein Science Munich (CIPSM), Munich, Germany.,Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), TUM, Freising, Germany
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31
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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] [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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32
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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] [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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33
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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] [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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34
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Willkomm S, Oellig CA, Zander A, Restle T, Keegan R, Grohmann D, Schneider S. Structural and mechanistic insights into an archaeal DNA-guided Argonaute protein. Nat Microbiol 2017; 2:17035. [PMID: 28319084 DOI: 10.1038/nmicrobiol.2017.35] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 02/10/2017] [Indexed: 12/17/2022]
Abstract
Argonaute (Ago) proteins in eukaryotes are known as key players in post-transcriptional gene silencing1, while recent studies on prokaryotic Agos hint at their role in the protection against invading DNA2,3. Here, we present crystal structures of the apo enzyme and a binary Ago-guide complex of the archaeal Methanocaldococcus jannaschii (Mj) Ago. Binding of a guide DNA leads to large structural rearrangements. This includes the structural transformation of a hinge region containing a switch helix, which has been shown for human Ago2 to be critical for the dynamic target search process4-6. To identify key residues crucial for MjAgo function, we analysed the effect of several MjAgo mutants. We observe that the nature of the 3' and 5' nucleotides in particular, as well as the switch helix, appear to impact MjAgo cleavage activity. In summary, we provide insights into the molecular mechanisms that drive DNA-guided DNA silencing by an archaeal Ago.
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Affiliation(s)
- Sarah Willkomm
- Institute of Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Christine A Oellig
- Center for Integrated Protein Science Munich CIPSM, Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Adrian Zander
- Institute of Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Tobias Restle
- Institute for Molecular Medicine, University of Lübeck, 23538 Lübeck, Germany
| | - Ronan Keegan
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, UK.,Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Dina Grohmann
- Institute of Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Sabine Schneider
- Center for Integrated Protein Science Munich CIPSM, Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany
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35
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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] [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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36
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Meekins DA, Zhang X, Battaile KP, Lovell S, Michel K. 1.45 Å resolution structure of SRPN18 from the malaria vector Anopheles gambiae. Acta Crystallogr F Struct Biol Commun 2016; 72:853-862. [PMID: 27917832 PMCID: PMC5137461 DOI: 10.1107/s2053230x16017854] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 11/08/2016] [Indexed: 12/28/2022] Open
Abstract
Serine protease inhibitors (serpins) in insects function within development, wound healing and immunity. The genome of the African malaria vector, Anopheles gambiae, encodes 23 distinct serpin proteins, several of which are implicated in disease-relevant physiological responses. A. gambiae serpin 18 (SRPN18) was previously categorized as non-inhibitory based on the sequence of its reactive-center loop (RCL), a region responsible for targeting and initiating protease inhibition. The crystal structure of A. gambiae SRPN18 was determined to a resolution of 1.45 Å, including nearly the entire RCL in one of the two molecules in the asymmetric unit. The structure reveals that the SRPN18 RCL is extremely short and constricted, a feature associated with noncanonical inhibitors or non-inhibitory serpin superfamily members. Furthermore, the SRPN18 RCL does not contain a suitable protease target site and contains a large number of prolines. The SRPN18 structure therefore reveals a unique RCL architecture among the highly conserved serpin fold.
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Affiliation(s)
| | - Xin Zhang
- Division of Biology, Kansas State University, USA
| | - Kevin P. Battaile
- IMCA–CAT, Hauptman–Woodward Medical Research Institute, Argonne National Laboratory, USA
| | - Scott Lovell
- Protein Structure Laboratory, Del Shankel Structural Biology Center, University of Kansas, USA
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37
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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] [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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38
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Li J, Wehmeyer G, Lovell S, Battaile KP, Egan SM. 1.65 Å resolution structure of the AraC-family transcriptional activator ToxT from Vibrio cholerae. Acta Crystallogr F Struct Biol Commun 2016; 72:726-31. [PMID: 27599865 PMCID: PMC5012214 DOI: 10.1107/s2053230x1601298x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 08/11/2016] [Indexed: 11/24/2022] Open
Abstract
ToxT is an AraC-family transcriptional activator protein that controls the expression of key virulence factors in Vibrio cholerae, the causative agent of cholera. ToxT directly activates the expression of the genes that encode the toxin-coregulated pilus and cholera toxin, and also positively auto-regulates its own expression from the tcp promoter. The crystal structure of ToxT has previously been solved at 1.9 Å resolution (PDB entry 3gbg). In this study, a crystal structure of ToxT at 1.65 Å resolution with a similar overall structure to the previously determined structure is reported. However, there are distinct differences between the two structures, particularly in the region that extends from Asp101 to Glu110. This region, which can influence ToxT activity but was disordered in the previous structure, can be traced entirely in the current structure.
