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Paketurytė-Latvė V, Smirnov A, Manakova E, Baranauskiene L, Petrauskas V, Zubrienė A, Matulienė J, Dudutienė V, Čapkauskaitė E, Zakšauskas A, Leitans J, Gražulis S, Tars K, Matulis D. From X-ray crystallographic structure to intrinsic thermodynamics of protein-ligand binding using carbonic anhydrase isozymes as a model system. IUCRJ 2024; 11:556-569. [PMID: 38856178 PMCID: PMC11220870 DOI: 10.1107/s2052252524004627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/17/2024] [Indexed: 06/11/2024]
Abstract
Carbonic anhydrase (CA) was among the first proteins whose X-ray crystal structure was solved to atomic resolution. CA proteins have essentially the same fold and similar active centers that differ in only several amino acids. Primary sulfonamides are well defined, strong and specific binders of CA. However, minor variations in chemical structure can significantly alter their binding properties. Over 1000 sulfonamides have been designed, synthesized and evaluated to understand the correlations between the structure and thermodynamics of their binding to the human CA isozyme family. Compound binding was determined by several binding assays: fluorescence-based thermal shift assay, stopped-flow enzyme activity inhibition assay, isothermal titration calorimetry and competition assay for enzyme expressed on cancer cell surfaces. All assays have advantages and limitations but are necessary for deeper characterization of these protein-ligand interactions. Here, the concept and importance of intrinsic binding thermodynamics is emphasized and the role of structure-thermodynamics correlations for the novel inhibitors of CA IX is discussed - an isozyme that is overexpressed in solid hypoxic tumors, and thus these inhibitors may serve as anticancer drugs. The abundant structural and thermodynamic data are assembled into the Protein-Ligand Binding Database to understand general protein-ligand recognition principles that could be used in drug discovery.
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Affiliation(s)
- Vaida Paketurytė-Latvė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Alexey Smirnov
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Elena Manakova
- Department of Protein - DNA Interactions, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Lina Baranauskiene
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Vytautas Petrauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Asta Zubrienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Jurgita Matulienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Virginija Dudutienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Edita Čapkauskaitė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Audrius Zakšauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Janis Leitans
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, 1067 Riga, Latvia
| | - Saulius Gražulis
- Sector of Crystallography and Chemical Informatics, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Kaspars Tars
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, 1067 Riga, Latvia
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
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Gilkes JM, Frampton RA, Board AJ, Hudson AO, Price TG, Morris VK, Crittenden DL, Muscroft‐Taylor AC, Sheen CR, Smith GR, Dobson RCJ. A new lysine biosynthetic enzyme from a bacterial endosymbiont shaped by genetic drift and genome reduction. Protein Sci 2024; 33:e5083. [PMID: 38924211 PMCID: PMC11201819 DOI: 10.1002/pro.5083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 05/16/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024]
Abstract
The effect of population bottlenecks and genome reduction on enzyme function is poorly understood. Candidatus Liberibacter solanacearum is a bacterium with a reduced genome that is transmitted vertically to the egg of an infected psyllid-a population bottleneck that imposes genetic drift and is predicted to affect protein structure and function. Here, we define the function of Ca. L. solanacearum dihydrodipicolinate synthase (CLsoDHDPS), which catalyzes the committed branchpoint reaction in diaminopimelate and lysine biosynthesis. We demonstrate that CLsoDHDPS is expressed in Ca. L. solanacearum and expression is increased ~2-fold in the insect host compared to in planta. CLsoDHDPS has decreased thermal stability and increased aggregation propensity, implying mutations have destabilized the enzyme but are compensated for through elevated chaperone expression and a stabilized oligomeric state. CLsoDHDPS uses a ternary-complex kinetic mechanism, which is to date unique among DHDPS enzymes, has unusually low catalytic ability, but an unusually high substrate affinity. Structural studies demonstrate that the active site is more open, and the structure of CLsoDHDPS with both pyruvate and the substrate analogue succinic-semialdehyde reveals that the product is both structurally and energetically different and therefore evolution has in this case fashioned a new enzyme. Our study suggests the effects of genome reduction and genetic drift on the function of essential enzymes and provides insights on bacteria-host co-evolutionary associations. We propose that bacteria with endosymbiotic lifestyles present a rich vein of interesting enzymes useful for understanding enzyme function and/or informing protein engineering efforts.
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Affiliation(s)
- Jenna M. Gilkes
- Biomolecular Interaction CentreSchool of Biological Sciences, University of CanterburyChristchurchNew Zealand
- The New Zealand Institute for Plant and Food Research LimitedLincolnNew Zealand
- Callaghan Innovation, University of CanterburyChristchurchNew Zealand
| | - Rebekah A. Frampton
- The New Zealand Institute for Plant and Food Research LimitedLincolnNew Zealand
| | - Amanda J. Board
- Biomolecular Interaction CentreSchool of Biological Sciences, University of CanterburyChristchurchNew Zealand
| | - André O. Hudson
- Rochester Institute of Technology, Thomas H. Gosnell School of Life SciencesRochesterNew YorkUSA
| | - Thomas G. Price
- Biomolecular Interaction CentreSchool of Chemical and Physical Sciences, University of CanterburyChristchurchNew Zealand
| | - Vanessa K. Morris
- Biomolecular Interaction CentreSchool of Biological Sciences, University of CanterburyChristchurchNew Zealand
| | - Deborah L. Crittenden
- Biomolecular Interaction CentreSchool of Chemical and Physical Sciences, University of CanterburyChristchurchNew Zealand
| | | | - Campbell R. Sheen
- Callaghan Innovation, University of CanterburyChristchurchNew Zealand
| | - Grant R. Smith
- The New Zealand Institute for Plant and Food Research LimitedLincolnNew Zealand
| | - Renwick C. J. Dobson
- Biomolecular Interaction CentreSchool of Biological Sciences, University of CanterburyChristchurchNew Zealand
- Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Molecular BiologyUniversity of MelbourneParkvilleVictoriaAustralia
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Baronas D, Knašienė B, Mickevičiūtė A, Jachno J, Naujalis E, Zubrienė A, Matulis D. Inhibitor binding to metal-substituted metalloenzyme: Sulfonamide affinity for carbonic anhydrase IX. J Inorg Biochem 2024; 256:112547. [PMID: 38581802 DOI: 10.1016/j.jinorgbio.2024.112547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 03/18/2024] [Accepted: 03/30/2024] [Indexed: 04/08/2024]
Abstract
Transition metal ions are structural and catalytic cofactors of many proteins including human carbonic anhydrase (CA), a Zn-dependent hydrolase. Sulfonamide inhibitors of CA recognize and form a coordination bond with the Zn ion located in the active site of the enzyme. The Zn ion may be removed or substituted with other metal ions. Such CA protein retains the structure and could serve as a tool to study metal ion role in the recognition and binding affinity of inhibitor molecules. We measured the affinities of selected divalent transition metal ions, including Mn, Fe, Co, Ni, Cu, Cd, Hg, and Zn to metal-free CA isozymes CA I, CA II, and CAIX by fluorescence-based thermal shift assay, prepared metal-substituted CAs, and determined binding of diverse sulfonamide compounds. Sulfonamide inhibitor binding to metal substituted CA followed a U-shape pH dependence. The binding was dissected to contributing binding-linked reactions and the intrinsic binding reaction affinity was calculated. This value is independent of pH and protonation reactions that occur simultaneously upon binding native CA and as demonstrated here, to metal substituted CA. Sulfonamide inhibitor binding to cancer-associated isozyme CAIX diminished in the order: Zn > Co > Hg > Cu > Cd > Mn > Ni. Energetic contribution of the inhibitor-metal coordination bond was determined for all above metals. The understanding of the principles of metal influence on ligand affinity and selectivity should help design new drugs targeting metalloenzymes.
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Affiliation(s)
- Denis Baronas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Birutė Knašienė
- Center for Physical Sciences and Technology, Saulėtekio 3, Vilnius LT-10257, Lithuania
| | - Aurelija Mickevičiūtė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Jelena Jachno
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Evaldas Naujalis
- Center for Physical Sciences and Technology, Saulėtekio 3, Vilnius LT-10257, Lithuania
| | - Asta Zubrienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania.
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Klett T, Schwer M, Ernst LN, Engelhardt MU, Jaag SJ, Masberg B, Knappe C, Lämmerhofer M, Gehringer M, Boeckler FM. Evaluation of a Covalent Library of Diverse Warheads (CovLib) Binding to JNK3, USP7, or p53. Drug Des Devel Ther 2024; 18:2653-2679. [PMID: 38974119 PMCID: PMC11226190 DOI: 10.2147/dddt.s466829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 06/12/2024] [Indexed: 07/09/2024] Open
Abstract
Purpose Over the last few years, covalent fragment-based drug discovery has gained significant importance. Thus, striving for more warhead diversity, we conceived a library consisting of 20 covalently reacting compounds. Our covalent fragment library (CovLib) contains four different warhead classes, including five α-cyanoacacrylamides/acrylates (CA), three epoxides (EO), four vinyl sulfones (VS), and eight electron-deficient heteroarenes with a leaving group (SNAr/SN). Methods After predicting the theoretical solubility of the fragments by LogP and LogS during the selection process, we determined their experimental solubility using a turbidimetric solubility assay. The reactivities of the different compounds were measured in a high-throughput 5,5'-dithiobis-(2-nitrobenzoic acid) DTNB assay, followed by a (glutathione) GSH stability assay. We employed the CovLib in a (differential scanning fluorimetry) DSF-based screening against different targets: c-Jun N-terminal kinase 3 (JNK3), ubiquitin-specific protease 7 (USP7), and the tumor suppressor p53. Finally, the covalent binding was confirmed by intact protein mass spectrometry (MS). Results In general, the purchased fragments turned out to be sufficiently soluble. Additionally, they covered a broad spectrum of reactivity. All investigated α-cyanoacrylamides/acrylates and all structurally confirmed epoxides turned out to be less reactive compounds, possibly due to steric hindrance and reversibility (for α-cyanoacrylamides/acrylates). The SNAr and vinyl sulfone fragments are either highly reactive or stable. DSF measurements with the different targets JNK3, USP7, and p53 identified reactive fragment hits causing a shift in the melting temperatures of the proteins. MS confirmed the covalent binding mode of all these fragments to USP7 and p53, while additionally identifying the SNAr-type electrophile SN002 as a mildly reactive covalent hit for p53. Conclusion The screening and target evaluation of the CovLib revealed first interesting hits. The highly cysteine-reactive fragments VS004, SN001, SN006, and SN007 covalently modify several target proteins and showed distinct shifts in the melting temperatures up to +5.1 °C and -9.1 °C.
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Affiliation(s)
- Theresa Klett
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Martin Schwer
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Larissa N Ernst
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Marc U Engelhardt
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Simon J Jaag
- Pharmaceutical (Bio-) Analysis, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Benedikt Masberg
- Pharmaceutical (Bio-) Analysis, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Cornelius Knappe
- Pharmaceutical (Bio-) Analysis, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Michael Lämmerhofer
- Pharmaceutical (Bio-) Analysis, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Matthias Gehringer
- Pharmaceutical Chemistry, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
- Medicinal Chemistry, Institute for Biomedical Engineering, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Frank M Boeckler
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
- Interfaculty Institute for Biomedical Informatics (IBMI), Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
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5
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Manning MC, Holcomb RE, Payne RW, Stillahn JM, Connolly BD, Katayama DS, Liu H, Matsuura JE, Murphy BM, Henry CS, Crommelin DJA. Stability of Protein Pharmaceuticals: Recent Advances. Pharm Res 2024:10.1007/s11095-024-03726-x. [PMID: 38937372 DOI: 10.1007/s11095-024-03726-x] [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: 03/25/2024] [Accepted: 06/03/2024] [Indexed: 06/29/2024]
Abstract
There have been significant advances in the formulation and stabilization of proteins in the liquid state over the past years since our previous review. Our mechanistic understanding of protein-excipient interactions has increased, allowing one to develop formulations in a more rational fashion. The field has moved towards more complex and challenging formulations, such as high concentration formulations to allow for subcutaneous administration and co-formulation. While much of the published work has focused on mAbs, the principles appear to apply to any therapeutic protein, although mAbs clearly have some distinctive features. In this review, we first discuss chemical degradation reactions. This is followed by a section on physical instability issues. Then, more specific topics are addressed: instability induced by interactions with interfaces, predictive methods for physical stability and interplay between chemical and physical instability. The final parts are devoted to discussions how all the above impacts (co-)formulation strategies, in particular for high protein concentration solutions.'
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Affiliation(s)
- Mark Cornell Manning
- Legacy BioDesign LLC, Johnstown, CO, USA.
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA.
| | - Ryan E Holcomb
- Legacy BioDesign LLC, Johnstown, CO, USA
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - Robert W Payne
- Legacy BioDesign LLC, Johnstown, CO, USA
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - Joshua M Stillahn
- Legacy BioDesign LLC, Johnstown, CO, USA
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | | | | | | | | | | | - Charles S Henry
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
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6
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de Oliveira Viana J, Sena Mendes M, Santos Castilho M, Olímpio de Moura R, Guimarães Barbosa E. Spiro-Acridine Compound as a Pteridine Reductase 1 Inhibitor: in silico Target Fishing and in vitro Studies. ChemMedChem 2024; 19:e202300545. [PMID: 38445815 DOI: 10.1002/cmdc.202300545] [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: 10/09/2023] [Revised: 02/20/2024] [Accepted: 03/05/2024] [Indexed: 03/07/2024]
Abstract
Among the many neglected tropical diseases, leishmaniasis ranks second in mortality rate and prevalence. In a previous study, acridine derivatives were synthesized and tested for their antileishmanial activity against L. chagasi. The most active compound identified in that study (1) showed a single digit IC50 value against the parasite (1.10 μg/mL), but its macromolecular target remained unknown. Aiming to overcome this limitation, this work exploited inverse virtual screening to identify compound 1's putative molecular mechanism of action. In vitro assays confirmed that compound 1 binds to Leishmania chagasi pteridine reductase 1 (LcPTR1), with moderate affinity (Kd=33,1 μM), according to differential scanning fluorimetry assay. Molecular dynamics simulations confirm the stability of LcPTR1-compound 1 complex, supporting a competitive mechanism of action. Therefore, the workflow presented in this work successfully identified PTR1 as a macromolecular target for compound 1, allowing the designing of novel potent antileishmanial compounds.
