1
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Giroud M, Kuhn B, Haap W. Drug Discovery Efforts to Identify Novel Treatments for Neglected Tropical Diseases - Cysteine Protease Inhibitors. Curr Med Chem 2024; 31:2170-2194. [PMID: 37916489 DOI: 10.2174/0109298673249097231017051733] [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: 02/14/2023] [Revised: 06/19/2023] [Accepted: 09/14/2023] [Indexed: 11/03/2023]
Abstract
BACKGROUND Neglected tropical diseases are a severe burden for mankind, affecting an increasing number of people around the globe. Many of those diseases are caused by protozoan parasites in which cysteine proteases play a key role in the parasite's pathogenesis. OBJECTIVE In this review article, we summarize the drug discovery efforts of the research community from 2017 - 2022 with a special focus on the optimization of small molecule cysteine protease inhibitors in terms of selectivity profiles or drug-like properties as well as in vivo studies. The cysteine proteases evaluated by this methodology include Cathepsin B1 from Schistosoma mansoni, papain, cruzain, falcipain, and rhodesain. METHODS Exhaustive literature searches were performed using the keywords "Cysteine Proteases" and "Neglected Tropical Diseases" including the years 2017 - 2022. Overall, approximately 3'000 scientific papers were retrieved, which were filtered using specific keywords enabling the focus on drug discovery efforts. RESULTS AND CONCLUSION Potent and selective cysteine protease inhibitors to treat neglected tropical diseases were identified, which progressed to pharmacokinetic and in vivo efficacy studies. As far as the authors are aware of, none of those inhibitors reached the stage of active clinical development. Either the inhibitor's potency or pharmacokinetic properties or safety profile or a combination thereof prevented further development of the compounds. More efforts with particular emphasis on optimizing pharmacokinetic and safety properties are needed, potentially by collaborations of academic and industrial research groups with complementary expertise. Furthermore, new warheads reacting with the catalytic cysteine should be exploited to advance the research field in order to make a meaningful impact on society.
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Affiliation(s)
- Maude Giroud
- Pharma Research and Early Development pRED, Roche Innovation Center Basel, Medicinal Chemistry, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, Basel, CH-4070, Switzerland
| | - Bernd Kuhn
- Pharma Research and Early Development pRED, Roche Innovation Center Basel, Medicinal Chemistry, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, Basel, CH-4070, Switzerland
| | - Wolfgang Haap
- Pharma Research and Early Development pRED, Roche Innovation Center Basel, Medicinal Chemistry, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, Basel, CH-4070, Switzerland
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2
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Rahmaninejad H, Pace T, Chun BJ, Kekenes-Huskey PM. Crowding within synaptic junctions influences the degradation of nucleotides by CD39 and CD73 ectonucleotidases. Biophys J 2022; 121:309-318. [PMID: 34922916 PMCID: PMC8790186 DOI: 10.1016/j.bpj.2021.12.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 11/01/2021] [Accepted: 12/07/2021] [Indexed: 01/21/2023] Open
Abstract
Synapsed cells can communicate using exocytosed nucleotides like adenosine triphosphate (ATP). Ectonucleotidases localized to synaptic junctions degrade nucleotides into metabolites like adenosine monophosphate (AMP) or adenosine. Oftentimes nucleotide degradation occurs in a sequential manner, of which ATP degradation by CD39 and CD73 is a representative example. Here, CD39 first converts ATP and adenosine diphosphate (ADP) into AMP, after which AMP is dephosphorylated into adenosine by CD73. Hence, the concerted activity of CD39 and CD73 can help shape cellular responses to extracellular ATP. In a previous study, we demonstrated that coupled CD39 and CD73 activity within synapse-like junctions is strongly controlled by the enzymes' co-localization, their surface charge densities, and the electrostatic potential of the surrounding cell membranes. In this study, we demonstrate that crowders within synaptic junctions, which can include globular proteins like cytokines and membrane-bound proteins, impact coupled CD39 and CD73 ectonucleotidase activity and, in turn, the availability of intrasynapse ATP. Specifically, we developed a spatially explicit, reaction-diffusion model for the coupled conversion of ATP → AMP and AMP → adenosine in a model synaptic junction with crowders that is solved via the finite element method. Our modeling results suggest that the association rate for ATP to CD39 is strongly influenced by the density of intrasynaptic protein crowders, as increasing crowder density generally suppressed ATP association kinetics. Much of this suppression can be rationalized based on a loss of configurational entropy. The surface charges of crowders can further influence the association rate, with the surprising result that favorable crowder-nucleotide electrostatic interactions can yield CD39 association rates that are faster than crowder-free configurations. However, attractive crowder-nucleotide interactions decrease the rate and efficiency of adenosine production, which in turn increases the availability of ATP and AMP within the synapse relative to crowder-free configurations. These findings highlight how CD39 and CD73 ectonucleotidase activity, electrostatics, and crowding within synapses influence the availability of nucleotides for intercellular communication.
