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Venturelli A, Guaitoli G, Vanossi D, Saitta F, Fessas D, Vitiello S, Malpezzi G, Aiello D, Ferrari S, Tondi D, Ponterini G, Paola Costi M. Intersite communication in dimeric enzymes highlighted by structural and thermodynamic analysis of didansyltyrosine binding to thymidylate synthases. Bioorg Chem 2024; 151:107663. [PMID: 39088977 DOI: 10.1016/j.bioorg.2024.107663] [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: 06/01/2024] [Revised: 07/17/2024] [Accepted: 07/18/2024] [Indexed: 08/03/2024]
Abstract
Intersite communication in dimeric enzymes, triggered by ligand binding, represents both a challenge and an opportunity in enzyme inhibition strategy. Though often understestimated, it can impact on the in vivo biological mechansim of an inhibitor and on its pharmacokinetics. Thymidylate synthase (TS) is a homodimeric enzyme present in almost all living organisms that plays a crucial role in DNA synthesis and cell replication. While its inhibition is a valid strategy in the therapy of several human cancers, designing specific inhibitors of bacterial TSs poses a challenge to the development of new anti-infective agents. N,O-didansyl-l-tyrosine (DDT) inhibits both Escherichia coli TS (EcTS) and Lactobacillus casei TS (LcTS). The available X-ray structure of the DDT:dUMP:EcTS ternary complex indicated an unexpected binding mode for DDT to EcTS, involving a rearrangement of the protein and addressing the matter of communication between the two active sites of an enzyme dimer. Combining molecular-level information on DDT binding to EcTS and LcTS extracted from structural and FRET-based fluorometric evidence with a thermodynamic characterization of these events obtained by fluorometric and calorimetric titrations, this study unveiled a negative cooperativity between the DDT bindings to the two monomers of each enzyme dimer. This result, complemented by the species-specific thermodynamic signatures of the binding events, implied that communication across the protein dimer was triggered by the first DDT binding. These findings could challenge the conventional understanding of TS inhibition and open the way for the development of novel TS inhibitors with a different mechanism of action and enhanced efficacy and specificity.
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Affiliation(s)
- Alberto Venturelli
- Dipartimento di Scienze della Vita, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Giambattista Guaitoli
- Dipartimento di Scienze della Vita, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy; Evotec SE, Biophysic - Essener Bogen 7, 22419 Hamburg, Germany
| | - Davide Vanossi
- Dipartimento di Scienze Chimiche e Geologiche, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Francesca Saitta
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, DeFENS, Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy
| | - Dimitrios Fessas
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, DeFENS, Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy
| | - Simone Vitiello
- Dipartimento di Scienze della Vita, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Giulia Malpezzi
- Dipartimento di Scienze della Vita, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy; Clinical and Experimental Medicine (CEM) PhD Program, University of Modena and Reggio Emilia, Via G. Campi 287, 41125 Modena, Italy
| | - Daniele Aiello
- Dipartimento di Scienze della Vita, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Stefania Ferrari
- Dipartimento di Scienze della Vita, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Donatella Tondi
- Dipartimento di Scienze della Vita, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Glauco Ponterini
- Dipartimento di Scienze della Vita, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy.
| | - Maria Paola Costi
- Dipartimento di Scienze della Vita, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy.
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Lee W. Mechanistic Insight into how β-Ketoacyl ACP Synthase I (KasA) Recognizes the Fatty Acid Chain Length of its Substrate. Chempluschem 2024; 89:e202300568. [PMID: 37983623 DOI: 10.1002/cplu.202300568] [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: 10/06/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 11/22/2023]
Abstract
β-ketoacyl ACP synthase I (KasA) has been considered as a promising drug target against Tuberculosis because it is known to play a pivotal role in the survival of Mycobacterium Tuberculosis, a causative agent of Tuberculosis. KasA catalyzes the reaction elongating only the acyl chain that is 16 carbon atoms in length or longer, but the molecular details of how KasA selectively recognizes only the substrate longer than a certain length still remain unknown. In the present study, this challenging subject is addressed, and to this end, molecular dynamics (MD) simulations and free energy calculations for actual substrate binding process are carried out. The results illustrate that the substrate specificity of KasA is highly linked to its cooperativity and this cooperativity is realized through the activation of catalytic residues. Through these results, the mechanistic details of how KasA can be selectively activated only by the substrate with a proper length are suggested.