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Affiliation(s)
- Jéssika de Oliveira Viana
- Bioinformatics Multidisciplinary Environment, Federal University of Rio Grande do Norte, University Campus I-Lagoa Nova, Natal, RN, 59078-970
| | - Marina Sena Mendes
- Department of Pharmacy, Federal University of Bahia, University Campus Ondina - Ondina, Salvador, BA, 40170-110
| | - Marcelo Santos Castilho
- Department of Pharmacy, Federal University of Bahia, University Campus Ondina - Ondina, Salvador, BA, 40170-110
| | - Ricardo Olímpio de Moura
- Department of Pharmacy, State University of Paraíba, University Campus I - Universitário, Campina, Grande - PB, 58429-500
| | - Euzébio Guimarães Barbosa
- Bioinformatics Multidisciplinary Environment, Federal University of Rio Grande do Norte, University Campus I-Lagoa Nova, Natal, RN, 59078-970
- Department of Pharmacy, Federal University of Rio Grande do Norte, University Campus I - Petrópolis, Natal, RN, 59012-570
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Kairys V, Baranauskiene L, Kazlauskiene M, Zubrienė A, Petrauskas V, Matulis D, Kazlauskas E. Recent advances in computational and experimental protein-ligand affinity determination techniques. Expert Opin Drug Discov 2024; 19:649-670. [PMID: 38715415 DOI: 10.1080/17460441.2024.2349169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 04/25/2024] [Indexed: 05/22/2024]
Abstract
INTRODUCTION Modern drug discovery revolves around designing ligands that target the chosen biomolecule, typically proteins. For this, the evaluation of affinities of putative ligands is crucial. This has given rise to a multitude of dedicated computational and experimental methods that are constantly being developed and improved. AREAS COVERED In this review, the authors reassess both the industry mainstays and the newest trends among the methods for protein - small-molecule affinity determination. They discuss both computational affinity predictions and experimental techniques, describing their basic principles, main limitations, and advantages. Together, this serves as initial guide to the currently most popular and cutting-edge ligand-binding assays employed in rational drug design. EXPERT OPINION The affinity determination methods continue to develop toward miniaturization, high-throughput, and in-cell application. Moreover, the availability of data analysis tools has been constantly increasing. Nevertheless, cross-verification of data using at least two different techniques and careful result interpretation remain of utmost importance.
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Affiliation(s)
- Visvaldas Kairys
- Department of Bioinformatics, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Lina Baranauskiene
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | | | - Asta Zubrienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Vytautas Petrauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Egidijus Kazlauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
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Fotsch C, Basu D, Case R, Chen Q, Koneru PC, Lo MC, Ngo R, Sharma P, Vaish A, Yi X, Zech SG, Hodder P. Creating a more strategic small molecule biophysical hit characterization workflow. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100159. [PMID: 38723666 DOI: 10.1016/j.slasd.2024.100159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/16/2024] [Accepted: 05/06/2024] [Indexed: 05/21/2024]
Abstract
To confirm target engagement of hits from our high-throughput screening efforts, we ran biophysical assays on several hundreds of hits from 15 different high-throughput screening campaigns. Analyzing the biophysical assay results from these screening campaigns led us to conclude that we could be more strategic in our biophysical analysis of hits by first confirming activity in a thermal shift assay (TSA) and then confirming activity in either a surface plasmon resonance (SPR) assay or a temperature-related intensity change (TRIC) assay. To understand how this new workflow shapes the quality of the final hits, we compared TSA/SPR or TSA/TRIC confirmed and unconfirmed hits to one another using four measures of compound quality: quantitative estimate of drug-likeness (QED), Pan-Assay Interference Compounds (PAINS), promiscuity, and aqueous solubility. In general, we found that the biophysically confirmed hits performed better in the compound quality metrics than the unconfirmed hits, demonstrating that our workflow not only confirmed target engagement of the hits but also enriched for higher quality hits.
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Affiliation(s)
- Christopher Fotsch
- Lead Discovery and Characterization Group, Amgen Research, Thousand Oaks CA, USA.
| | - Debaleena Basu
- Lead Discovery and Characterization Group, Amgen Research, South San Francisco CA, USA
| | - Ryan Case
- Lead Discovery and Characterization Group, Amgen Research, South San Francisco CA, USA
| | - Qing Chen
- Lead Discovery and Characterization Group, Amgen Research, Thousand Oaks CA, USA
| | - Pratibha C Koneru
- Lead Discovery and Characterization Group, Amgen Research, South San Francisco CA, USA
| | - Mei-Chu Lo
- Lead Discovery and Characterization Group, Amgen Research, South San Francisco CA, USA
| | - Rachel Ngo
- Lead Discovery and Characterization Group, Amgen Research, South San Francisco CA, USA
| | - Pooja Sharma
- Lead Discovery and Characterization Group, Amgen Research, Thousand Oaks CA, USA
| | - Amit Vaish
- Lead Discovery and Characterization Group, Amgen Research, Thousand Oaks CA, USA
| | - Xiang Yi
- Lead Discovery and Characterization Group, Amgen Research, South San Francisco CA, USA
| | - Stephan G Zech
- Lead Discovery and Characterization Group, Amgen Research, Thousand Oaks CA, USA
| | - Peter Hodder
- Lead Discovery and Characterization Group, Amgen Research, Thousand Oaks CA, USA
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Stincone P, Naimi A, Saviola AJ, Reher R, Petras D. Decoding the molecular interplay in the central dogma: An overview of mass spectrometry-based methods to investigate protein-metabolite interactions. Proteomics 2024; 24:e2200533. [PMID: 37929699 DOI: 10.1002/pmic.202200533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/15/2023] [Accepted: 10/23/2023] [Indexed: 11/07/2023]
Abstract
With the emergence of next-generation nucleotide sequencing and mass spectrometry-based proteomics and metabolomics tools, we have comprehensive and scalable methods to analyze the genes, transcripts, proteins, and metabolites of a multitude of biological systems. Despite the fascinating new molecular insights at the genome, transcriptome, proteome and metabolome scale, we are still far from fully understanding cellular organization, cell cycles and biology at the molecular level. Significant advances in sensitivity and depth for both sequencing as well as mass spectrometry-based methods allow the analysis at the single cell and single molecule level. At the same time, new tools are emerging that enable the investigation of molecular interactions throughout the central dogma of molecular biology. In this review, we provide an overview of established and recently developed mass spectrometry-based tools to probe metabolite-protein interactions-from individual interaction pairs to interactions at the proteome-metabolome scale.
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Affiliation(s)
- Paolo Stincone
- University of Tuebingen, CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Infection Medicine, Tuebingen, Germany
- University of Tuebingen, Center for Plant Molecular Biology, Tuebingen, Germany
| | - Amira Naimi
- University of Marburg, Institute of Pharmaceutical Biology and Biotechnology, Marburg, Germany
| | | | - Raphael Reher
- University of Marburg, Institute of Pharmaceutical Biology and Biotechnology, Marburg, Germany
| | - Daniel Petras
- University of Tuebingen, CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Infection Medicine, Tuebingen, Germany
- University of California Riverside, Department of Biochemistry, Riverside, USA
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10
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Song M, Sun Y, Hu Y, Wang C, Jin Y, Liu Y, Da Y, Zhao Q, Zheng R, Li L. Comprehensive quantifications of tumour microenvironment to predict the responsiveness to immunotherapy and prognosis for paediatric neuroblastomas. Int Immunopharmacol 2024; 133:112145. [PMID: 38691920 DOI: 10.1016/j.intimp.2024.112145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/18/2024] [Accepted: 04/20/2024] [Indexed: 05/03/2024]
Abstract
Treatment strategies for paediatric neuroblastoma as well as many other cancers are limited by the unfavourable tumour microenvironment (TME). In this study, the TMEs of neuroblastoma were grouped by their genetic signatures into four distinct subtypes: immune enriched, immune desert, non-proliferative and fibrotic. An Immune Score and a Proliferation Score were constructed based on the molecular features of the subtypes to quantify the immune microenvironment or malignancy degree of cancer cells in neuroblastoma, respectively. The Immune Score correlated with a patient's response to immunotherapy; the Proliferation Score was an independent prognostic biomarker for neuroblastoma and proved to be more accurate than the existing clinical predictors. This double scoring system was further validated and the conserved molecular pattern associated with immune landscape and malignancy degree was confirmed. Axitinib and BI-2536 were confirmed as candidate drugs for neuroblastoma by the double scoring system. Both in vivo and in vitro experiments demonstrated that axitinib-induced pyroptosis of neuroblastoma cells activated anti-tumour immunity and inhibited tumour growth; BI-2536 induced cell cycle arrest at the S phase in neuroblastoma cells. The comprehensive double scoring system of neuroblastoma may predict prognosis and screen for therapeutic strategies which could provide personalized treatments.
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Affiliation(s)
- Mingkun Song
- Tianjin Institute of Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), State Key Laboratory of Experimental Hematology, Department of Immunology, Tianjin Medical University, Tianjin 300070, China; Department of Paediatrics, Tianjin Medical University General Hospital, Tianjin 300052, China; Department of Paediatric Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Yiming Sun
- Tianjin Institute of Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), State Key Laboratory of Experimental Hematology, Department of Immunology, Tianjin Medical University, Tianjin 300070, China
| | - Yikai Hu
- Tianjin Institute of Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), State Key Laboratory of Experimental Hematology, Department of Immunology, Tianjin Medical University, Tianjin 300070, China
| | - Chong Wang
- Tianjin Institute of Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), State Key Laboratory of Experimental Hematology, Department of Immunology, Tianjin Medical University, Tianjin 300070, China; Class of 2019, Program in Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Yan Jin
- Department of Paediatric Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Yun Liu
- Department of Paediatric Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Yurong Da
- Tianjin Institute of Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), State Key Laboratory of Experimental Hematology, Department of Immunology, Tianjin Medical University, Tianjin 300070, China.
| | - Qiang Zhao
- Department of Paediatric Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China.
| | - Rongxiu Zheng
- Department of Paediatrics, Tianjin Medical University General Hospital, Tianjin 300052, China.
| | - Long Li
- Tianjin Institute of Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), State Key Laboratory of Experimental Hematology, Department of Immunology, Tianjin Medical University, Tianjin 300070, China; Department of Paediatric Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China.
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11
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Maruyama T, Takahashi Y, Hiro K, Murase K, Kojima H, Okabe T, Yamauchi Y, Sato R. Discovery of Novel Binders to Sterol Regulatory Element-Binding Protein-1 by High-Throughput Screening. ACS Med Chem Lett 2024; 15:667-676. [PMID: 38994455 PMCID: PMC11238716 DOI: 10.1021/acsmedchemlett.4c00067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/26/2024] [Accepted: 04/11/2024] [Indexed: 07/13/2024] Open
Abstract
Sterol regulatory element-binding protein-1 (SREBP-1) is a transcription factor that regulates the expression of genes related to fatty acid biosynthesis. Its high expression and activation in obesity and associated metabolic diseases make it a potential therapeutic target. However, the role of SREBP-1 in the development and exacerbation of these diseases remains unclear, partly because of the impossibility of inhibiting its function because of the lack of specific inhibitors. Here, we aimed to identify small-molecule compounds that directly bind to SREBP-1 using the recombinant N-terminal region of SREBP-1a, which is required for its transcriptional activity. A high-throughput screening campaign was conducted using a thermal shift assay and surface plasmon resonance assay to evaluate the compound affinity and specificity, which resulted in the identification of two compounds. Future analysis of their structure-activity relationships may lead to the development of specific SREBP-1 inhibitors, thereby potentially validating SREBP-1 as a therapeutic target for obesity and resultant atherosclerotic diseases.
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Affiliation(s)
- Takashi Maruyama
- Food
Biochemistry Laboratory, Department of Applied Biological Chemistry,
Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Yu Takahashi
- Food
Biochemistry Laboratory, Department of Applied Biological Chemistry,
Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Kahori Hiro
- Food
Biochemistry Laboratory, Department of Applied Biological Chemistry,
Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Kohji Murase
- The
Bioorganic Chemistry Laboratory, Department of Applied Biological
Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Hirotatsu Kojima
- Drug
Discovery Initiative, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Takayoshi Okabe
- Drug
Discovery Initiative, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yoshio Yamauchi
- Food
Biochemistry Laboratory, Department of Applied Biological Chemistry,
Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Ryuichiro Sato
- Nutri-Life
Science Laboratory, Department of Applied Biological Chemistry, Graduate
School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
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12
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Akabane T, Suzuki N, Ikeda K, Yonezawa T, Nagatoishi S, Matsumura H, Yoshizawa T, Tsuchiya W, Kamino S, Tsumoto K, Ishimaru K, Katoh E, Hirotsu N. THOUSAND-GRAIN WEIGHT 6, which is an IAA-glucose hydrolase, preferentially recognizes the structure of the indole ring. Sci Rep 2024; 14:6778. [PMID: 38514802 PMCID: PMC10958001 DOI: 10.1038/s41598-024-57506-z] [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: 01/19/2024] [Accepted: 03/19/2024] [Indexed: 03/23/2024] Open
Abstract
An indole-3-acetic acid (IAA)-glucose hydrolase, THOUSAND-GRAIN WEIGHT 6 (TGW6), negatively regulates the grain weight in rice. TGW6 has been used as a target for breeding increased rice yield. Moreover, the activity of TGW6 has been thought to involve auxin homeostasis, yet the details of this putative TGW6 activity remain unclear. Here, we show the three-dimensional structure and substrate preference of TGW6 using X-ray crystallography, thermal shift assays and fluorine nuclear magnetic resonance (19F NMR). The crystal structure of TGW6 was determined at 2.6 Å resolution and exhibited a six-bladed β-propeller structure. Thermal shift assays revealed that TGW6 preferably interacted with indole compounds among the tested substrates, enzyme products and their analogs. Further analysis using 19F NMR with 1,134 fluorinated fragments emphasized the importance of indole fragments in recognition by TGW6. Finally, docking simulation analyses of the substrate and related fragments in the presence of TGW6 supported the interaction specificity for indole compounds. Herein, we describe the structure and substrate preference of TGW6 for interacting with indole fragments during substrate recognition. Uncovering the molecular details of TGW6 activity will stimulate the use of this enzyme for increasing crop yields and contributes to functional studies of IAA glycoconjugate hydrolases in auxin homeostasis.