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Affiliation(s)
- Hadi Rahmaninejad
- Department of Physics, Virginia Tech, Blacksburg,Corresponding author
| | - Tom Pace
- Department of Cell & Molecular Physiology, Loyola University Chicago, Chicago,Corresponding author
| | - Byeong Jae Chun
- Department of Cell & Molecular Physiology, Loyola University Chicago, Chicago
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3
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Kondrat S, von Lieres E. Mechanisms and Effects of Substrate Channelling in Enzymatic Cascades. Methods Mol Biol 2022; 2487:27-50. [PMID: 35687228 DOI: 10.1007/978-1-0716-2269-8_3] [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] [Indexed: 06/15/2023]
Abstract
Substrate or metabolite channelling is a transfer of intermediates produced by one enzyme to the sequential enzyme of a reaction cascade or metabolic pathway, without releasing them entirely into bulk. Despite an enormous effort and more than three decades of research, substrate channelling remains the subject of continuing debates and active investigation. Herein, we review the benefits and mechanisms of substrate channelling in vivo and in vitro. We discuss critically the effects that substrate channelling can have on enzymatic cascades, including speeding up or slowing down reaction cascades and protecting intermediates from sequestration and enzymes' surroundings from toxic or otherwise detrimental intermediates. We also discuss how macromolecular crowding affects substrate channelling and point out the galore of open questions.
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Affiliation(s)
- Svyatoslav Kondrat
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland.
- Max-Planck-Institut für Intelligente Systeme, Stuttgart, Germany.
- IV. Institut für Theoretische Physik, Universität Stuttgart, Stuttgart, Germany.
| | - Eric von Lieres
- Forschungszentrum Jülich, IBG-1: Biotechnology, Jülich, Germany
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4
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Mhashal AR, Major DT. Temperature-Dependent Kinetic Isotope Effects in R67 Dihydrofolate Reductase from Path-Integral Simulations. J Phys Chem B 2021; 125:1369-1377. [PMID: 33522797 PMCID: PMC7883348 DOI: 10.1021/acs.jpcb.0c10318] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/05/2021] [Indexed: 11/28/2022]
Abstract
Calculation of temperature-dependent kinetic isotope effects (KIE) in enzymes presents a significant theoretical challenge. Additionally, it is not trivial to identify enzymes with available experimental accurate intrinsic KIEs in a range of temperatures. In the current work, we present a theoretical study of KIEs in the primitive R67 dihydrofolate reductase (DHFR) enzyme and compare with experimental work. The advantage of R67 DHFR is its significantly lower kinetic complexity compared to more evolved DHFR isoforms. We employ mass-perturbation-based path-integral simulations in conjunction with umbrella sampling and a hybrid quantum mechanics-molecular mechanics Hamiltonian. We obtain temperature-dependent KIEs in good agreement with experiments and ascribe the temperature-dependent KIEs primarily to zero-point energy effects. The active site in the primitive enzyme is found to be poorly preorganized, which allows excessive water access to the active site and results in loosely bound reacting ligands.