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Affiliation(s)
- Jiaqin Li
- Department of Molecular Bioscience, The University of Kansas, 8031 Haworth, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA
| | - Graham Wehmeyer
- Department of Molecular Bioscience, The University of Kansas, 8031 Haworth, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA
| | - Scott Lovell
- Protein Structure Laboratory, Shankel Structural Biology Center, The University of Kansas, 2034 Becker Drive, Lawrence, KS 66047, USA
| | - Kevin P. Battaile
- IMCA-CAT, Hauptman–Woodward Medical Research Institute, 9700 South Cass Avenue, Building 435A, Argonne, IL 60439, USA
| | - Susan M. Egan
- Department of Molecular Bioscience, The University of Kansas, 8031 Haworth, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA
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39
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Kumar R, Qi Y, Matsumura H, Lovell S, Yao H, Battaile KP, Im W, Moënne-Loccoz P, Rivera M. Replacing Arginine 33 for Alanine in the Hemophore HasA from Pseudomonas aeruginosa Causes Closure of the H32 Loop in the Apo-Protein. Biochemistry 2016; 55:2622-31. [PMID: 27074415 DOI: 10.1021/acs.biochem.6b00239] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Previous characterization of hemophores from Serratia marcescens (HasAs), Pseudomonas aeruginosa (HasAp), and Yersinia pestis (HasAyp) showed that hemin binds between two loops, where it is axially coordinated by H32 and Y75. The Y75 loop is structurally conserved in all three hemophores and harbors conserved ligand Y75. The other loop contains H32 in HasAs and HasAp, but a noncoordinating Q32 in HasAyp. The H32 loop in apo-HasAs and apo-HasAp is in an open conformation, which places H32 about 30 Å from the hemin-binding site. Hence, hemin binding onto the Y75 loop of HasAs or HasAp triggers a large relocation of the H32 loop from an open- to a closed-loop conformation and enables coordination of the hemin-iron by H32. In comparison, the Q32 loop in apo-HasAyp is in the closed conformation, and hemin binding occurs with minimal reorganization and without coordinative interactions with the Q32 loop. Studies in crystallo and in solution have established that the open H32 loop in apo-HasAp and apo-HasAs is well structured and minimally affected by conformational dynamics. In this study we address the intriguing issue of the stability of the H32 loop in apo-HasAp and how hemin binding triggers its relocation. We address this question with a combination of NMR spectroscopy, X-ray crystallography, and molecular dynamics simulations and find that R33 is critical to the stability of the open H32 loop. Replacing R33 with A causes the H32 loop in R33A apo-HasAp to adopt a conformation similar to that of holo-HasAp. Finally, stopped-flow absorption and resonance Raman analyses of hemin binding to apo-R33A HasAp indicate that the closed H32 loop slows down the insertion of the heme inside the binding pocket, presumably as it obstructs access to the hydrophobic platform on the Y75 loop, but accelerates the completion of the heme iron coordination.