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Affiliation(s)
- Wook Lee
- Department of Biochemistry, Kangwon National University, Chuncheon, 24341, Korea
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Arabpour Shiraz Z, Sohrabi N, Eslami Moghadam M, Oftadeh M. Spectroscopic study and molecular simulation: Bovine serum albumin binding with anticancer Pt complex of amyl dithiocarbamate ligand. Heliyon 2023; 9:e20090. [PMID: 37809783 PMCID: PMC10559868 DOI: 10.1016/j.heliyon.2023.e20090] [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: 06/04/2023] [Revised: 09/11/2023] [Accepted: 09/11/2023] [Indexed: 10/10/2023] Open
Abstract
Until now, many methods have been proposed to treat cancer, such as radiation therapy and drug therapy, but none of them have caused a complete cure for cancer. Heavy metal complexes such as cisplatin are among the compounds used as drugs in chemotherapy against cancer cells. These compounds cause cell death and have anti-cancer properties, but they have side effects. The biochemical mechanism of cisplatin is related to its interaction with DNA through covalent binding. To reduce the toxicity of metallodrugs, new complexes can be designed containing S, S- bidentate ligands such as diethyldithiocarbamate. Moreover, anti-cancer compounds probably interact with proteins, such as HSA, before passing the cancerous cell membrane and DNA as a target. So, the function of proteins and their stabilities are expected to change. In this research, the mode of binding of [Pt (bpy) (amyl.dtc)]NO3 complex with BSA was evaluated by various thermodynamic methods. Negative binding enthalpy and entropy changes amounts show that the connection between the Platinum compound and BSA occurs via the van Der Waals type of hydrogen bond. The negative Gibbs free energy change was obtained through isothermal titration, which showed interaction proceeds spontaneously. Moreover, the emission titration data showed that protein fluorescence quenching by platinum agent titration is static. Binding, quenching constants, and binding site number were obtained by the Stern-Volmer equation, and only one binding site was determined for this interaction. A Scatchard plot with a positive slope shows the Pt agent-BSA formation is proceeding positively cooperative. The kinetic study displayed that the absorption monitoring followed the second-order model. Finally, molecular docking simulation showed that the position of the Pt agent on protein is placed I under region II.
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Affiliation(s)
| | - Nasrin Sohrabi
- Chemistry Department, Payame Noor University, 19395-4697, Tehran, Iran
| | | | - Mohsen Oftadeh
- Chemistry Department, Payame Noor University, 19395-4697, Tehran, Iran
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4
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Arabpour Shiraz Z, Sohrabi N, Eslami Moghadam M, Oftadeh M. Molecular docking and spectroscopic study of bovine serum albumin interaction with new anticancer Pt complex with isopentyl dithiocarbamate ligand. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2023; 43:65-85. [PMID: 37452787 DOI: 10.1080/15257770.2023.2233576] [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: 04/13/2023] [Revised: 06/20/2023] [Accepted: 07/01/2023] [Indexed: 07/18/2023]
Abstract
Although cisplatin is useful in the treatment of cancer, it has a series of side effects that limit its use. Dithiocarbamates reduce the toxicity of platinum due to their structure and the presence of S, and N donating groups. In this article, the interaction of [Pt(bpy)(isopentyl.dtc)]NO3, where bpy is bipyridine and isopentyl.dtc is isopentyl-dithiocarbamate, with BSA, bovine serum albumin has been studied. The molecular binding method, including UV-Vis and fluorescence titration, was carried out in conditions including pH = 7.4 and temperatures of 27 and 37 °C. The negative values of enthalpy (ΔH°b) and entropy (ΔS°b) show that the driving forces of this interaction are hydrogen and van der Waals, and the negative value of the Gibbs free energy, ΔG°b indicates that the interaction proceeds spontaneously. The fluorescence results showed that the quenching mechanism is the static type and the Stern Volmer constant, KSV, was also obtained. The fluorescence titration method data displayed that the quenching mechanism is static. Binding constant (Kb), binding point (n), Hill coefficients, nH, Hill constant, KH, number of binding sites, g, BSA melting temperature, Tm, were also obtained. Finally, the molecular docking method result shows the binding constant, Ki and binding free energy for the platinum complex are -6.53 and 16.39 kcal mol-1, respectively, and also the proper position of binding on BSA can be considered the site I in the subdomain IIA.