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Affiliation(s)
- Anil R. Mhashal
- Department of Chemistry and Institute
for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Dan Thomas Major
- Department of Chemistry and Institute
for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
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5
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Rahmaninejad H, Pace T, Bhatt S, Sun B, Kekenes-Huskey P. Co-localization and confinement of ecto-nucleotidases modulate extracellular adenosine nucleotide distributions. PLoS Comput Biol 2020; 16:e1007903. [PMID: 32584811 PMCID: PMC7316229 DOI: 10.1371/journal.pcbi.1007903] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 04/22/2020] [Indexed: 12/30/2022] Open
Abstract
Nucleotides comprise small molecules that perform critical signaling roles in biological systems. Adenosine-based nucleotides, including adenosine tri-, di-, and mono-phosphate, are controlled through their rapid degradation by diphosphohydrolases and ecto-nucleotidases (NDAs). The interplay between nucleotide signaling and degradation is especially important in synapses formed between cells, which create signaling 'nanodomains'. Within these 'nanodomains', charged nucleotides interact with densely-packed membranes and biomolecules. While the contributions of electrostatic and steric interactions within such nanodomains are known to shape diffusion-limited reaction rates, less is understood about how these factors control the kinetics of nucleotidase activity. To quantify these factors, we utilized reaction-diffusion numerical simulations of 1) adenosine triphosphate (ATP) hydrolysis into adenosine monophosphate (AMP) and 2) AMP into adenosine (Ado) via two representative nucleotidases, CD39 and CD73. We evaluate these sequentially-coupled reactions in nanodomain geometries representative of extracellular synapses, within which we localize the nucleotidases. With this model, we find that 1) nucleotidase confinement reduces reaction rates relative to an open (bulk) system, 2) the rates of AMP and ADO formation are accelerated by restricting the diffusion of substrates away from the enzymes, and 3) nucleotidase co-localization and the presence of complementary (positive) charges to ATP enhance reaction rates, though the impact of these contributions on nucleotide pools depends on the degree to which the membrane competes for substrates. As a result, these contributions integratively control the relative concentrations and distributions of ATP and its metabolites within the junctional space. Altogether, our studies suggest that CD39 and CD73 nucleotidase activity within junctional spaces can exploit their confinement and favorable electrostatic interactions to finely control nucleotide signaling.
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Affiliation(s)
- Hadi Rahmaninejad
- Department of Physics and Astronomy, University of Kentucky, Lexington, Kentucky, United States of America
| | - Tom Pace
- Department of Physics and Astronomy, University of Kentucky, Lexington, Kentucky, United States of America
| | - Shashank Bhatt
- Paul Laurence Dunbar High School, Lexington, Kentucky, United States of America
| | - Bin Sun
- Department of Chemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Peter Kekenes-Huskey
- Department of Cell & Molecular Physiology, Loyola University Chicago, Chicago, Illinois, United States of America
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6
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Sathyanarayanan N, Cannone G, Gakhar L, Katagihallimath N, Sowdhamini R, Ramaswamy S, Vinothkumar KR. Molecular basis for metabolite channeling in a ring opening enzyme of the phenylacetate degradation pathway. Nat Commun 2019; 10:4127. [PMID: 31511507 PMCID: PMC6739347 DOI: 10.1038/s41467-019-11931-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 08/13/2019] [Indexed: 02/06/2023] Open
Abstract
Substrate channeling is a mechanism for the internal transfer of hydrophobic, unstable or toxic intermediates from the active site of one enzyme to another. Such transfer has previously been described to be mediated by a hydrophobic tunnel, the use of electrostatic highways or pivoting and by conformational changes. The enzyme PaaZ is used by many bacteria to degrade environmental pollutants. PaaZ is a bifunctional enzyme that catalyzes the ring opening of oxepin-CoA and converts it to 3-oxo-5,6-dehydrosuberyl-CoA. Here we report the structures of PaaZ determined by electron cryomicroscopy with and without bound ligands. The structures reveal that three domain-swapped dimers of the enzyme form a trilobed structure. A combination of small-angle X-ray scattering (SAXS), computational studies, mutagenesis and microbial growth experiments suggests that the key intermediate is transferred from one active site to the other by a mechanism of electrostatic pivoting of the CoA moiety, mediated by a set of conserved positively charged residues.