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Affiliation(s)
| | | | - Hirotoshi Matsumura
- Division of Environmental & Biomolecular Systems, Institute of Environmental Health, Oregon Health and Science University , 3181 SW Sam Jackson Park Road, Oregon 97239, United States
| | - Scott Lovell
- Protein Structure Lab, Del Shankel Structural Biology Center, University of Kansas , 2034 Becker Drive, Lawrence, Kansas 66047, United States
| | | | - Kevin P Battaile
- IMCA-CAT, Hauptman Woodward Medical Research Institute , 9700 South Cass Avenue, Building 435A, Argonne, Illinois 60439, United States
| | | | - Pierre Moënne-Loccoz
- Division of Environmental & Biomolecular Systems, Institute of Environmental Health, Oregon Health and Science University , 3181 SW Sam Jackson Park Road, Oregon 97239, United States
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40
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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] [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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41
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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 PMCID: PMC4822980 DOI: 10.1107/s2053230x1600217x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 02/04/2016] [Indexed: 12/18/2022] Open
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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42
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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] [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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43
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Barta ML, Battaile KP, Lovell S, Hefty PS. Hypothetical protein CT398 (CdsZ) interacts with σ(54) (RpoN)-holoenzyme and the type III secretion export apparatus in Chlamydia trachomatis. Protein Sci 2015; 24:1617-32. [PMID: 26173998 DOI: 10.1002/pro.2746] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 07/06/2015] [Indexed: 12/22/2022]
Abstract
A significant challenge to bacteriology is the relatively large proportion of proteins that lack sufficient sequence similarity to support functional annotation (i.e. hypothetical proteins). The aim of this study was to apply protein structural homology to gain insights into a candidate protein of unknown function (CT398) within the medically important, obligate intracellular bacterium Chlamydia trachomatis. C. trachomatis is a major human pathogen responsible for numerous infections throughout the world that can lead to blindness and infertility. A 2.12 Å crystal structure of hypothetical protein CT398 was determined that was comprised of N-terminal coiled-coil and C-terminal Zn-ribbon domains. The structure of CT398 displayed a high degree of structural similarity to FlgZ (Flagellar-associated zinc-ribbon domain protein) from Helicobacter pylori. This observation directed analyses of candidate protein partners of CT398, revealing interactions with two paralogous type III secretion system (T3SS) ATPase-regulators (CdsL and FliH) and the alternative sigma factor RpoN (σ(54) ). Furthermore, genetic introduction of a conditional expression, affinity-tagged construct into C. trachomatis enabled the purification of a CT398-RpoN-holoenzyme complex, suggesting a potential role for CT398 in modulating transcriptional activity during infection. The interactions reported here, in tandem with previous FlgZ studies in H. pylori, indicate that CT398 functions as a regulator of several key areas of chlamydial biology throughout the developmental cycle. Accordingly, we propose that CT398 be named CdsZ (Contact-dependent secretion-associated zinc-ribbon domain protein).
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Affiliation(s)
- Michael L Barta
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045
| | - Kevin P Battaile
- IMCA-CAT, Hauptman-Woodward Medical Research Institute, Argonne, Illinois
| | - Scott Lovell
- Protein Structure Laboratory, Del Shankel Structural Biology Center, University of Kansas, Lawrence, KS, 66045
| | - P Scott Hefty
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045
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44
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Karplus PA, Diederichs K. Assessing and maximizing data quality in macromolecular crystallography. Curr Opin Struct Biol 2015. [PMID: 26209821 DOI: 10.1016/j.sbi.2015.07.003] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The quality of macromolecular crystal structures depends, in part, on the quality and quantity of the data used to produce them. Here, we review recent shifts in our understanding of how to use data quality indicators to select a high resolution cutoff that leads to the best model, and of the potential to greatly increase data quality through the merging of multiple measurements from multiple passes of single crystals or from multiple crystals. Key factors supporting this shift are the introduction of more robust correlation coefficient based indicators of the precision of merged data sets as well as the recognition of the substantial useful information present in extensive amounts of data once considered too weak to be of value.
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Affiliation(s)
- P Andrew Karplus
- Department of Biochemistry & Biophysics, Oregon State University, Corvallis, OR 97331, USA.
| | - Kay Diederichs
- University of Konstanz, Faculty of Biology, Box 647, D-78457 Konstanz, Germany.
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45
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Menting J, Lawrence C, Kong GW, Margetts M, Ward C, Lawrence M. Structural Congruency of Ligand Binding to the Insulin and Insulin/Type 1 Insulin-like Growth Factor Hybrid Receptors. Structure 2015; 23:1271-82. [DOI: 10.1016/j.str.2015.04.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 04/10/2015] [Accepted: 04/14/2015] [Indexed: 10/23/2022]
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Alexeeva M, Åberg E, Engh RA, Rothweiler U. The structure of a dual-specificity tyrosine phosphorylation-regulated kinase 1A-PKC412 complex reveals disulfide-bridge formation with the anomalous catalytic loop HRD(HCD) cysteine. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1207-15. [PMID: 25945585 DOI: 10.1107/s1399004715005106] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 03/12/2015] [Indexed: 01/12/2023]
Abstract
Dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) is a protein kinase associated with neuronal development and brain physiology. The DYRK kinases are very unusual with respect to the sequence of the catalytic loop, in which the otherwise highly conserved arginine of the HRD motif is replaced by a cysteine. This replacement, along with the proximity of a potential disulfide-bridge partner from the activation segment, implies a potential for redox control of DYRK family activities. Here, the crystal structure of DYRK1A bound to PKC412 is reported, showing the formation of the disulfide bridge and associated conformational changes of the activation loop. The DYRK kinases represent emerging drug targets for several neurological diseases as well as cancer. The observation of distinct activation states may impact strategies for drug targeting. In addition, the characterization of PKC412 binding offers new insights for DYRK inhibitor discovery.