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Affiliation(s)
| | - Nasrin Sohrabi
- Chemistry Department, Payame Noor University, Tehran, I. R. Iran
| | | | - Mohsen Oftadeh
- Chemistry Department, Payame Noor University, Tehran, I. R. Iran
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Bonin JP, Sapienza PJ, Lee AL. Dynamic allostery in substrate binding by human thymidylate synthase. eLife 2022; 11:79915. [PMID: 36200982 PMCID: PMC9536839 DOI: 10.7554/elife.79915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 08/31/2022] [Indexed: 11/25/2022] Open
Abstract
Human thymidylate synthase (hTS) is essential for DNA replication and therefore a therapeutic target for cancer. Effective targeting requires knowledge of the mechanism(s) of regulation of this 72 kDa homodimeric enzyme. Here, we investigate the mechanism of binding cooperativity of the nucleotide substrate. We have employed exquisitely sensitive methyl-based CPMG and CEST NMR experiments enabling us to identify residues undergoing bifurcated linear 3-state exchange, including concerted switching between active and inactive conformations in the apo enzyme. The inactive state is populated to only ~1.3%, indicating that conformational selection contributes negligibly to the cooperativity. Instead, methyl rotation axis order parameters, determined by 2H transverse relaxation rates, suggest that rigidification of the enzyme upon substrate binding is responsible for the entropically-driven cooperativity. Lack of the rigidification in product binding and substrate binding to an N-terminally truncated enzyme, both non-cooperative, support this idea. In addition, the lack of this rigidification in the N-terminal truncation indicates that interactions between the flexible N-terminus and the rest of the protein, which are perturbed by substrate binding, play a significant role in the cooperativity—a novel mechanism of dynamic allostery. Together, these findings yield a rare depth of insight into the substrate binding cooperativity of an essential enzyme.
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Affiliation(s)
- Jeffrey P Bonin
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina
| | - Paul J Sapienza
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina
| | - Andrew L Lee
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina
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Arabpour Shiraz Z, Sohrabi N, Eslami Moghadam M, Oftadeh M. Dynamic and Thermodynamic Investigation on the Interaction of Bovine Serum Albumin with an Anticancer Pt Complex Containing Dithiocarbamate Using Molecular Docking and Spectroscopic Methods. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2058027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
| | - Nasrin Sohrabi
- Chemistry Department, Payame Noor University (PNU), Tehran, Iran
| | | | - Mohsen Oftadeh
- Chemistry Department, Payame Noor University (PNU), Tehran, Iran
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Rajakumara E, Abhishek S, Nitin K, Saniya D, Bajaj P, Schwaneberg U, Davari MD. Structure and Cooperativity in Substrate-Enzyme Interactions: Perspectives on Enzyme Engineering and Inhibitor Design. ACS Chem Biol 2022; 17:266-280. [PMID: 35041385 DOI: 10.1021/acschembio.1c00500] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Enzyme-based synthetic chemistry provides a green way to synthesize industrially important chemical scaffolds and provides incomparable substrate specificity and unmatched stereo-, regio-, and chemoselective product formation. However, using biocatalysts at an industrial scale has its challenges, like their narrow substrate scope, limited stability in large-scale one-pot reactions, and low expression levels. These limitations can be overcome by engineering and fine-tuning these biocatalysts using advanced protein engineering methods. A detailed understanding of the enzyme structure and catalytic mechanism and its structure-function relationship, cooperativity in binding of substrates, and dynamics of substrate-enzyme-cofactor complexes is essential for rational enzyme engineering for a specific purpose. This Review covers all these aspects along with an in-depth categorization of various industrially and pharmaceutically crucial bisubstrate enzymes based on their reaction mechanisms and their active site and substrate/cofactor-binding site structures. As the bisubstrate enzymes constitute around 60% of the known industrially important enzymes, studying their mechanism of actions and structure-activity relationship gives significant insight into deciding the targets for protein engineering for developing industrial biocatalysts. Thus, this Review is focused on providing a comprehensive knowledge of the bisubstrate enzymes' structure, their mechanisms, and protein engineering approaches to develop them into industrial biocatalysts.