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Affiliation(s)
- Nitish Sathyanarayanan
- Institute for Stem Cell Science and Regenerative Medicine, GKVK Campus, Bellary Road, Bangalore, India
- Institute of Trans-Disciplinary Health Sciences and Technology (TDU), Bangalore, India
| | - Giuseppe Cannone
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
| | - Lokesh Gakhar
- Protein Crystallography Facility and Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Nainesh Katagihallimath
- Institute for Stem Cell Science and Regenerative Medicine, GKVK Campus, Bellary Road, Bangalore, India
- Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences TIFR, GKVK Campus, Bellary Road, Bangalore, India
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences TIFR, GKVK Campus, Bellary Road, Bangalore, India
| | - Subramanian Ramaswamy
- Institute for Stem Cell Science and Regenerative Medicine, GKVK Campus, Bellary Road, Bangalore, India.
| | - Kutti R Vinothkumar
- National Centre for Biological Sciences TIFR, GKVK Campus, Bellary Road, Bangalore, India.
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7
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Kuzmak A, Carmali S, von Lieres E, Russell AJ, Kondrat S. Can enzyme proximity accelerate cascade reactions? Sci Rep 2019; 9:455. [PMID: 30679600 PMCID: PMC6345930 DOI: 10.1038/s41598-018-37034-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 11/26/2018] [Indexed: 01/23/2023] Open
Abstract
The last decade has seen an exponential expansion of interest in conjugating multiple enzymes of cascades in close proximity to each other, with the overarching goal being to accelerate the overall reaction rate. However, some evidence has emerged that there is no effect of proximity channeling on the reaction velocity of the popular GOx-HRP cascade, particularly in the presence of a competing enzyme (catalase). Herein, we rationalize these experimental results quantitatively. We show that, in general, proximity channeling can enhance reaction velocity in the presence of competing enzymes, but in steady state a significant enhancement can only be achieved for diffusion-limited reactions or at high concentrations of competing enzymes. We provide simple equations to estimate the effect of channeling quantitatively and demonstrate that proximity can have a more pronounced effect under crowding conditions in vivo, particularly that crowding can enhance the overall rates of channeled cascade reactions.
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Affiliation(s)
- Andrij Kuzmak
- Department for Theoretical Physics, I. Franko National University of Lviv, Lviv, Ukraine
| | - Sheiliza Carmali
- Department of Chemistry, Aarhus University, 8000, Aarhus C, Denmark.,Center for Polymer-Based Protein Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA, 15213, USA
| | - Eric von Lieres
- Forschungszentrum Jülich, IBG-1: Biotechnology, 52425, Jülich, Germany
| | - Alan J Russell
- Center for Polymer-Based Protein Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA, 15213, USA.,Department of Chemical Engineering, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | - Svyatoslav Kondrat
- Forschungszentrum Jülich, IBG-1: Biotechnology, 52425, Jülich, Germany. .,Department of Complex Systems, Institute of Physical Chemistry, Warsaw, Poland.