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Affiliation(s)
- Marina Alexeeva
- Department of Chemistry, The Norwegian Structural Biology Centre, The Arctic University of Norway, 9037 Tromsø, Norway
| | - Espen Åberg
- Department of Chemistry, The Norwegian Structural Biology Centre, The Arctic University of Norway, 9037 Tromsø, Norway
| | - Richard A Engh
- Department of Chemistry, The Norwegian Structural Biology Centre, The Arctic University of Norway, 9037 Tromsø, Norway
| | - Ulli Rothweiler
- Department of Chemistry, The Norwegian Structural Biology Centre, The Arctic University of Norway, 9037 Tromsø, Norway
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Kankanamalage ACG, 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 PMCID: PMC4484267 DOI: 10.1021/jm5019934] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [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)
| | - Yunjeong Kim
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506
| | | | | | | | | | - Kevin R. Alliston
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260
| | - Nurjahan Mehzabeen
- Protein Structure Laboratory, The University of Kansas, Lawrence, Kansas 66047
| | - Kevin P. Battaile
- IMCA-CAT, Hauptman-Woodward Medical Research Institute, APS Argonne National Laboratory, Argonne, IL 60439
| | - Scott Lovell
- Protein Structure Laboratory, The University of Kansas, Lawrence, Kansas 66047
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506
| | - William C. Groutas
- Protein Structure Laboratory, The University of Kansas, Lawrence, Kansas 66047
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48
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Yao H, Rui H, Kumar R, Eshelman K, Lovell S, Battaile KP, Im W, Rivera M. Concerted motions networking pores and distant ferroxidase centers enable bacterioferritin function and iron traffic. Biochemistry 2015; 54:1611-27. [PMID: 25640193 DOI: 10.1021/bi501255r] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
X-ray crystallography, molecular dynamics (MD) simulations, and biochemistry were utilized to investigate the effect of introducing hydrophobic interactions in the 4-fold (N148L and Q151L) and B-pores (D34F) of Pseudomonas aeruginosa bacterioferritin B (BfrB) on BfrB function. The structures show only local structural perturbations and confirm the anticipated hydrophobic interactions. Surprisingly, structures obtained after soaking crystals in Fe2+-containing crystallization solution revealed that although iron loads into the ferroxidase centers of the mutants, the side chains of ferroxidase ligands E51 and H130 do not reorganize to bind the iron ions, as is seen in the wt BfrB structures. Similar experiments with a double mutant (C89S/K96C) prepared to introduce changes outside the pores show competent ferroxidase centers that function akin to those in wt BfrB. MD simulations comparing wt BfrB with the D34F and N148L mutants show that the mutants exhibit significantly reduced flexibility and reveal a network of concerted motions linking ferroxidase centers and 4-fold and B-pores, which are important for imparting ferroxidase centers in BfrB with the required flexibility to function efficiently. In agreement, the efficiency of Fe2+ oxidation and uptake of the 4-fold and B-pore mutants in solution is significantly compromised relative to wt or C89S/K96C BfrB. Finally, our structures show a large number of previously unknown iron binding sites in the interior cavity and B-pores of BfrB, which reveal in unprecedented detail conduits followed by iron and phosphate ions across the BfrB shell, as well as paths in the interior cavity that may facilitate nucleation of the iron phosphate mineral.