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Affiliation(s)
- Tatsuki Akabane
- Graduate School of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura, Oura, Gunma, 374-0193, Japan
| | - Nobuhiro Suzuki
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Kazuyoshi Ikeda
- Medicinal Chemistry Data Intelligence Unit, Drug Development Data Intelligence Platform Group, Medical Sciences Innovation Hub Program (MIH), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- Division of Physics for Life Functions, Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen Minato-ku, Tokyo, 105-8512, Japan
| | - Tomoki Yonezawa
- Division of Physics for Life Functions, Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen Minato-ku, Tokyo, 105-8512, Japan
| | - Satoru Nagatoishi
- School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Hiroyoshi Matsumura
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga, 525-8577, Japan
| | - Takuya Yoshizawa
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga, 525-8577, Japan
| | - Wataru Tsuchiya
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Satoshi Kamino
- CRYO SHIP Incorporated, 1-266-3, Sakuragi-cho, Omiya-ku, Saitama, Saitama, 330-0854, Japan
| | - Kouhei Tsumoto
- School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Ken Ishimaru
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Etsuko Katoh
- Department of Food and Nutritional Sciences, Toyo University, 1-1-1 Izumino, Itakura, Oura, Gunma, 374-0193, Japan.
| | - Naoki Hirotsu
- Graduate School of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura, Oura, Gunma, 374-0193, Japan.
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13
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Pham TL, Conde González MR, Fazliev S, Kishore A, Comba P, Thomas F. Relationship of Thermostability and Binding Affinity in Metal-binding WW-Domain Minireceptors. Chembiochem 2024; 25:e202300715. [PMID: 38127995 DOI: 10.1002/cbic.202300715] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 12/23/2023]
Abstract
The design of metallo-miniproteins advances our understanding of the structural and functional roles of metals in proteins. We recently designed a metal-binding WW domain, WW-CA-Nle, which displays three histidine residues on its surface for coordination of divalent metals Ni(II), Zn(II) and Cu(II). However, WW-CA-Nle is a molten globule in the apo state and thus showed only moderate binding affinities with Kd values in the μM regime. In this report, we hypothesize that improved thermal stability of the apo state of the metal binding WW-domain scaffold should lead to improved preorganization of the metal-binding site and consequently to higher metal-binding affinities. By redesigning WW-CA-Nle, we obtained WW-CA variants, WW-CA-min and WW-CA-ANG, which were fully folded in the apo states and displayed moderate to excellent thermostabilities in the apo and holo states. We were able to show that the improved thermal stabilities led to improved metal binding, which was reflected in Kd values that were at least one order of magnitude lower compared to WW-CA-Nle. EPR spectroscopy and ITC measurements revealed a better defined and predisposed metal binding site in WW-CA-ANG.
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Affiliation(s)
- Truc Lam Pham
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Marcos R Conde González
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
- Max Planck School Matter to Life
| | - Sunnatullo Fazliev
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
- Max Planck School Matter to Life
- Max Planck Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany
| | - Agi Kishore
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
- Max Planck School Matter to Life
- Institute of Inorganic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Peter Comba
- Institute of Inorganic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Franziska Thomas
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
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14
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Hait S, Kundu S. Revisiting structural organization of proteins at high temperature from a network perspective. Comput Biol Chem 2024; 108:107978. [PMID: 37956471 DOI: 10.1016/j.compbiolchem.2023.107978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/08/2023] [Accepted: 10/29/2023] [Indexed: 11/15/2023]
Abstract
Interactions between distantly placed amino acids in the primary chain (long-range) play a very crucial role in the formation and stabilization of the tertiary structure of a protein, while interactions between closely placed amino acids in the primary chain (short-range) mostly stabilize the secondary structures. Every protein needs to maintain marginal stability in order to perform its physiological functions in its native environment. The requirements for this stability in mesophilic and thermophilic proteins are different. Thermophilic proteins need to form more interactions as well as more stable interactions to survive in the extreme environment, they live in. Here, we aim to find out how the interacting amino acids in three-dimensional space are positioned in the primary chains in thermophilic and mesophilic. How does this arrangement help thermophiles to maintain their structural integrity at high temperatures? Working on a dataset of 1560 orthologous pairs we perceive that thermophiles are not only enriched with long-range interactions, they feature bigger connected clusters and higher network densities compared to their mesophilic orthologs, at higher interaction strengths between the amino acids. Moreover, we have observed the enrichment of different types of interactions at different secondary structural regions.
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Affiliation(s)
- Suman Hait
- Department of Biophysics, Molecular Biology and Bioinformatics, 92, Acharya Prafulla Chandra Road, Kolkata 700009, India.
| | - Sudip Kundu
- Department of Biophysics, Molecular Biology and Bioinformatics, 92, Acharya Prafulla Chandra Road, Kolkata 700009, India.
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15
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Gooran N, Kopra K. Fluorescence-Based Protein Stability Monitoring-A Review. Int J Mol Sci 2024; 25:1764. [PMID: 38339045 PMCID: PMC10855643 DOI: 10.3390/ijms25031764] [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: 12/31/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
Proteins are large biomolecules with a specific structure that is composed of one or more long amino acid chains. Correct protein structures are directly linked to their correct function, and many environmental factors can have either positive or negative effects on this structure. Thus, there is a clear need for methods enabling the study of proteins, their correct folding, and components affecting protein stability. There is a significant number of label-free methods to study protein stability. In this review, we provide a general overview of these methods, but the main focus is on fluorescence-based low-instrument and -expertise-demand techniques. Different aspects related to thermal shift assays (TSAs), also called differential scanning fluorimetry (DSF) or ThermoFluor, are introduced and compared to isothermal chemical denaturation (ICD). Finally, we discuss the challenges and comparative aspects related to these methods, as well as future opportunities and assay development directions.
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Affiliation(s)
| | - Kari Kopra
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland;
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16
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Chen B, Zhang Q, Zhong X, Zhang X, Liu X, Wang H, Yang F, Zhang J, Huang J, Wong YK, Luo P, Wang J, Sun J. Dopamine modification of glycolytic enzymes impairs glycolysis: possible implications for Parkinson's disease. Cell Commun Signal 2024; 22:75. [PMID: 38287374 PMCID: PMC10823740 DOI: 10.1186/s12964-024-01478-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/05/2024] [Indexed: 01/31/2024] Open
Abstract
BACKGROUND Parkinson's disease (PD), a chronic and severe neurodegenerative disease, is pathologically characterized by the selective loss of nigrostriatal dopaminergic neurons. Dopamine (DA), the neurotransmitter produced by dopaminergic neurons, and its metabolites can covalently modify proteins, and dysregulation of this process has been implicated in neuronal loss in PD. However, much remains unknown about the protein targets. METHODS In the present work, we designed and synthesized a dopamine probe (DA-P) to screen and identify the potential protein targets of DA using activity-based protein profiling (ABPP) technology in combination with liquid chromatography-tandem mass spectrometry (LC-MS/MS). In situ pull-down assays, cellular thermal shift assays (CETSAs) and immunofluorescence were performed to confirm the DA modifications on these hits. To investigate the effects of DA modifications, we measured the enzymatic activities of these target proteins, evaluated glycolytic stress and mitochondrial respiration by Seahorse tests, and systematically analyzed the changes in metabolites with unbiased LC-MS/MS-based non-targeted metabolomics profiling. RESULTS We successfully identified three glycolytic proteins, aldolase A, α-enolase and pyruvate kinase M2 (PKM2), as the binding partners of DA. DA bound to Glu166 of α-enolase, Cys49 and Cys424 of PKM2, and Lys230 of aldolase A, inhibiting the enzymatic activities of α-enolase and PKM2 and thereby impairing ATP synthesis, resulting in mitochondrial dysfunction. CONCLUSIONS Recent research has revealed that enhancing glycolysis can offer protection against PD. The present study identified that the glycolytic pathway is vulnerable to disruption by DA, suggesting a promising avenue for potential therapeutic interventions. Safeguarding glycolysis against DA-related disruption could be a potential therapeutic intervention for PD.
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Affiliation(s)
- Bing Chen
- Shenzhen Clinical Research Center for Geriatrics and Shenzhen Institute of Respiratory Disease, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
- Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, China
| | - Qian Zhang
- Shenzhen Clinical Research Center for Geriatrics and Shenzhen Institute of Respiratory Disease, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- School of Traditional Chinese Medicine and School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Xiaoru Zhong
- Shenzhen Clinical Research Center for Geriatrics and Shenzhen Institute of Respiratory Disease, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Xinwei Zhang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xin Liu
- Shenzhen Clinical Research Center for Geriatrics and Shenzhen Institute of Respiratory Disease, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Hongyang Wang
- Shenzhen Clinical Research Center for Geriatrics and Shenzhen Institute of Respiratory Disease, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Fan Yang
- Shenzhen Clinical Research Center for Geriatrics and Shenzhen Institute of Respiratory Disease, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
- Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, China
| | - Jingjing Zhang
- Shenzhen Clinical Research Center for Geriatrics and Shenzhen Institute of Respiratory Disease, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
- Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, China
| | - Jingnan Huang
- Shenzhen Clinical Research Center for Geriatrics and Shenzhen Institute of Respiratory Disease, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Yin-Kwan Wong
- Shenzhen Clinical Research Center for Geriatrics and Shenzhen Institute of Respiratory Disease, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Piao Luo
- Shenzhen Clinical Research Center for Geriatrics and Shenzhen Institute of Respiratory Disease, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- School of Traditional Chinese Medicine and School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Jigang Wang
- Shenzhen Clinical Research Center for Geriatrics and Shenzhen Institute of Respiratory Disease, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China.
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
- School of Traditional Chinese Medicine and School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China.
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, China.
| | - Jichao Sun
- Shenzhen Clinical Research Center for Geriatrics and Shenzhen Institute of Respiratory Disease, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China.
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17
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Kelley EH, Minasov G, Konczak K, Shuvalova L, Brunzelle JS, Shukla S, Beulke M, Thabthimthong T, Olsen KW, Inniss NL, Satchell KJF, Becker DP. Biochemical and Structural Analysis of the Bacterial Enzyme Succinyl-Diaminopimelate Desuccinylase (DapE) from Acinetobacter baumannii. ACS OMEGA 2024; 9:3905-3915. [PMID: 38284080 PMCID: PMC10809365 DOI: 10.1021/acsomega.3c08231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 01/30/2024]
Abstract
There is an urgent need for new antibiotics given the rise of antibiotic resistance, and succinyl-diaminopimelate desuccinylase (DapE, E.C. 3.5.1.18) has emerged as a promising bacterial enzyme target. DapE from Haemophilus influenzae (HiDapE) has been studied and inhibitors identified, but it is essential to explore DapE from different species to assess selective versus broad-spectrum therapeutics. We have determined the structure of DapE from the ESKAPE pathogen Acinetobacter baumannii (AbDapE) and studied inhibition by known inhibitors of HiDapE. AbDapE is inhibited by captopril and sulfate comparable to HiDapE, but AbDapE was not significantly inhibited by a known indoline sulfonamide HiDapE inhibitor. Captopril and sulfate both stabilize HiDapE by increasing the thermal melting temperature (Tm) in thermal shift assays. By contrast, sulfate decreases the stability of the AbDapE enzyme, whereas captopril increases the stability. Further, we report two crystal structures of selenomethionine-substituted AbDapE in the closed conformation, one with AbDapE in complex with succinate derived from enzymatic hydrolysis of N6-methyl-l,l-SDAP substrate and acetate (PDB code 7T1Q, 2.25 Å resolution), and a crystal structure of AbDapE with bound succinate along with l-(S)-lactate, a product of degradation of citric acid from the crystallization buffer during X-ray irradiation (PDB code 8F8O, 2.10 Å resolution).