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8
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Chen W, Yao X, Huang Z, Mao F, Guan L, Tang Y, Jiang H, Li J, Huang J, Jiang L, Zhu J. Novel dual inhibitors against FP-2 and PfDHFR as potential antimalarial agents: Design, synthesis and biological evaluation. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2017.11.041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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9
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Eun C. Effect of surface curvature on diffusion-limited reactions on a curved surface. J Chem Phys 2018; 147:184112. [PMID: 29141428 DOI: 10.1063/1.5005038] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
To investigate how the curvature of a reactive surface can affect reaction kinetics, we use a simple model in which a diffusion-limited bimolecular reaction occurs on a curved surface that is hollowed inward, flat, or extended outward while keeping the reactive area on the surface constant. By numerically solving the diffusion equation for this model using the finite element method, we find that the rate constant is a non-linear function of the surface curvature and that there is an optimal curvature providing the maximum value of the rate constant, which indicates that a spherical reactant whose entire surface is reactive (a uniformly reactive sphere) is not the most reactive species for a given reactive surface area. We discuss how this result arises from the interplay between two opposing effects: the exposedness of the reactive area to its partner reactants, which causes the rate constant to increase as the curvature increases, and the competition occurring on the reactive surface, which decreases the rate constant. This study helps us to understand the role of curvature in surface reactions and allows us to rationally design reactants that provide a high reaction rate.
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Affiliation(s)
- Changsun Eun
- Department of Chemistry, Hankuk University of Foreign Studies, Yongin 17035, South Korea
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10
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Corral MG, Haywood J, Stehl LH, Stubbs KA, Murcha MW, Mylne JS. Targeting plant DIHYDROFOLATE REDUCTASE with antifolates and mechanisms for genetic resistance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:727-742. [PMID: 29876984 DOI: 10.1111/tpj.13983] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/16/2018] [Accepted: 05/21/2018] [Indexed: 06/08/2023]
Abstract
The folate biosynthetic pathway and its key enzyme dihydrofolate reductase (DHFR) is a popular target for drug development due to its essential role in the synthesis of DNA precursors and some amino acids. Despite its importance, little is known about plant DHFRs, which, like the enzymes from the malarial parasite Plasmodium, are bifunctional, possessing DHFR and thymidylate synthase (TS) domains. Here using genetic knockout lines we confirmed that either DHFR-TS1 or DHFR-TS2 (but not DHFR-TS3) was essential for seed development. Screening mutated Arabidopsis thaliana seeds for resistance to antimalarial DHFR-inhibitor drugs pyrimethamine and cycloguanil identified causal lesions in DHFR-TS1 and DHFR-TS2, respectively, near the predicted substrate-binding site. The different drug resistance profiles for the plants, enabled by the G137D mutation in DHFR-TS1 and the A71V mutation in DHFR-TS2, were consistent with biochemical studies using recombinant proteins and could be explained by structural models. These findings provide a great improvement in our understanding of plant DHFR-TS and suggest how plant-specific inhibitors might be developed, as DHFR is not currently targeted by commercial herbicides.
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Affiliation(s)
- Maxime G Corral
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Joel Haywood
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Luca H Stehl
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
- Faculty of Biology, The University of Freiburg, Schaenzlestrasse 1, Freiburg, 79104, Germany
| | - Keith A Stubbs
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Monika W Murcha
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Joshua S Mylne
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
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11
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Chen W, Huang Z, Wang W, Mao F, Guan L, Tang Y, Jiang H, Li J, Huang J, Jiang L, Zhu J. Discovery of new antimalarial agents: Second-generation dual inhibitors against FP-2 and PfDHFR via fragments assembely. Bioorg Med Chem 2017; 25:6467-6478. [DOI: 10.1016/j.bmc.2017.10.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 10/07/2017] [Accepted: 10/16/2017] [Indexed: 02/02/2023]
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12
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Poshyvailo L, von Lieres E, Kondrat S. Does metabolite channeling accelerate enzyme-catalyzed cascade reactions? PLoS One 2017; 12:e0172673. [PMID: 28234973 PMCID: PMC5325314 DOI: 10.1371/journal.pone.0172673] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 02/08/2017] [Indexed: 12/30/2022] Open
Abstract
Metabolite or substrate channeling is a direct transfer of metabolites from one enzyme to the next enzyme in a cascade. Among many potential advantages of substrate channeling, acceleration of the total reaction rate is considered as one of the most important and self-evident. However, using a simple model, supported by stochastic simulations, we show that it is not always the case; particularly at long times (i.e. in steady state) and high substrate concentrations, a channeled reaction cannot be faster, and can even be slower, than the original non-channeled cascade reaction. In addition we show that increasing the degree of channeling may lead to an increase of the metabolite pool size. We substantiate that the main advantage of channeling likely lies in protecting metabolites from degradation or competing side reactions.