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Affiliation(s)
- Eerappa Rajakumara
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Suman Abhishek
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Kulhar Nitin
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Dubey Saniya
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Priyanka Bajaj
- National Institute of Pharmaceutical Education and Research (NIPER), NH-44, Balanagar, Hyderabad 500037, India
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074 Aachen, Germany
| | - Mehdi D. Davari
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
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8
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Falconer RJ, Schuur B, Mittermaier AK. Applications of isothermal titration calorimetry in pure and applied research from 2016 to 2020. J Mol Recognit 2021; 34:e2901. [PMID: 33975380 DOI: 10.1002/jmr.2901] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/02/2021] [Accepted: 04/26/2021] [Indexed: 02/06/2023]
Abstract
The last 5 years have seen a series of advances in the application of isothermal titration microcalorimetry (ITC) and interpretation of ITC data. ITC has played an invaluable role in understanding multiprotein complex formation including proteolysis-targeting chimeras (PROTACS), and mitochondrial autophagy receptor Nix interaction with LC3 and GABARAP. It has also helped elucidate complex allosteric communication in protein complexes like trp RNA-binding attenuation protein (TRAP) complex. Advances in kinetics analysis have enabled the calculation of kinetic rate constants from pre-existing ITC data sets. Diverse strategies have also been developed to study enzyme kinetics and enzyme-inhibitor interactions. ITC has also been applied to study small molecule solvent and solute interactions involved in extraction, separation, and purification applications including liquid-liquid separation and extractive distillation. Diverse applications of ITC have been developed from the analysis of protein instability at different temperatures, determination of enzyme kinetics in suspensions of living cells to the adsorption of uremic toxins from aqueous streams.
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Affiliation(s)
- Robert J Falconer
- School of Chemical Engineering & Advanced Materials, University of Adelaide, Adelaide, South Australia, Australia
| | - Boelo Schuur
- Faculty of Science and Technology, University of Twente, Enschede, Netherlands
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Bonin JP, Lee AL. Backbone and ILVM methyl resonance assignments of human thymidylate synthase in apo and substrate bound forms. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:197-202. [PMID: 33486616 PMCID: PMC7979492 DOI: 10.1007/s12104-021-10006-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/08/2021] [Indexed: 06/12/2023]
Abstract
Human thymidylate synthase (hTS) is a 72 kDa homodimeric enzyme responsible for the conversion of deoxyuridine monophosphate (dUMP) to deoxythymidine monophosphate (dTMP), making it the sole source of de novo dTMP in human cells. As a result, hTS is an attractive anti-cancer therapeutic target. Additionally, hTS is known to possess a number of interesting biophysical features, including adoption of active and inactive conformations, positively cooperative substrate binding, half-the-sites activity, and interacting with its own mRNA. The physical mechanisms underlying these properties, and how they may be leveraged to guide therapeutic development, are yet to be fully explored. Here, as a preface to detailed NMR characterization, we present backbone amide and ILVM methyl resonance assignments for hTS in apo and dUMP bound forms. In addition, we present backbone amide resonance assignments for hTS bound to a substrate analog and the native cofactor.
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Affiliation(s)
- Jeffrey P Bonin
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Andrew L Lee
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, USA.
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, USA.
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Byun JA, Akimoto M, VanSchouwen B, Lazarou TS, Taylor SS, Melacini G. Allosteric pluripotency as revealed by protein kinase A. SCIENCE ADVANCES 2020; 6:eabb1250. [PMID: 32596469 PMCID: PMC7304965 DOI: 10.1126/sciadv.abb1250] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 05/08/2020] [Indexed: 05/03/2023]
Abstract
The functional response of a signaling system to an allosteric stimulus often depends on subcellular conditions, a phenomenon known as pluripotent allostery. For example, a single allosteric modulator, Rp-cAMPS, of the prototypical protein kinase A (PKA) switches from antagonist to agonist depending on MgATP levels. However, the mechanism underlying such pluripotent allostery has remained elusive for decades. Using nuclear magnetic resonance spectroscopy, ensemble models, kinase assays, and molecular dynamics simulations, we show that allosteric pluripotency arises from surprisingly divergent responses of highly homologous tandem domains. The differential responses perturb domain-domain interactions and remodel the free-energy landscape of inhibitory excited states sampled by the regulatory subunit of PKA. The resulting activation threshold values are comparable to the effective free energy of regulatory and catalytic subunit binding, which depends on metabolites, substrates, and mutations, explaining pluripotent allostery and warranting a general redefinition of allosteric targets to include specific subcellular environments.
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Affiliation(s)
- J. A. Byun
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4M1, Canada
| | - M. Akimoto
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON L8S 4M1, Canada
| | - B. VanSchouwen
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON L8S 4M1, Canada
| | - T. S. Lazarou
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON L8S 4M1, Canada
| | - S. S. Taylor
- Departments of Chemistry and Biochemistry and Pharmacology, University of California San Diego, La Jolla, CA 92093, USA
| | - G. Melacini
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4M1, Canada
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON L8S 4M1, Canada
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Reviving Protein-Observed 19F Lineshape Analysis for Deep Insight into Protein-Ligand Binding Events. Biophys J 2020; 118:2333-2335. [DOI: 10.1016/j.bpj.2020.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 04/01/2020] [Indexed: 11/23/2022] Open
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