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Affiliation(s)
- Emma H. Kelley
- Department
of Chemistry and Biochemistry, Loyola University
Chicago, 1032 West Sheridan Road, Chicago, Illinois 60660, United States
| | - George Minasov
- Department
of Microbiology-Immunology, Northwestern
University, Feinberg School of Medicine, Chicago, Illinois 60611, United States
- Center
for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Katherine Konczak
- Department
of Chemistry and Biochemistry, Loyola University
Chicago, 1032 West Sheridan Road, Chicago, Illinois 60660, United States
| | - Ludmilla Shuvalova
- Department
of Pharmacology, Northwestern University,
Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Joseph S. Brunzelle
- Northwestern
Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, Illinois 60439, United States
| | - Shantanu Shukla
- Department
of Microbiology-Immunology, Northwestern
University, Feinberg School of Medicine, Chicago, Illinois 60611, United States
- Center
for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Megan Beulke
- Department
of Chemistry and Biochemistry, Loyola University
Chicago, 1032 West Sheridan Road, Chicago, Illinois 60660, United States
| | - Teerana Thabthimthong
- Department
of Chemistry and Biochemistry, Loyola University
Chicago, 1032 West Sheridan Road, Chicago, Illinois 60660, United States
| | - Kenneth W. Olsen
- Department
of Chemistry and Biochemistry, Loyola University
Chicago, 1032 West Sheridan Road, Chicago, Illinois 60660, United States
| | - Nicole L. Inniss
- Department
of Microbiology-Immunology, Northwestern
University, Feinberg School of Medicine, Chicago, Illinois 60611, United States
- Center
for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Karla J. F. Satchell
- Department
of Microbiology-Immunology, Northwestern
University, Feinberg School of Medicine, Chicago, Illinois 60611, United States
- Center
for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Daniel P. Becker
- Department
of Chemistry and Biochemistry, Loyola University
Chicago, 1032 West Sheridan Road, Chicago, Illinois 60660, United States
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18
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Kim Y, Miller WT. Contrasting Effects of Cancer-Associated Mutations in EphA3 and EphB2 Kinases. Biochemistry 2024. [PMID: 38252844 DOI: 10.1021/acs.biochem.3c00674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Erythropoietin-producing hepatoma (Eph) receptors are a family of tyrosine kinases that can act as tumor promoters or tumor suppressors, depending on the receptor and cancer cell type. Cancer-associated somatic mutations have been identified in all Eph receptors, but in most cases, the functional effects of the mutations are unknown. In this study, we expressed and purified the kinase domains of wild-type (WT) EphA3 and EphB2 along with 16 cancer-associated mutants. We identified mutations that decrease EphA3 activity and both activating and inhibitory mutations in EphB2. To shed light on the mechanisms by which the mutations altered kinase activity, we measured the thermal stabilities of the enzymes and performed steady-state kinetic experiments. We also expressed the full-length receptors in HEK293T cells to determine the cellular effects. WT EphB2 promoted downstream ERK signaling, while a kinase-inactive mutant (S706F) was similar to the control cells. In contrast, WT EphA3 (but not loss-of-function mutants) inhibited ERK signaling. The reciprocal effects of EphB2 and EphA3 on ERK phosphorylation in HEK293T cells were also evident in Ras-GTP loading. Thus, consistent with the dual roles of Eph receptors as tumor promoters and tumor suppressors, somatic mutations have the potential to increase or decrease Eph function, resulting in changes in the downstream signaling transduction.
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Affiliation(s)
- Yunyoung Kim
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York 11794, United States
| | - W Todd Miller
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York 11794, United States
- Department of Veterans Affairs Medical Center, Northport, New York 11768, United States
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19
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Breindl M, Spitzer D, Gerasimaitė R, Kairys V, Schubert T, Henfling R, Schwartz U, Lukinavičius G, Manelytė L. Biochemical and cellular insights into the Baz2B protein, a non-catalytic subunit of the chromatin remodeling complex. Nucleic Acids Res 2024; 52:337-354. [PMID: 38000389 PMCID: PMC10783490 DOI: 10.1093/nar/gkad1096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 09/21/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Baz2B is a regulatory subunit of the ATP-dependent chromatin remodeling complexes BRF1 and BRF5, which control access to DNA during DNA-templated processes. Baz2B has been implicated in several diseases and also in unhealthy ageing, however limited information is available on the domains and cellular roles of Baz2B. To gain more insight into the Baz2B function, we biochemically characterized the TAM (Tip5/ARBP/MBD) domain with the auxiliary AT-hook motifs and the bromodomain (BRD). We observed alterations in histone code recognition in bromodomains carrying cancer-associated point mutations, suggesting their potential involvement in disease. Furthermore, the depletion of Baz2B in the Hap1 cell line resulted in altered cell morphology, reduced colony formation and perturbed transcriptional profiles. Despite that, super-resolution microscopy images revealed no changes in the overall chromatin structure in the absence of Baz2B. These findings provide insights into the biological function of Baz2B.
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Affiliation(s)
- Matthias Breindl
- Biochemistry III, University of Regensburg, Regensburg DE-93053, Germany
| | - Dominika Spitzer
- Biochemistry III, University of Regensburg, Regensburg DE-93053, Germany
| | - Rūta Gerasimaitė
- Chromatin Labeling and Imaging Group, Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, DE-37077 Göttingen, Germany
| | - Visvaldas Kairys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | | | - Ramona Henfling
- Biochemistry III, University of Regensburg, Regensburg DE-93053, Germany
| | - Uwe Schwartz
- NGS Analysis Center, University of Regensburg, Regensburg DE-93053, Germany
| | - Gražvydas Lukinavičius
- Chromatin Labeling and Imaging Group, Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, DE-37077 Göttingen, Germany
| | - Laura Manelytė
- Biochemistry III, University of Regensburg, Regensburg DE-93053, Germany
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20
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Wu T, Hornsby M, Zhu L, Yu JC, Shokat KM, Gestwicki JE. Protocol for performing and optimizing differential scanning fluorimetry experiments. STAR Protoc 2023; 4:102688. [PMID: 37943662 PMCID: PMC10663957 DOI: 10.1016/j.xpro.2023.102688] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/21/2023] [Accepted: 10/12/2023] [Indexed: 11/12/2023] Open
Abstract
Differential scanning fluorimetry (DSF) is a widely used technique for determining the apparent melting temperature (Tma) of a purified protein. Here, we present a protocol for performing and optimizing DSF experiments. We describe steps for designing and performing the experiment, analyzing data, and optimization. We provide benchmarks for typical Tmas and ΔTmas, standard assay conditions, and upper and lower limits of commonly altered experimental variables. We also detail common pitfalls of DSF and ways to avoid, identify, and overcome them.
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Affiliation(s)
- Taiasean Wu
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michael Hornsby
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 941583, USA
| | - Lawrence Zhu
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Joshua C Yu
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kevan M Shokat
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 941583, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California, San Francisco, San Francisco, CA 94158, USA.
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21
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Sun S, Zheng Z, Wang J, Li F, He A, Lai K, Zhang S, Lu JH, Tian R, Tan CSH. Improved in situ characterization of protein complex dynamics at scale with thermal proximity co-aggregation. Nat Commun 2023; 14:7697. [PMID: 38001062 PMCID: PMC10673876 DOI: 10.1038/s41467-023-43526-2] [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: 02/23/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
Cellular activities are carried out vastly by protein complexes but large repertoire of protein complexes remains functionally uncharacterized which necessitate new strategies to delineate their roles in various cellular processes and diseases. Thermal proximity co-aggregation (TPCA) is readily deployable to characterize protein complex dynamics in situ and at scale. We develop a version termed Slim-TPCA that uses fewer temperatures increasing throughputs by over 3X, with new scoring metrics and statistical evaluation that result in minimal compromise in coverage and detect more relevant complexes. Less samples are needed, batch effects are minimized while statistical evaluation cost is reduced by two orders of magnitude. We applied Slim-TPCA to profile K562 cells under different duration of glucose deprivation. More protein complexes are found dissociated, in accordance with the expected downregulation of most cellular activities, that include 55S ribosome and respiratory complexes in mitochondria revealing the utility of TPCA to study protein complexes in organelles. Protein complexes in protein transport and degradation are found increasingly assembled unveiling their involvement in metabolic reprogramming during glucose deprivation. In summary, Slim-TPCA is an efficient strategy for characterization of protein complexes at scale across cellular conditions, and is available as Python package at https://pypi.org/project/Slim-TPCA/ .
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Affiliation(s)
- Siyuan Sun
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Zhenxiang Zheng
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Jun Wang
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Fengming Li
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - An He
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Kunjia Lai
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Shuang Zhang
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen, Guangdong, China
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Zhuhai, Macau SAR, China
| | - Jia-Hong Lu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Zhuhai, Macau SAR, China
| | - Ruijun Tian
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Chris Soon Heng Tan
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen, Guangdong, China.
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22
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Mahran R, Vello N, Komulainen A, Malakoutikhah M, Härmä H, Kopra K. Isothermal chemical denaturation assay for monitoring protein stability and inhibitor interactions. Sci Rep 2023; 13:20066. [PMID: 37973851 PMCID: PMC10654576 DOI: 10.1038/s41598-023-46720-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 11/03/2023] [Indexed: 11/19/2023] Open
Abstract
Thermal shift assay (TSA) with altered temperature has been the most widely used method for monitoring protein stability for drug research. However, there is a pressing need for isothermal techniques as alternatives. This urgent demand arises from the limitations of TSA, which can sometimes provide misleading ranking of protein stability and fail to accurately reflect protein stability under physiological conditions. Although differential scanning fluorimetry has significantly improved throughput in comparison to differential scanning calorimetry and differential static light scattering throughput, all these methods exhibit moderate sensitivity. In contrast, current isothermal chemical denaturation (ICD) techniques may not offer the same throughput capabilities as TSA, but it provides more precise information about protein stability and interactions. Unfortunately, ICD also suffers from limited sensitivity, typically in micromolar range. We have developed a novel method to overcome these challenges, namely throughput and sensitivity. The novel Förster Resonance Energy Transfer (FRET)-Probe as an external probe is highly applicable to isothermal protein stability monitoring but also to conventional TSA. We have investigated ICD for multiple proteins with focus on KRASG12C with covalent inhibitors and three chemical denaturants performed at nanomolar protein concentration. Data showed corresponding inhibitor-induced stabilization of KRASG12C to those reported by nucleotide exchange assay.
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Affiliation(s)
- Randa Mahran
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland.
| | - Niklas Vello
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | - Anita Komulainen
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | | | - Harri Härmä
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | - Kari Kopra
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
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23
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Vitharana S, Stillahn JM, Katayama DS, Henry CS, Manning MC. Application of Formulation Principles to Stability Issues Encountered During Processing, Manufacturing, and Storage of Drug Substance and Drug Product Protein Therapeutics. J Pharm Sci 2023; 112:2724-2751. [PMID: 37572779 DOI: 10.1016/j.xphs.2023.08.003] [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: 10/14/2022] [Revised: 07/24/2023] [Accepted: 08/07/2023] [Indexed: 08/14/2023]
Abstract
The field of formulation and stabilization of protein therapeutics has become rather extensive. However, most of the focus has been on stabilization of the final drug product. Yet, proteins experience stress and degradation through the manufacturing process, starting with fermentaition. This review describes how formulation principles can be applied to stabilize biopharmaceutical proteins during bioprocessing and manufacturing, considering each unit operation involved in prepration of the drug substance. In addition, the impact of the container on stabilty is discussed as well.
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Affiliation(s)
| | - Joshua M Stillahn
- Legacy BioDesign LLC, Johnstown, CO 80534, USA; Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
| | | | - Charles S Henry
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
| | - Mark Cornell Manning
- Legacy BioDesign LLC, Johnstown, CO 80534, USA; Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA.
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24
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Zhang F, Chen F, Zhong M, Shen R, Zhao Z, Wei H, Zhang B, Fang J. Imaging of Carbonic Anhydrase Level in Epilepsy with an Environment-Sensitive Fluorescent Probe. Anal Chem 2023; 95:14833-14841. [PMID: 37747928 DOI: 10.1021/acs.analchem.3c01368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Carbonic anhydrases (CAs) participate in various physiological and pathological activities by catalyzing the interconversion between carbon dioxide and bicarbonate ions. Under normal circumstances, they guarantee that the relevant biological reactions in our body occur within an appropriate time scale. Abnormal expression or activity alteration of CAs is closely related to the pathogenesis of diverse diseases. This work reports an inhibitor-directed fluorescent probe FMRs-CA for the detection of CAs. Excellent selectivity, favorable biocompatibility, and desirable blood-brain barrier (BBB) penetration endow the probe with the ability to image the fluctuation of CAs in cells and mice. We achieved in situ visualization of the increased CAs in hypoxic cells with this probe. Additionally, probe FMRs-CA was mainly enriched within the liver and gradually metabolized by the liver. With the help of FMRs-CA, the increase of CAs in epileptic mouse brains was revealed first from the perspective of imaging, providing the mechanism connection between abnormal CA expressions and epilepsy.
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Affiliation(s)
- Fang Zhang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Fan Chen
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Miao Zhong
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Ruipeng Shen
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Zhengjia Zhao
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Haopai Wei
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Baoxin Zhang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Jianguo Fang
- School of Chemistry and Chemical Engineering, Nanjing University of Science & Technology, Nanjing, Jiangsu 210094, China
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25
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Silva J, Omar N, Sittaramane V, Cowell JK. Identification of small molecules that suppress cell invasion and metastasis promoted by WASF3 activation. Heliyon 2023; 9:e20662. [PMID: 37867831 PMCID: PMC10585217 DOI: 10.1016/j.heliyon.2023.e20662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 09/30/2023] [Accepted: 10/03/2023] [Indexed: 10/24/2023] Open
Abstract
The WASF3 gene promotes cancer cell invasion and metastasis, and genetic inactivation leads to suppression of metastasis. To identify small molecules that might interfere with WASF3 function, we performed an in silico docking study to the regulatory pocket of WASF3 using the National Cancer Institute (NCI) diversity set VI small molecule library. Compounds that showed the maximum likelihood of interaction with WASF3 were screened for their effect on cell movement in breast and prostate cancer cells, a well-established predictor of invasion and metastasis. Three hit compounds were identified that affected cell movement, and the same compounds also suppressed cell migration and invasion in vitro in both MDA-MB-231 breast cancer cells and Du145 prostate cancer cells. Using a zebrafish metastasis assay, one of these compounds, NSC670283, showed significant suppression of metastasis in vivo while not affecting cell proliferation. NSC670283 showed a consistent effect on suppression of invasion and metastasis, and cellular temperature shift assays provided support for physical interaction with WASF3. In addition, suppression of cell movement and invasion was accompanied by a decrease in actin filament polymerization. The data in this study suggest that these small molecules inhibit cancer cell invasion and metastasis, and to our knowledge, it is the first identification of a small molecule that can potentially inhibit WASF3-directed metastasis, laying the foundation for medicinal chemistry approaches to enhance the potency of the identified compounds.