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Affiliation(s)
- Liubov Poshyvailo
- Forschungszentrum Jülich, IBG-1: Biotechnology, Jülich, Germany
- Forschungszentrum Jülich, IEK-7: Institute of Energy and Climate Research, Jülich, Germany
| | - Eric von Lieres
- Forschungszentrum Jülich, IBG-1: Biotechnology, Jülich, Germany
| | - Svyatoslav Kondrat
- Forschungszentrum Jülich, IBG-1: Biotechnology, Jülich, Germany
- * E-mail: ,
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13
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Tang Z, Roberts CC, Chang CEA. Understanding ligand-receptor non-covalent binding kinetics using molecular modeling. FRONT BIOSCI-LANDMRK 2017; 22:960-981. [PMID: 27814657 PMCID: PMC5470370 DOI: 10.2741/4527] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Kinetic properties may serve as critical differentiators and predictors of drug efficacy and safety, in addition to the traditionally focused binding affinity. However the quantitative structure-kinetics relationship (QSKR) for modeling and ligand design is still poorly understood. This review provides an introduction to the kinetics of drug binding from a fundamental chemistry perspective. We focus on recent developments of computational tools and their applications to non-covalent binding kinetics.
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Affiliation(s)
- Zhiye Tang
- Department of Chemistry, University of California, Riverside, CA 92521
| | | | - Chia-En A Chang
- Department of Chemistry, University of California, Riverside, CA 92521,
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14
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Marques SM, Daniel L, Buryska T, Prokop Z, Brezovsky J, Damborsky J. Enzyme Tunnels and Gates As Relevant Targets in Drug Design. Med Res Rev 2016; 37:1095-1139. [PMID: 27957758 DOI: 10.1002/med.21430] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/11/2016] [Accepted: 11/07/2016] [Indexed: 12/28/2022]
Abstract
Many enzymes contain tunnels and gates that are essential to their function. Gates reversibly switch between open and closed conformations and thereby control the traffic of small molecules-substrates, products, ions, and solvent molecules-into and out of the enzyme's structure via molecular tunnels. Many transient tunnels and gates undoubtedly remain to be identified, and their functional roles and utility as potential drug targets have received comparatively little attention. Here, we describe a set of general concepts relating to the structural properties, function, and classification of these interesting structural features. In addition, we highlight the potential of enzyme tunnels and gates as targets for the binding of small molecules. The different types of binding that are possible and the potential pharmacological benefits of such targeting are discussed. Twelve examples of ligands bound to the tunnels and/or gates of clinically relevant enzymes are used to illustrate the different binding modes and to explain some new strategies for drug design. Such strategies could potentially help to overcome some of the problems facing medicinal chemists and lead to the discovery of more effective drugs.