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Affiliation(s)
- Huili Yao
- Department of Chemistry, ‡Del Shankel Structural Biology Center, and §Department of Molecular Biosciences and Center for Bioinformatics, University of Kansas , Multidisciplinary Research Building, 2030 Becker Drive, Lawrence, Kansas 66047, United States
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49
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Zhang X, Meekins DA, An C, Zolkiewski M, Battaile KP, Kanost MR, Lovell S, Michel K. Structural and inhibitory effects of hinge loop mutagenesis in serpin-2 from the malaria vector Anopheles gambiae. J Biol Chem 2014; 290:2946-56. [PMID: 25525260 DOI: 10.1074/jbc.m114.625665] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Serpin-2 (SRPN2) is a key negative regulator of the melanization response in the malaria vector Anopheles gambiae. SRPN2 irreversibly inhibits clip domain serine proteinase 9 (CLIPB9), which functions in a serine proteinase cascade culminating in the activation of prophenoloxidase and melanization. Silencing of SRPN2 in A. gambiae results in spontaneous melanization and decreased life span and is therefore a promising target for vector control. The previously determined structure of SRPN2 revealed a partial insertion of the hinge region of the reactive center loop (RCL) into β sheet A. This partial hinge insertion participates in heparin-linked activation in other serpins, notably antithrombin III. SRPN2 does not contain a heparin binding site, and any possible mechanistic function of the hinge insertion was previously unknown. To investigate the function of the SRPN2 hinge insertion, we developed three SRPN2 variants in which the hinge regions are either constitutively expelled or inserted and analyzed their structure, thermostability, and inhibitory activity. We determined that constitutive hinge expulsion resulted in a 2.7-fold increase in the rate of CLIPB9Xa inhibition, which is significantly lower than previous observations of allosteric serpin activation. Furthermore, we determined that stable insertion of the hinge region did not appreciably decrease the accessibility of the RCL to CLIPB9. Together, these results indicate that the partial hinge insertion in SRPN2 does not participate in the allosteric activation observed in other serpins and instead represents a molecular trade-off between RCL accessibility and efficient formation of an inhibitory complex with the cognate proteinase.
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Affiliation(s)
- Xin Zhang
- From the Division of Biology, Kansas State University, Manhattan, Kansas 66506
| | - David A Meekins
- From the Division of Biology, Kansas State University, Manhattan, Kansas 66506
| | - Chunju An
- From the Division of Biology, Kansas State University, Manhattan, Kansas 66506, the Department of Entomology, College of Agriculture and Biotechnology, China Agricultural University, Beijing, China
| | - Michal Zolkiewski
- the Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506
| | - Kevin P Battaile
- Industrial Macromolecular Crystallography Association Collaborative Access Team, Hauptman-Woodward Medical Research Institute, Advanced Photon Source Argonne National Laboratory, Argonne, Illinois 60439, and
| | - Michael R Kanost
- the Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506
| | - Scott Lovell
- the Protein Structure Laboratory, Del Shankel Structural Biology Center, University of Kansas, Lawrence, Kansas 66407
| | - Kristin Michel
- From the Division of Biology, Kansas State University, Manhattan, Kansas 66506,
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50
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Kemege KE, Hickey JM, Barta ML, Wickstrum J, Balwalli N, Lovell S, Battaile KP, Hefty PS. Chlamydia trachomatis protein CT009 is a structural and functional homolog to the key morphogenesis component RodZ and interacts with division septal plane localized MreB. Mol Microbiol 2014; 95:365-82. [PMID: 25382739 DOI: 10.1111/mmi.12855] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2014] [Indexed: 11/28/2022]
Abstract
Cell division in Chlamydiae is poorly understood as apparent homologs to most conserved bacterial cell division proteins are lacking and presence of elongation (rod shape) associated proteins indicate non-canonical mechanisms may be employed. The rod-shape determining protein MreB has been proposed as playing a unique role in chlamydial cell division. In other organisms, MreB is part of an elongation complex that requires RodZ for proper function. A recent study reported that the protein encoded by ORF CT009 interacts with MreB despite low sequence similarity to RodZ. The studies herein expand on those observations through protein structure, mutagenesis and cellular localization analyses. Structural analysis indicated that CT009 shares high level of structural similarity to RodZ, revealing the conserved orientation of two residues critical for MreB interaction. Substitutions eliminated MreB protein interaction and partial complementation provided by CT009 in RodZ deficient Escherichia coli. Cellular localization analysis of CT009 showed uniform membrane staining in Chlamydia. This was in contrast to the localization of MreB, which was restricted to predicted septal planes. MreB localization to septal planes provides direct experimental observation for the role of MreB in cell division and supports the hypothesis that it serves as a functional replacement for FtsZ in Chlamydia.
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Affiliation(s)
- Kyle E Kemege
- Department of Molecular Biosciences, University of Kansas, Haworth Hall, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA
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