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Affiliation(s)
- Jeane Silva
- The Georgia Cancer Center, 1410 Laney Walker Blvd., Augusta, GA 30912, Georgia
- Department of Interdisciplinary Health Sciences, College of Allied Sciences, Augusta University, GA, 30912, Georgia
| | - Nivin Omar
- Department of Pathology, Medical College of Georgia, Augusta University, GA, 30912, Georgia
| | - Vinoth Sittaramane
- Department of Biology, Georgia Southern University, Statesboro, GA 30458, Georgia
| | - John K. Cowell
- The Georgia Cancer Center, 1410 Laney Walker Blvd., Augusta, GA 30912, Georgia
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26
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Djelid H, Flahaut S, Oudjama Y, Wauven CV, Kacem Chaouche N. High NaCl concentrations induce the resistance to thermal denaturation of an extremely halotolerant (salt-activated) β-mannanase from Bacillus velezensis H1. World J Microbiol Biotechnol 2023; 39:304. [PMID: 37691038 DOI: 10.1007/s11274-023-03754-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/06/2023] [Indexed: 09/12/2023]
Abstract
β-mannanase catalyzes the hydrolysis of mannans β-1,4-mannosidic linkages to produce industrially relevant oligosaccharides. These enzymes have numerous important applications in the detergent, food, and feed industries, particularly those that are resistant to harsh environmental conditions such as salts and heat. While, moderately salt-tolerant β-mannanases are already reported, existence of a high halotolerant β-mannanase is still elusive. This study aims to report the first purification and characterization of ManH1, an extremely halotolerant β-mannanase from the halotolerant B. velezensis strain H1. Electrospray ionization quadrupole time-of-flight mass spectrometry (ESI-Q-TOF-MS) analysis revealed a single major peak with a molecular mass of 37.8 kDa demonstrating its purity. The purified enzyme showed a good thermostability as no activity was lost after a 48 h incubation under optimal conditions of 50 °C and pH 5.5. The enzyme's salt activation nature was revealed when its maximum activity was obtained in the presence of 4 M NaCl, it doubled compared to the no-salt condition. Moreover, NaCl strengthens its resistance to thermal denaturation, as its melting temperature (Tm) increased steadily with increasing NaCl concentrations reaching 75.5 °C in the presence of 2.5 M NaCl. The Km and Vmax values were 5.63 mg/mL and 333.33 µmol/min/mL, respectively, using carob galactomannan (CG) as a substrate. The enzyme showed a significant ability to produce manno-oligosaccharides (MOS) from lignocellulosic biomass releasing 13 mg/mL of reducing sugars from olive mill wastes (OMW) after 24 h incubation. The results revealed that this enzyme may have significant commercial values for agro-waste treatment, and other potential applications.
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Affiliation(s)
- Hadjer Djelid
- Laboratoire de Mycologie, de Biotechnologie et de l'Activité Microbienne (LaMyBAM), Département de Biologie Appliquée, FSNV, Université des Frères Mentouri, Constantine 1, Constantine, 25017, Algeria.
- Laboratoire de microbiologie appliquée, Ecole interfacultaire de Bioingénieurs, Université Libre de Bruxelles, Campus du CERIA, Bât. 4B, 1 avenue Emile Gryson, Brussels, 1070, Belgium.
| | - Sigrid Flahaut
- Laboratoire de microbiologie appliquée, Ecole interfacultaire de Bioingénieurs, Université Libre de Bruxelles, Campus du CERIA, Bât. 4B, 1 avenue Emile Gryson, Brussels, 1070, Belgium
| | | | | | - Noreddine Kacem Chaouche
- Laboratoire de Mycologie, de Biotechnologie et de l'Activité Microbienne (LaMyBAM), Département de Biologie Appliquée, FSNV, Université des Frères Mentouri, Constantine 1, Constantine, 25017, Algeria
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27
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Kim Y, Ahmed S, Miller WT. Colorectal cancer-associated mutations impair EphB1 kinase function. J Biol Chem 2023; 299:105115. [PMID: 37527777 PMCID: PMC10463257 DOI: 10.1016/j.jbc.2023.105115] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/03/2023] Open
Abstract
Erythropoietin-producing hepatoma (Eph) receptor tyrosine kinases regulate the migration and adhesion of cells that are required for many developmental processes and adult tissue homeostasis. In the intestinal epithelium, Eph signaling controls the positioning of cell types along the crypt-villus axis. Eph activity can suppress the progression of colorectal cancer (CRC). The most frequently mutated Eph receptor in metastatic CRC is EphB1. However, the functional effects of EphB1 mutations are mostly unknown. We expressed and purified the kinase domains of WT and five cancer-associated mutant EphB1 and developed assays to assess the functional effects of the mutations. Using purified proteins, we determined that CRC-associated mutations reduce the activity and stability of the folded structure of EphB1. By mammalian cell expression, we determined that CRC-associated mutant EphB1 receptors inhibit signal transducer and activator of transcription 3 and extracellular signal-regulated kinases 1 and 2 signaling. In contrast to the WT, the mutant EphB1 receptors are unable to suppress the migration of human CRC cells. The CRC-associated mutations also impair cell compartmentalization in an assay in which EphB1-expressing cells are cocultured with ligand (ephrin B1)-expressing cells. These results suggest that somatic mutations impair the kinase-dependent tumor suppressor function of EphB1 in CRC.
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Affiliation(s)
- Yunyoung Kim
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York, USA
| | - Sultan Ahmed
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York, USA
| | - W Todd Miller
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York, USA; Department of Veterans Affairs Medical Center, Northport, New York, USA.
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28
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Cardenal Peralta C, Vandroux P, Neumann-Arnold L, Panvert M, Fagart J, Seufert W, Mechulam Y, Schmitt E. Binding of human Cdc123 to eIF2γ. J Struct Biol 2023; 215:108006. [PMID: 37507029 DOI: 10.1016/j.jsb.2023.108006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/18/2023] [Accepted: 07/25/2023] [Indexed: 07/30/2023]
Abstract
Eukaryotic initiation factor 2 (eIF2) plays a key role in protein synthesis and in its regulation. The assembly of this heterotrimeric factor is facilitated by Cdc123, a member of the ATP grasp family that binds the γ subunit of eIF2. Notably, some mutations related to MEHMO syndrome, an X-linked intellectual disability, affect Cdc123-mediated eIF2 assembly. The mechanism of action of Cdc123 is unclear and structural information for the human protein is awaited. Here, the crystallographic structure of human Cdc123 (Hs-Cdc123) bound to domain 3 of human eIF2γ (Hs-eIF2γD3) was determined. The structure shows that the domain 3 of eIF2γ is bound to domain 1 of Cdc123. In addition, the long C-terminal region of Hs-Cdc123 provides a link between the ATP and Hs-eIF2γD3 binding sites. A thermal shift assay shows that ATP is tightly bound to Cdc123 whereas the affinity of ADP is much smaller. Yeast cell viability experiments, western blot analysis and two-hybrid assays show that ATP is important for the function of Hs-Cdc123 in eIF2 assembly. These data and recent findings allow us to propose a refined model to explain the mechanism of action of Cdc123 in eIF2 assembly.
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Affiliation(s)
- Cristina Cardenal Peralta
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Paul Vandroux
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Lea Neumann-Arnold
- Department of Genetics, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Michel Panvert
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Jérôme Fagart
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Wolfgang Seufert
- Department of Genetics, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany.
| | - Yves Mechulam
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Emmanuelle Schmitt
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France.
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29
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Burgos MI, Dassie SA, Fidelio GD. The effect of denaturants on protein thermal stability analyzed through a theoretical model considering multiple binding sites. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140920. [PMID: 37207817 DOI: 10.1016/j.bbapap.2023.140920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/02/2023] [Accepted: 05/05/2023] [Indexed: 05/21/2023]
Abstract
A novel mathematical development applied to protein ligand binding thermodynamics is proposed, which allows the simulation, and therefore the analysis of the effects of multiple and independent binding sites to the Native and/or Unfolded protein conformations, with different binding constant values. Protein stability is affected when it binds to a small number of high affinity ligands or to a high number of low affinity ligands. Differential scanning calorimetry (DSC) measures released or absorbed energy of thermally induced structural transitions of biomolecules. This paper presents the general theoretical development for the analysis of thermograms of proteins obtained for n-ligands bound to the native protein and m-ligands bound to their unfolded form. In particular, the effect of ligands with low affinity and with a high number of binding sites (n and/or m > 50) is analyzed. If the interaction with the native form of the protein is the one that predominates, they are considered stabilizers and if the binding with the unfolded species predominates, it is expected a destabilizing effect. The formalism presented here can be adapted to fitting routines in order to simultaneously obtain the unfolding energy and ligand binding energy of the protein. The effect of guanidinium chloride on bovine serum albumin thermal stability, was successfully analyzed with the model considering low number of middle affinity binding sites to the native state and a high number of weak binding sites to the unfolded state.
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Affiliation(s)
- M Ines Burgos
- Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina; Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Ciudad Universitaria, X5000HUA Córdoba, Argentina.
| | - Sergio A Dassie
- Departamento de Fisicoquímica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina; Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), CONICET, Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - Gerardo D Fidelio
- Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina; Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Ciudad Universitaria, X5000HUA Córdoba, Argentina
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30
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Ford A, Breitgoff F, Pasquini M, MacKenzie A, McElroy S, Baker S, Abrusci P, Varzandeh S, Bird L, Gavard A, Damerell D, Redhead M. Application of particle swarm optimization to understand the mechanism of action of allosteric inhibitors of the enzyme HSD17β13. PATTERNS (NEW YORK, N.Y.) 2023; 4:100733. [PMID: 37223265 PMCID: PMC10201303 DOI: 10.1016/j.patter.2023.100733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 09/06/2022] [Accepted: 03/24/2023] [Indexed: 05/25/2023]
Abstract
Understanding a drug candidate's mechanism of action is crucial for its further development. However, kinetic schemes are often complex and multi-parametric, especially for proteins in oligomerization equilibria. Here, we demonstrate the use of particle swarm optimization (PSO) as a method to select between different sets of parameters that are too far apart in the parameter space to be found by conventional approaches. PSO is based upon the swarming of birds: each bird in the flock assesses multiple landing spots while at the same time sharing that information with its neighbors. We applied this approach to the kinetics of HSD17β13 enzyme inhibitors, which displayed unusually large thermal shifts. Thermal shift data for HSD17β13 indicated that the inhibitor shifted the oligomerization equilibrium toward the dimeric state. Validation of the PSO approach was provided by experimental mass photometry data. These results encourage further exploration of multi-parameter optimization algorithms as tools in drug discovery.
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Affiliation(s)
- Amy Ford
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford OX4 4GE, UK
| | - Frauke Breitgoff
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford OX4 4GE, UK
| | - Miriam Pasquini
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford OX4 4GE, UK
| | | | - Stuart McElroy
- Bioascent, Bo'Ness Road, Chapelhall, Motherwell ML1 5SH, UK
| | - Steve Baker
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford OX4 4GE, UK
| | - Patrizia Abrusci
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford OX4 4GE, UK
| | - Simon Varzandeh
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford OX4 4GE, UK
| | - Louise Bird
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford OX4 4GE, UK
| | - Angeline Gavard
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford OX4 4GE, UK
| | - David Damerell
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford OX4 4GE, UK
| | - Martin Redhead
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford OX4 4GE, UK
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Khan AM, Atia-Tul-Wahab, Farooq S, Ullah A, Choudhary MI. Repurposing of US-FDA approved drugs against SARS-CoV-2 main protease (M pro) by using STD-NMR spectroscopy, in silico studies and antiviral assays. Int J Biol Macromol 2023; 234:123540. [PMID: 36740128 PMCID: PMC9896891 DOI: 10.1016/j.ijbiomac.2023.123540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/21/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023]
Abstract
SARS-CoV-2 Main protease (Mpro) is a well-known drug target against SARS-CoV-2 infection. Identification of Mpro inhibitors is vigorously pursued due to its crucial role in viral replication. The present study was aimed to identify Mpro inhibitors via repurposing of US-FDA approved drugs by STD-NMR spectroscopy. In this study, 156 drugs and natural compounds were evaluated against Mpro. Among them, 10 drugs were found to be interacting with Mpro, including diltiazem HCl (1), mefenamic acid (2), losartan potassium (3), mexiletine HCl (4), glaucine HBr (5), trimebutine maleate (6), flurbiprofen (7), amantadine HCl (8), dextromethorphan (9), and lobeline HCl (10) in STD-NMR spectroscopy. Their interactions were compared with three standards (Repurposed anti-viral drugs), dexamethasone, chloroquine phosphate, and remdesivir. Thermal stability of Mpro and dissociation constant (Kd) of six interacting drugs were also determined using DSF. RMSD plots in MD simulation studies showed the formation of stable protein-ligand complexes. They were further examined for their antiviral activity by plaque reduction assay against SARS-CoV-2, which showed 55-100% reduction in viral plaques. This study demonstrates the importance of drug repurposing against emerging and neglected diseases. This study also exhibits successful application of STD-NMR spectroscopy combined with plaque reduction assay in rapid identification of potential anti-viral agents.
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Affiliation(s)
- Abdul Mateen Khan
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Atia-Tul-Wahab
- Dr. Panjwani Center for Molecular and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan.
| | - Saba Farooq
- National Institute of Virology, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Asmat Ullah
- Dr. Panjwani Center for Molecular and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - M Iqbal Choudhary
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan; Dr. Panjwani Center for Molecular and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan; Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
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32
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Svilenov HL, Delhommel F, Siebenmorgen T, Rührnößl F, Popowicz GM, Reiter A, Sattler M, Brockmeyer C, Buchner J. Extrinsic stabilization of antiviral ACE2-Fc fusion proteins targeting SARS-CoV-2. Commun Biol 2023; 6:386. [PMID: 37031320 PMCID: PMC10082628 DOI: 10.1038/s42003-023-04762-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/24/2023] [Indexed: 04/10/2023] Open
Abstract
The angiotensin-converting enzyme 2 (ACE2) is a viral receptor used by sarbecoviruses to infect cells. Fusion proteins comprising extracellular ACE2 domains and the Fc part of immunoglobulins exhibit high virus neutralization efficiency, but the structure and stability of these molecules are poorly understood. We show that although the hinge between the ACE2 and the IgG4-Fc is highly flexible, the conformational dynamics of the two ACE2 domains is restricted by their association. Interestingly, the conformational stability of the ACE2 moiety is much lower than that of the Fc part. We found that chemical compounds binding to ACE2, such as DX600 and MLN4760, can be used to strongly increase the thermal stability of the ACE2 by different mechanisms. Together, our findings reveal a general concept for stabilizing the labile receptor segments of therapeutic antiviral fusion proteins by chemical compounds.
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Affiliation(s)
- Hristo L Svilenov
- Center for Functional Protein Assemblies (CPA) and School of Natural Sciences, Department of Bioscience, Technical University of Munich, 85748, Garching, Germany.
- Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium.
| | - Florent Delhommel
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Bavarian NMR Center, School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching, 85748, Munich, Germany
| | - Till Siebenmorgen
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Bavarian NMR Center, School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching, 85748, Munich, Germany
| | - Florian Rührnößl
- Center for Functional Protein Assemblies (CPA) and School of Natural Sciences, Department of Bioscience, Technical University of Munich, 85748, Garching, Germany
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Bavarian NMR Center, School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching, 85748, Munich, Germany
| | | | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Bavarian NMR Center, School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching, 85748, Munich, Germany
| | | | - Johannes Buchner
- Center for Functional Protein Assemblies (CPA) and School of Natural Sciences, Department of Bioscience, Technical University of Munich, 85748, Garching, Germany.
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33
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Wang H, Hu L, Li H, Lai YT, Wei X, Xu X, Cao Z, Cao H, Wan Q, Chang YY, Xu A, Zhou Q, Jiang G, He ML, Sun H. Mitochondrial ATP synthase as a direct molecular target of chromium(III) to ameliorate hyperglycaemia stress. Nat Commun 2023; 14:1738. [PMID: 36977671 PMCID: PMC10050403 DOI: 10.1038/s41467-023-37351-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
Chromium(III) is extensively used as a supplement for muscle development and the treatment of diabetes mellitus. However, its mode of action, essentiality, and physiological/pharmacological effects have been a subject of scientific debate for over half a century owing to the failure in identifying the molecular targets of Cr(III). Herein, by integrating fluorescence imaging with a proteomic approach, we visualized the Cr(III) proteome being mainly localized in the mitochondria, and subsequently identified and validated eight Cr(III)-binding proteins, which are predominately associated with ATP synthesis. We show that Cr(III) binds to ATP synthase at its beta subunit via the catalytic residues of Thr213/Glu242 and the nucleotide in the active site. Such a binding suppresses ATP synthase activity, leading to the activation of AMPK, improving glucose metabolism, and rescuing mitochondria from hyperglycaemia-induced fragmentation. The mode of action of Cr(III) in cells also holds true in type II diabetic male mice. Through this study, we resolve the long-standing question of how Cr(III) ameliorates hyperglycaemia stress at the molecular level, opening a new horizon for further exploration of the pharmacological effects of Cr(III).
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Affiliation(s)
- Haibo Wang
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pok Fu Lam, Hong Kong S.A.R., P.R. China
| | - Ligang Hu
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pok Fu Lam, Hong Kong S.A.R., P.R. China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, P.R. China
| | - Hongyan Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pok Fu Lam, Hong Kong S.A.R., P.R. China
| | - Yau-Tsz Lai
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pok Fu Lam, Hong Kong S.A.R., P.R. China
| | - Xueying Wei
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pok Fu Lam, Hong Kong S.A.R., P.R. China
| | - Xiaohan Xu
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pok Fu Lam, Hong Kong S.A.R., P.R. China
| | - Zhenkun Cao
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pok Fu Lam, Hong Kong S.A.R., P.R. China
| | - Huiming Cao
- Institute of Environment and Health, Jianghan University, Wuhan, 430056, P.R. China
| | - Qianya Wan
- Department of Biomedical Science, City University of Hong Kong, Kowloon Tong, Hong Kong, P.R. China
| | - Yuen-Yan Chang
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pok Fu Lam, Hong Kong S.A.R., P.R. China
| | - Aimin Xu
- Department of Pharmacology and Pharmacy, and State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, 21 Sassoon Road, Pok Fu Lam, Hong Kong, P.R. China
| | - Qunfang Zhou
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, P.R. China
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, P.R. China
| | - Ming-Liang He
- Department of Biomedical Science, City University of Hong Kong, Kowloon Tong, Hong Kong, P.R. China
| | - Hongzhe Sun
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pok Fu Lam, Hong Kong S.A.R., P.R. China.
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Rosenberg EM, Jian X, Soubias O, Yoon HY, Yadav MP, Hammoudeh S, Pallikkuth S, Akpan I, Chen PW, Maity TK, Jenkins LM, Yohe ME, Byrd RA, Randazzo PA. The small molecule inhibitor NAV-2729 has a complex target profile including multiple ADP-ribosylation factor regulatory proteins. J Biol Chem 2023; 299:102992. [PMID: 36758799 PMCID: PMC10023970 DOI: 10.1016/j.jbc.2023.102992] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 02/11/2023] Open
Abstract
The ADP-ribosylation factor (Arf) GTPases and their regulatory proteins are implicated in cancer progression. NAV-2729 was previously identified as a specific inhibitor of Arf6 that reduced progression of uveal melanoma in an orthotopic xenograft. Here, our goal was to assess the inhibitory effects of NAV-2729 on the proliferation of additional cell types. We found NAV-2729 inhibited proliferation of multiple cell lines, but Arf6 expression did not correlate with NAV-2729 sensitivity, and knockdown of Arf6 affected neither cell viability nor sensitivity to NAV-2729. Furthermore, binding to native Arf6 was not detected; however, we determined that NAV-2729 inhibited both Arf exchange factors and Arf GTPase-activating proteins. ASAP1, a GTPase-activating protein linked to cancer progression, was further investigated. We demonstrated that NAV-2729 bound to the PH domain of ASAP1 and changed ASAP1 cellular distribution. However, ASAP1 knockdown did not fully recapitulate the cytoskeletal effects of NAV-2729 nor affect cell proliferation. Finally, our screens identified 48 other possible targets of NAV-2729. These results illustrate the complexities of defining targets of small molecules and identify NAV-2729 as a model PH domain-binding inhibitor.
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Affiliation(s)
- Eric M Rosenberg
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Xiaoying Jian
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Olivier Soubias
- Center for Structural Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Hye-Young Yoon
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Mukesh P Yadav
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Sarah Hammoudeh
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Sandeep Pallikkuth
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Itoro Akpan
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Pei-Wen Chen
- Department of Biology, Williams College, Williamstown, Massachusetts, USA
| | - Tapan K Maity
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Lisa M Jenkins
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Marielle E Yohe
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA; Laboratory of Cell and Developmental Signaling, Center for Cancer Research, Frederick, Maryland, USA
| | - R Andrew Byrd
- Center for Structural Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Paul A Randazzo
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA.
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35
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Rowlands H, Tschapalda K, Blackett C, Ivanov D, Plant D, Shaw J, Thomas A, Packer M, Arnold L, Holdgate GA. High throughput screening of 0.5 Million compounds against CRAF using Alpha CETSA Ⓡ. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2023; 28:102-110. [PMID: 36736830 DOI: 10.1016/j.slasd.2023.01.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/13/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023]
Abstract
The cellular thermal shift assay (CETSA®) has increasingly been used in early drug discovery to provide a measure of cellular target engagement. Traditionally, CETSA has been employed for bespoke questions with small to medium throughput and has predominantly been applied during hit validation rather than in hit identification. Using a CETSA screen versus the kinase CRAF, we assessed 3 key questions: (1) technical feasibility - could the CETSA methodology technically be applied at truly high throughput scale? (2) relevance - could hits suitable for further optimisation be identified? (3) reliability - would the approach identify known chemical equity. Here, we describe the first large scale AlphaLISA SureFire based CETSA (Alpha CETSA) approach allowing us to screen a large library of almost 0.5 million compounds. We discuss the issues overcome in automating and executing the screen and describe the resulting screen output.
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Affiliation(s)
- Hannah Rowlands
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | - Kirsten Tschapalda
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | - Carolyn Blackett
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | - Delyan Ivanov
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | - Darren Plant
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | - Joseph Shaw
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | | | | | | | - Geoffrey A Holdgate
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK.
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36
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Bai N, Adeshina Y, Bychkov I, Xia Y, Gowthaman R, Miller SA, Gupta AK, Johnson DK, Lan L, Golemis EA, Makhov PB, Xu L, Pillai MM, Boumber Y, Karanicolas J. Rationally designed inhibitors of the Musashi protein-RNA interaction by hotspot mimicry. RESEARCH SQUARE 2023:rs.3.rs-2395172. [PMID: 36711552 PMCID: PMC9882606 DOI: 10.21203/rs.3.rs-2395172/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
RNA-binding proteins (RBPs) are key post-transcriptional regulators of gene expression, and thus underlie many important biological processes. Here, we developed a strategy that entails extracting a "hotspot pharmacophore" from the structure of a protein-RNA complex, to create a template for designing small-molecule inhibitors and for exploring the selectivity of the resulting inhibitors. We demonstrate this approach by designing inhibitors of Musashi proteins MSI1 and MSI2, key regulators of mRNA stability and translation that are upregulated in many cancers. We report this novel series of MSI1/MSI2 inhibitors is specific and active in biochemical, biophysical, and cellular assays. This study extends the paradigm of "hotspots" from protein-protein complexes to protein-RNA complexes, supports the "druggability" of RNA-binding protein surfaces, and represents one of the first rationally-designed inhibitors of non-enzymatic RNA-binding proteins. Owing to its simplicity and generality, we anticipate that this approach may also be used to develop inhibitors of many other RNA-binding proteins; we also consider the prospects of identifying potential off-target interactions by searching for other RBPs that recognize their cognate RNAs using similar interaction geometries. Beyond inhibitors, we also expect that compounds designed using this approach can serve as warheads for new PROTACs that selectively degrade RNA-binding proteins.
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Affiliation(s)
- Nan Bai
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia PA 19111
- Department of Molecular Biosciences, University of Kansas, Lawrence KS 66045
| | - Yusuf Adeshina
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia PA 19111
- Center for Computational Biology, University of Kansas, Lawrence KS 66045
| | - Igor Bychkov
- Division of Hematology/Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Yan Xia
- Department of Molecular Biosciences, University of Kansas, Lawrence KS 66045
| | - Ragul Gowthaman
- Center for Computational Biology, University of Kansas, Lawrence KS 66045
| | - Sven A. Miller
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia PA 19111
| | - Abhishek K. Gupta
- Section of Hematology, Yale Cancer Center, New Haven CT 06520
- Department of Pathology, Yale University School of Medicine, New Haven CT 06520
| | - David K. Johnson
- Center for Computational Biology, University of Kansas, Lawrence KS 66045
| | - Lan Lan
- Department of Molecular Biosciences, University of Kansas, Lawrence KS 66045
| | - Erica A. Golemis
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia PA 19111
- Department of Cancer and Cellular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140
| | - Petr B. Makhov
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia PA 19111
| | - Liang Xu
- Department of Molecular Biosciences, University of Kansas, Lawrence KS 66045
- Department of Radiation Oncology, University of Kansas Medical Center, Kansas City KS 66160
| | - Manoj M. Pillai
- Section of Hematology, Yale Cancer Center, New Haven CT 06520
- Department of Pathology, Yale University School of Medicine, New Haven CT 06520
| | - Yanis Boumber
- Division of Hematology/Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - John Karanicolas
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia PA 19111
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, PA 19140
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37
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Bai N, Adeshina Y, Bychkov I, Xia Y, Gowthaman R, Miller SA, Gupta AK, Johnson DK, Lan L, Golemis EA, Makhov PB, Xu L, Pillai MM, Boumber Y, Karanicolas J. Rationally designed inhibitors of the Musashi protein-RNA interaction by hotspot mimicry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.09.523326. [PMID: 36711508 PMCID: PMC9882015 DOI: 10.1101/2023.01.09.523326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
RNA-binding proteins (RBPs) are key post-transcriptional regulators of gene expression, and thus underlie many important biological processes. Here, we developed a strategy that entails extracting a "hotspot pharmacophore" from the structure of a protein-RNA complex, to create a template for designing small-molecule inhibitors and for exploring the selectivity of the resulting inhibitors. We demonstrate this approach by designing inhibitors of Musashi proteins MSI1 and MSI2, key regulators of mRNA stability and translation that are upregulated in many cancers. We report this novel series of MSI1/MSI2 inhibitors is specific and active in biochemical, biophysical, and cellular assays. This study extends the paradigm of "hotspots" from protein-protein complexes to protein-RNA complexes, supports the "druggability" of RNA-binding protein surfaces, and represents one of the first rationally-designed inhibitors of non-enzymatic RNA-binding proteins. Owing to its simplicity and generality, we anticipate that this approach may also be used to develop inhibitors of many other RNA-binding proteins; we also consider the prospects of identifying potential off-target interactions by searching for other RBPs that recognize their cognate RNAs using similar interaction geometries. Beyond inhibitors, we also expect that compounds designed using this approach can serve as warheads for new PROTACs that selectively degrade RNA-binding proteins.
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Affiliation(s)
- Nan Bai
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia PA 19111
- Department of Molecular Biosciences, University of Kansas, Lawrence KS 66045
| | - Yusuf Adeshina
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia PA 19111
- Center for Computational Biology, University of Kansas, Lawrence KS 66045
| | - Igor Bychkov
- Division of Hematology/Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Yan Xia
- Department of Molecular Biosciences, University of Kansas, Lawrence KS 66045
| | - Ragul Gowthaman
- Center for Computational Biology, University of Kansas, Lawrence KS 66045
| | - Sven A. Miller
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia PA 19111
| | | | - David K. Johnson
- Center for Computational Biology, University of Kansas, Lawrence KS 66045
| | - Lan Lan
- Department of Molecular Biosciences, University of Kansas, Lawrence KS 66045
| | - Erica A. Golemis
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia PA 19111
- Department of Cancer and Cellular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140
| | - Petr B. Makhov
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia PA 19111
| | - Liang Xu
- Department of Molecular Biosciences, University of Kansas, Lawrence KS 66045
- Department of Radiation Oncology, University of Kansas Medical Center, Kansas City KS 66160
| | - Manoj M. Pillai
- Section of Hematology, Yale Cancer Center, New Haven CT 06520
- Department of Pathology, Yale University School of Medicine, New Haven CT 06520
| | - Yanis Boumber
- Division of Hematology/Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - John Karanicolas
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia PA 19111
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, PA 19140
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Cardona HRA, Froes TQ, Souza BCD, Leite FHA, Brandão HN, Buaruang J, Kijjoa A, Alves CQ. Thermal shift assays of marine-derived fungal metabolites from Aspergillus fischeri MMERU 23 against Leishmania major pteridine reductase 1 and molecular dynamics studies. J Biomol Struct Dyn 2022; 40:11968-11976. [PMID: 34415221 DOI: 10.1080/07391102.2021.1966510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Marine-derived fungi are a promising source of bioactive molecules, especially species from extreme habitats. Although several secondary metabolites such as meroterpenoids and alkaloids have been isolated from cultures of Aspergillus fischeri, obtained from terrestrial habitats, there is no report on compounds isolated from marine-derived strains. Many metabolites isolated from marine-derived fungi exhibited a myriad of biological activities. Marine natural products have shown to be an important source of bioactive compounds and can assist in the discovery of molecules with affinity against validated targets from exclusive strains of parasites of medical importance such as pteridine reductase 1 (PTR1), from Leishmania major, which is essential for cell growth. Leishmaniasis is responsible for approximately 65,000 annual deaths. Despite the mortality data, drugs available for the treatment of patients are insufficient and have moderate therapeutic efficacy in addition to serious adverse effects, which make the development of new drugs urgent. The previously described aszonalenin (ASL), aszonapyrone A (ASP), acetylaszonalenin (ACZ), and helvolic acid (HAC) were isolated from the ethyl acetate extract of the culture of a marine sponge-associated A. fischeri MMERU 23 and their affinities against PTR1 were determined by ThermoFluor®. Among the tested compounds, only ACZ showed dose-dependent affinity against PTR1. Moreover, complementary molecular dynamics studies (t = 100 000 ps) have showed that this molecule performs hydrogen bonds with key residues at the active site for more than 60% of the productive trajectory time. The results indicate that ACZ could be a promising PTR1 inhibitor and a potential candidate for development of antileishmanial drug.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Thamires Q Froes
- Faculdade de Farmácia, Universidade Federal da Bahia, Salvador, Brazil
| | - Bruno C De Souza
- Departamento de Saúde, Universidade Estadual Feira de Santana, Bahia, Brazil
| | - Franco H A Leite
- Departamento de Saúde, Universidade Estadual Feira de Santana, Bahia, Brazil
| | - Hugo Neves Brandão
- Departamento de Saúde, Universidade Estadual Feira de Santana, Bahia, Brazil
| | - Jamrearn Buaruang
- Marine Microbe Environment Research Unit, Division of Environmental Science, Faculty of Science, Ramkhamhaeng University, Bangkok, Thailand
| | - Anake Kijjoa
- ICBAS-Instituto de Ciências Biomédicas Abel Salazar and CIIMAR, Universidade do Porto, Porto, Portugal
| | - Clayton Q Alves
- Departamento de Ciências Exatas, Universidade Estadual de Feira de Santana, Bahia, Brazil
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39
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Cho KB, Shukla SP, Kannan M, Zhang H, Amina SJ, Zhou S, Chen Y, Molligan JF, Taneja V, Mohan C, Udugamasooriya DG, Guo B. A peptoid interleukin‐15 receptor antagonist suppresses inflammation and arthritis in mice. Clin Transl Immunology 2022; 11:e1432. [PMCID: PMC9686008 DOI: 10.1002/cti2.1432] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 10/13/2022] [Accepted: 11/11/2022] [Indexed: 11/27/2022] Open
Abstract
Objective To discover a novel peptoid antagonist that targets the interleukin‐15 (IL‐15) receptor and to evaluate its therapeutic efficacy in the treatment of inflammation and arthritis. Methods A new compound (IFRA3, interleukin‐15 receptor antagonist 3) was discovered using a unique on‐bead two‐colour combinatorial cell screening of a peptoid library. The interaction of IFRA3 with IL‐15 receptor was assessed by in vitro pull‐down and thermal shift assays. The efficacy of IFRA3 in treating inflammation and arthritis was evaluated in mouse models. Results IFRA3Q1 (a tetrameric derivative of IFRA3) inhibited the activity of IL‐15 and suppressed CTLL‐2 cell proliferation (which depends on IL‐15 activity). IFRA3Q1 exhibited strong in vivo anti‐inflammatory activity in carrageenan‐induced inflammation in mice. Furthermore, IFRA3Q1 inhibited collagen‐induced arthritis in DBA/1J mice. Conclusion By binding to and inhibiting the function of IL‐15 receptor, IFRA3Q1 exhibited significant anti‐arthritis activity. Our findings suggest that IFRA3Q1 represents a new paradigm for arthritis therapy by targeting IL‐15 signalling.
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Affiliation(s)
- Kwang Bog Cho
- Department of Pharmacological and Pharmaceutical SciencesUniversity of HoustonHoustonTXUSA
| | - Satya Prakash Shukla
- Department of Pharmacological and Pharmaceutical SciencesUniversity of HoustonHoustonTXUSA
| | - Maheshkumar Kannan
- Department of Pharmacological and Pharmaceutical SciencesUniversity of HoustonHoustonTXUSA
| | - Haowen Zhang
- Department of Pharmacological and Pharmaceutical SciencesUniversity of HoustonHoustonTXUSA
| | - Sundus Jabeen Amina
- Department of Pharmacological and Pharmaceutical SciencesUniversity of HoustonHoustonTXUSA
| | - Shuang Zhou
- Department of Pharmacological and Pharmaceutical SciencesUniversity of HoustonHoustonTXUSA
| | - Yanping Chen
- Department of Biomedical EngineeringUniversity of HoustonHoustonTXUSA
| | | | - Veena Taneja
- Department of Immunology and RheumatologyMayo ClinicRochesterMNUSA
| | - Chandra Mohan
- Department of Biomedical EngineeringUniversity of HoustonHoustonTXUSA
| | | | - Bin Guo
- Department of Pharmacological and Pharmaceutical SciencesUniversity of HoustonHoustonTXUSA
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40
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Aggarwal S, Tanwar N, Singh A, Munde M. Formation of Protamine and Zn-Insulin Assembly: Exploring Biophysical Consequences. ACS OMEGA 2022; 7:41044-41057. [PMID: 36406544 PMCID: PMC9670714 DOI: 10.1021/acsomega.2c04419] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
The insulin-protamine interaction is at the core of the mode of action in many insulin formulations (Zn + insulin + protamine) and to treat diabetes, in which protamine is added to the stable form of hexameric insulin (Zn-insulin). However, due to the unavailability of quantitative data and a high-resolution structure, the binding mechanism of the insulin-protamine complex remains unknown. In this study, it was observed that Zn-insulin experiences destabilization as observed by the loss of secondary structure in circular dichroism (CD), and reduction in thermal stability in melting study, upon protamine binding. In isothermal titration calorimetry (ITC), it was found that the interactions were mostly enthalpically driven. This is in line with the positive ΔC m value (+880 cal mol-1), indicating the role of hydrophilic interactions in the complex formation, with the exposure of hydrophobic residues to the solvent, which was firmly supported by the 8-anilino-1-naphthalene sulfonate (ANS) binding study. The stoichiometry (N) value in ITC suggests the multiple insulin molecules binding to the protamine chain, which is consistent with the picture of the condensation of insulin in the presence of protamine. Atomic force microscopy (AFM) suggested the formation of a heterogeneous Zn-insulin-protamine complex. In fluorescence, Zn-insulin experiences strong Tyr quenching, suggesting that the location of the protamine-binding site is near Tyr, which is also supported by the molecular docking study. Since Tyr is critical in the stabilization of insulin self-assembly, its interaction with protamine may impair insulin's self-association ability and thermodynamic stability while at the same time promoting its flexible conformation desired for better biological activity.
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41
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Huang W, Yang S, Cheng YS, Sima N, Sun W, Shen M, Braisted JC, Lu W, Zheng W. Terfenadine resensitizes doxorubicin activity in drug-resistant ovarian cancer cells via an inhibition of CaMKII/CREB1 mediated ABCB1 expression. Front Oncol 2022; 12:1068443. [PMID: 36439493 PMCID: PMC9684669 DOI: 10.3389/fonc.2022.1068443] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 10/25/2022] [Indexed: 10/23/2023] Open
Abstract
Ovarian cancer is one of the most lethal gynecological malignancies. Recurrence or acquired chemoresistance is the leading cause of ovarian cancer therapy failure. Overexpression of ATP-binding cassette subfamily B member 1 (ABCB1), commonly known as P-glycoprotein, correlates closely with multidrug resistance (MDR). However, the mechanism underlying aberrant ABCB1 expression remains unknown. Using a quantitative high-throughput combinational screen, we identified that terfenadine restored doxorubicin sensitivity in an MDR ovarian cancer cell line. In addition, RNA-seq data revealed that the Ca2+-mediated signaling pathway in the MDR cells was abnormally regulated. Moreover, our research demonstrated that terfenadine directly bound to CAMKIID to prevent its autophosphorylation and inhibit the activation of the cAMP-responsive element-binding protein 1 (CREB1)-mediated pathway. Direct inhibition of CAMKII or CREB1 had the same phenotypic effects as terfenadine in the combined treatment, including lower expression of ABCB1 and baculoviral IAP repeat-containing 5 (BIRC5, also known as survivin) and increased doxorubicin-induced apoptosis. In this study, we demonstrate that aberrant regulation of the Ca2+-mediated CAMKIID/CREB1 pathway contributes to ABCB1 over-expression and MDR creation and that CAMKIID and CREB1 are attractive targets for restoring doxorubicin efficacy in ABCB1-mediated MDR ovarian cancer.
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Affiliation(s)
- Wei Huang
- Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Shu Yang
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Yu-Shan Cheng
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Ni Sima
- Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Wei Sun
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Min Shen
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Bethesda, MD, United States
| | - John C. Braisted
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Weiguo Lu
- Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Women’s Reproductive Health Research Laboratory of Zhejiang Province, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Wei Zheng
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Bethesda, MD, United States
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Alaofi AL, Shahid M, Raish M, Ansari MA, Syed R, Kalam MA. Identification of Doxorubicin as Repurposing Inhibitory Drug for MERS-CoV PLpro. Molecules 2022; 27:7553. [PMID: 36364379 PMCID: PMC9654812 DOI: 10.3390/molecules27217553] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 10/26/2022] [Accepted: 10/30/2022] [Indexed: 07/29/2023] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV), belonging to the betacoronavirus genus can cause severe respiratory illnesses, accompanied by pneumonia, multiorgan failure, and ultimately death. CoVs have the ability to transgress species barriers and spread swiftly into new host species, with human-to-human transmission causing epidemic diseases. Despite the severe public health threat of MERS-CoV, there are currently no vaccines or drugs available for its treatment. MERS-CoV papain-like protease (PLpro) is a key enzyme that plays an important role in its replication. In the present study, we evaluated the inhibitory activities of doxorubicin (DOX) against the recombinant MERS-CoV PLpro by employing protease inhibition assays. Hydrolysis of fluorogenic peptide from the Z-RLRGG-AMC-peptide bond in the presence of DOX showed an IC50 value of 1.67 μM at 30 min. Subsequently, we confirmed the interaction between DOX and MERS-CoV PLpro by thermal shift assay (TSA), and DOX increased ΔTm by ~20 °C, clearly indicating a coherent interaction between the MERS-CoV PL protease and DOX. The binding site of DOX on MERS-CoV PLpro was assessed using docking techniques and molecular dynamic (MD) simulations. DOX bound to the thumb region of the catalytic domain of the MERS-CoV PLpro. MD simulation results showed flexible BL2 loops, as well as other potential residues, such as R231, R233, and G276 of MERS-CoV PLpro. Development of drug repurposing is a remarkable opportunity to quickly examine the efficacy of different aspects of treating various diseases. Protease inhibitors have been found to be effective against MERS-CoV to date, and numerous candidates are currently undergoing clinical trials to prove this. Our effort follows a in similar direction.
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Affiliation(s)
- Ahmed L. Alaofi
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
- College of Pharmacy Building 23, Pharmaceutics Department, King Saud University, Ground Floor, Office AA 79, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Mudassar Shahid
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Mohammad Raish
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Mushtaq Ahmad Ansari
- Department of Phamacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Rabbani Syed
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Mohd Abul Kalam
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
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Linkuvienė V, Zubrienė A, Matulis D. Intrinsic affinity of protein - ligand binding by differential scanning calorimetry. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140830. [PMID: 35934299 DOI: 10.1016/j.bbapap.2022.140830] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/28/2022] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
Differential scanning calorimetry (DSC) determines the enthalpy change upon protein unfolding and the melting temperature of the protein. Performing DSC of a protein in the presence of increasing concentrations of specifically-binding ligand yields a series of curves that can be fit to obtain the protein-ligand dissociation constant as done in the fluorescence-based thermal shift assay (FTSA, ThermoFluor, DSF). The enthalpy of unfolding, as directly determined by DSC, helps improving the precision of the fit. If the ligand binding is linked to protonation reactions, the intrinsic binding constant can be determined by performing the affinity determination at a series of pH values. Here, the intrinsic, pH-independent, affinity of acetazolamide binding to carbonic anhydrase (CA) II was determined. A series of high-affinity ligands binding to CAIX, an anticancer drug target, and CAII showed recognition and selectivity for the anticancer isozyme. Performing the DSC experiment in buffers of highly different enthalpies of protonation enabled to observe the ligand unbinding-linked protonation reactions and estimate the intrinsic enthalpy of binding. The heat capacity of combined unfolding and unbinding was determined by varying the ligand concentrations. Taken together, these parameters provided a detailed thermodynamic picture of the linked ligand binding and protein unfolding process.
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Affiliation(s)
- Vaida Linkuvienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania
| | - Asta Zubrienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania.
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44
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Jaklin M, Hritz J, Hribar-Lee B. A new fibrillization mechanism of β-lactoglobulin in glycine solutions. Int J Biol Macromol 2022; 216:414-425. [PMID: 35803407 PMCID: PMC10039397 DOI: 10.1016/j.ijbiomac.2022.06.182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/15/2022] [Accepted: 06/27/2022] [Indexed: 11/26/2022]
Abstract
Even though amyloid aggregates were discovered many years ago the mechanism of their formation is still a mystery. Because of their connection to many of untreatable neurodegenerative diseases the motivation for finding a common aggregation path is high. We report a new high heat induced fibrillization path of a model protein β-lactoglobulin (BLG) when incubated in glycine instead of water at pH 2. By combining atomic force microscopy (AFM), transmission emission microscopy (TEM), dynamic light scattering (DLS) and circular dichroism (CD) we predict that the basic building blocks of fibrils made in glycine are not peptides, but rather spheroid oligomers of different height that form by stacking of ring-like structures. Spheroid oligomers linearly align to form fibrils by opening up and combining. We suspect that glycine acts as an hydrolysation inhibitor which consequently promotes a different fibrillization path. By combining the known data on fibrillization in water with our experimental conclusions we come up with a new fibrillization scheme for BLG. We show that by changing the fibrillization conditions just by small changes in buffer composition can dramatically change the aggregation pathway and the effect of buffer shouldn't be neglected. Fibrils seen in our study are also gaining more and more attention because of their pore-like structure and a possible cytotoxic mechanism by forming pernicious ion-channels. By preparing them in a simple model system as BLG we opened a new way to study their formation.
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Affiliation(s)
- Matej Jaklin
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Večna pot 113, Ljubljana SI-1000, Slovenia
| | - Jozef Hritz
- CEITEC Masaryk University Kamenice 5, Brno 625 00, Czech Republic; Department of Chemistry, Faculty of Science, Masaryk University Kamenice 5, Brno 625 00, Czech Republic
| | - Barbara Hribar-Lee
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Večna pot 113, Ljubljana SI-1000, Slovenia.
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45
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Vincent T, Gaillet B, Garnier A. Optimization of operation conditions for improved cytochrome
P450BM3
enzymatic reaction yield. CAN J CHEM ENG 2022. [DOI: 10.1002/cjce.24232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Thierry Vincent
- Department of Chemical Engineering Université Laval Québec City Québec Canada
| | - Bruno Gaillet
- Department of Chemical Engineering Université Laval Québec City Québec Canada
| | - Alain Garnier
- Department of Chemical Engineering Université Laval Québec City Québec Canada
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46
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Wagner MP, Formaglio P, Gorgette O, Dziekan JM, Huon C, Berneburg I, Rahlfs S, Barale JC, Feinstein SI, Fisher AB, Ménard D, Bozdech Z, Amino R, Touqui L, Chitnis CE. Human peroxiredoxin 6 is essential for malaria parasites and provides a host-based drug target. Cell Rep 2022; 39:110923. [PMID: 35705035 DOI: 10.1016/j.celrep.2022.110923] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 03/30/2022] [Accepted: 05/17/2022] [Indexed: 11/30/2022] Open
Abstract
The uptake and digestion of host hemoglobin by malaria parasites during blood-stage growth leads to significant oxidative damage of membrane lipids. Repair of lipid peroxidation damage is crucial for parasite survival. Here, we demonstrate that Plasmodium falciparum imports a host antioxidant enzyme, peroxiredoxin 6 (PRDX6), during hemoglobin uptake from the red blood cell cytosol. PRDX6 is a lipid-peroxidation repair enzyme with phospholipase A2 (PLA2) activity. Inhibition of PRDX6 with a PLA2 inhibitor, Darapladib, increases lipid-peroxidation damage in the parasite and disrupts transport of hemoglobin-containing vesicles to the food vacuole, causing parasite death. Furthermore, inhibition of PRDX6 synergistically reduces the survival of artemisinin-resistant parasites following co-treatment of parasite cultures with artemisinin and Darapladib. Thus, PRDX6 is a host-derived drug target for development of antimalarial drugs that could help overcome artemisinin resistance.
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Affiliation(s)
- Matthias Paulus Wagner
- Institut Pasteur, Université de Paris, Malaria Parasite Biology and Vaccines Unit, Paris, France
| | - Pauline Formaglio
- Institut Pasteur, Université de Paris, Malaria Infection and Immunity Unit, Paris, France
| | - Olivier Gorgette
- Institut Pasteur, Department of Cell Biology and Infection, Centre for Innovation and Technological Research, Ultrastructural Bioimaging Unit, Paris, France
| | - Jerzy Michal Dziekan
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Christèle Huon
- Institut Pasteur, Université de Paris, Malaria Parasite Biology and Vaccines Unit, Paris, France
| | - Isabell Berneburg
- Biochemistry and Molecular Biology, Interdisciplinary Research Centre, Justus Liebig University Giessen, Giessen, Germany
| | - Stefan Rahlfs
- Biochemistry and Molecular Biology, Interdisciplinary Research Centre, Justus Liebig University Giessen, Giessen, Germany
| | - Jean-Christophe Barale
- Institut Pasteur, Université de Paris, CNRS UMR 3528, Structural Microbiology Unit, Paris, France; Institut Pasteur, Pasteur International Unit, Pasteur International Network, Malaria Translational Research Unit, Phnom Penh, Cambodia and Paris, France
| | | | - Aron B Fisher
- Peroxitech, Inc., Philadelphia, PA, USA; Institute for Environmental Medicine, Department of Physiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Didier Ménard
- Institut Pasteur, Université de Paris, INSERM U1201, Malaria Genetics and Resistance Unit, Paris, France; Dynamics of Host-Pathogen Interactions, EA 7292, IPPTS, Strasbourg University, Strasbourg, France
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Rogerio Amino
- Institut Pasteur, Université de Paris, Malaria Infection and Immunity Unit, Paris, France
| | - Lhousseine Touqui
- Cystic Fibrosis, Physiopathology and Phenogenomics, INSERM Unit 938, Saint-Antoine, Paris, France; Institut Pasteur, Université de Paris, Laboratory of Cystic Fibrosis and Chronic Bronchopathies, Paris, France
| | - Chetan E Chitnis
- Institut Pasteur, Université de Paris, Malaria Parasite Biology and Vaccines Unit, Paris, France.
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Gedgaudas M, Baronas D, Kazlauskas E, Petrauskas V, Matulis D. Thermott: a comprehensive online tool for protein–ligand binding constant determination. Drug Discov Today 2022; 27:2076-2079. [DOI: 10.1016/j.drudis.2022.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/17/2022] [Accepted: 05/10/2022] [Indexed: 11/28/2022]
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48
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Beta and Gamma Amino Acid-Substituted Benzenesulfonamides as Inhibitors of Human Carbonic Anhydrases. Pharmaceuticals (Basel) 2022; 15:ph15040477. [PMID: 35455474 PMCID: PMC9033141 DOI: 10.3390/ph15040477] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/24/2022] [Accepted: 04/07/2022] [Indexed: 02/06/2023] Open
Abstract
A series of novel benzenesulfonamide derivatives were synthesized bearing para-N β,γ-amino acid or para-N β-amino acid and thiazole moieties and their binding to the human carbonic anhydrase (CA) isozymes determined. These enzymes are involved in various illnesses, such as glaucoma, altitude sickness, epilepsy, obesity, and even cancer. There are numerous compounds that are inhibitors of CA and used as pharmaceuticals. However, most of them bind to most CA isozymes with little selectivity. The design of high affinity and selectivity towards one CA isozyme remains a significant challenge. The beta and gamma amino acid-substituted compound affinities were determined by the fluorescent thermal shift assay and isothermal titration calorimetry for all 12 catalytically active human carbonic anhydrase isozymes, showing the full affinity and selectivity profile. The structures of several compounds were determined by X-ray crystallography, and the binding mode in the active site of CA enzyme was shown.
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49
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Bril’kov MS, Dobrovolska O, Ødegård-Fougner Ø, Turcu DC, Strømland Ø, Underhaug J, Aasland R, Halskau Ø. Binding Specificity of ASHH2 CW Domain Toward H3K4me1 Ligand Is Coupled to Its Structural Stability Through Its α1-Helix. Front Mol Biosci 2022; 9:763750. [PMID: 35495628 PMCID: PMC9043364 DOI: 10.3389/fmolb.2022.763750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 02/25/2022] [Indexed: 11/14/2022] Open
Abstract
The CW domain binds to histone tail modifications found in different protein families involved in epigenetic regulation and chromatin remodeling. CW domains recognize the methylation state of the fourth lysine on histone 3 and could, therefore, be viewed as a reader of epigenetic information. The specificity toward different methylation states such as me1, me2, or me3 depends on the particular CW subtype. For example, the CW domain of ASHH2 methyltransferase binds preferentially to H3K4me1, and MORC3 binds to both H3K4me2 and me3 modifications, while ZCWPW1 is more specific to H3K4me3. The structural basis for these preferential bindings is not well understood, and recent research suggests that a more complete picture will emerge if dynamical and energetic assessments are included in the analysis of interactions. This study uses fold assessment by NMR in combination with mutagenesis, ITC affinity measurements, and thermal denaturation studies to investigate possible couplings between ASHH2 CW selectivity toward H3K4me1 and the stabilization of the domain and loops implicated in binding. The key elements of the binding site—the two tryptophans and the α1-helix form and maintain the binding pocket— were perturbed by mutagenesis and investigated. Results show that the α1-helix maintains the overall stability of the fold via the I915 and L919 residues and that the correct binding consolidates the loops designated as η1 and η3, as well as the C-terminal. This consolidation is incomplete for H3K4me3 binding to CW, which experiences a decrease in overall thermal stability on binding. Loop mutations not directly involved in the binding site, nonetheless, affect the equilibrium positions of the key residues.
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Affiliation(s)
- Maxim S. Bril’kov
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- Department of Pharmacy, University of Tromsø, Tromsø, Norway
| | - Olena Dobrovolska
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Øyvind Ødegård-Fougner
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- Department of Molecular Cell Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo, Norway
| | - Diana C. Turcu
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | | | - Jarl Underhaug
- Department of Chemistry, University of Bergen, Bergen, Norway
| | - Rein Aasland
- Department of Biosciences, University of Oslo, Oslo, Norway
- *Correspondence: Rein Aasland, ; Øyvind Halskau,
| | - Øyvind Halskau
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- *Correspondence: Rein Aasland, ; Øyvind Halskau,
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Thomas PW, Cho EJ, Bethel CR, Smisek T, Ahn YC, Schroeder JM, Thomas CA, Dalby KN, Beckham JT, Crowder MW, Bonomo RA, Fast W. Discovery of an Effective Small-Molecule Allosteric Inhibitor of New Delhi Metallo-β-lactamase (NDM). ACS Infect Dis 2022; 8:811-824. [PMID: 35353502 DOI: 10.1021/acsinfecdis.1c00577] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
To identify novel inhibitors of the carbapenemase New Delhi metallo-β-lactamase (NDM) as possible therapeutic compounds, we conducted a high-throughput screen of a 43,358-compound library. One of these compounds, a 2-quinazolinone linked through a diacylhydrazine to a phenyl ring (QDP-1) (IC50 = 7.9 ± 0.5 μM), was characterized as a slow-binding reversible inhibitor (Kiapp = 4 ± 2 μM) with a noncompetitive mode of inhibition in which substrate and inhibitor enhance each other's binding affinity. These studies, along with differential scanning fluorimetry, zinc quantitation, and selectivity studies, support an allosteric mechanism of inhibition. Cotreatment with QDP-1 effectively lowers minimum inhibitory concentrations of carbapenems for a panel of resistant Escherichia coli and Klebsiella pneumoniae clinical isolates expressing NDM-1 but not for those expressing only serine carbapenemases. QDP-1 represents a novel allosteric approach for NDM drug development for potential use alone or with other NDM inhibitors to counter carbapenem resistance in enterobacterales.
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Affiliation(s)
- Pei W. Thomas
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Eun Jeong Cho
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
- Targeted Therapeutic Drug Discovery and Development Program, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Christopher R. Bethel
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States
| | - Thomas Smisek
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Yeong-Chan Ahn
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - John M. Schroeder
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Caitlyn A. Thomas
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Kevin N. Dalby
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
- Targeted Therapeutic Drug Discovery and Development Program, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Josh T. Beckham
- Texas Institute for Discovery Education in Science, University of Texas, Austin, Texas 78712, United States
| | - Michael W. Crowder
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Robert A. Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
- Departments of Pharmacology, Molecular Biology & Microbiology, and Proteomics & Bioinformatics, Case Western Reserve University, Cleveland, Ohio 44106, United States
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio 44106, United States
| | - Walter Fast
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
- LaMontagne Center for Infectious Disease, University of Texas, Austin, Texas 78712, United States
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