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Affiliation(s)
- Sergio M Marques
- Loschmidt Laboratories, Faculty of Science, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, RECETOX, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Lukas Daniel
- Loschmidt Laboratories, Faculty of Science, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, RECETOX, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic
| | - Tomas Buryska
- Loschmidt Laboratories, Faculty of Science, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, RECETOX, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Faculty of Science, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, RECETOX, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic
| | - Jan Brezovsky
- Loschmidt Laboratories, Faculty of Science, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, RECETOX, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Faculty of Science, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, RECETOX, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic
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15
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Kekenes-Huskey PM, Scott CE, Atalay S. Quantifying the Influence of the Crowded Cytoplasm on Small Molecule Diffusion. J Phys Chem B 2016; 120:8696-706. [PMID: 27327486 DOI: 10.1021/acs.jpcb.6b03887] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cytosolic crowding can influence the thermodynamics and kinetics of in vivo chemical reactions. Most significantly, proteins and nucleic acid crowders reduce the accessible volume fraction, ϕ, available to a diffusing substrate, thereby reducing its effective diffusion rate, Deff, relative to its rate in bulk solution. However, Deff can be further hindered or even enhanced, when long-range crowder/diffuser interactions are significant. To probe these effects, we numerically estimated Deff values for small, charged molecules in representative, cytosolic protein lattices up to 0.1 × 0.1 × 0.1 μm(3) in volume via the homogenized Smoluchowski electro-diffusion equation. We further validated our predictions against Deff estimates from ϕ-dependent analytical relationships, such as the Maxwell-Garnett (MG) bound, as well as explicit solutions of the time-dependent electro-diffusion equation. We find that in typical, moderately crowded cell cytoplasm (ϕ ≈ 0.8), Deff is primarily determined by ϕ; in other words, diverse protein shapes and heterogeneous distributions only modestly impact Deff. However, electrostatic interactions between diffusers and crowders, particularly at low electrolyte ionic strengths, can substantially modulate Deff. These findings help delineate the extent that cytoplasmic crowders influence small molecule diffusion, which ultimately may shape the efficiency and timing of intracellular signaling pathways. More generally, the quantitative agreement between computationally expensive solutions of the time-dependent electro-diffusion equation and its comparatively cheaper homogenized form suggest that the latter is a broadly effective model for diffusion in wide-ranging, crowded biological media.
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Affiliation(s)
- Peter M Kekenes-Huskey
- Department of Chemistry, University of Kentucky , Lexington, Kentucky 40506, United States
| | - Caitlin E Scott
- Department of Chemistry, University of Kentucky , Lexington, Kentucky 40506, United States
| | - Selcuk Atalay
- Department of Chemistry, University of Kentucky , Lexington, Kentucky 40506, United States
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16
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Kekenes-Huskey PM, Eun C, McCammon JA. Enzyme localization, crowding, and buffers collectively modulate diffusion-influenced signal transduction: Insights from continuum diffusion modeling. J Chem Phys 2016; 143:094103. [PMID: 26342355 DOI: 10.1063/1.4929528] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Biochemical reaction networks consisting of coupled enzymes connect substrate signaling events with biological function. Substrates involved in these reactions can be strongly influenced by diffusion "barriers" arising from impenetrable cellular structures and macromolecules, as well as interactions with biomolecules, especially within crowded environments. For diffusion-influenced reactions, the spatial organization of diffusion barriers arising from intracellular structures, non-specific crowders, and specific-binders (buffers) strongly controls the temporal and spatial reaction kinetics. In this study, we use two prototypical biochemical reactions, a Goodwin oscillator, and a reaction with a periodic source/sink term to examine how a diffusion barrier that partitions substrates controls reaction behavior. Namely, we examine how conditions representative of a densely packed cytosol, including reduced accessible volume fraction, non-specific interactions, and buffers, impede diffusion over nanometer length-scales. We find that diffusion barriers can modulate the frequencies and amplitudes of coupled diffusion-influenced reaction networks, as well as give rise to "compartments" of decoupled reactant populations. These effects appear to be intensified in the presence of buffers localized to the diffusion barrier. These findings have strong implications for the role of the cellular environment in tuning the dynamics of signaling pathways.
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Affiliation(s)
| | - Changsun Eun
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, California 92093-0365, USA
| | - J A McCammon
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, California 92093-0365, USA
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17
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Abstract
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Electrostatic effects
are ubiquitous in protein interactions and
are found to be pervasive in the complement system as well. The interaction
between complement fragment C3d and complement receptor 2 (CR2) has
evolved to become a link between innate and adaptive immunity. Electrostatic
interactions have been suggested to be the driving factor for the
association of the C3d:CR2 complex. In this study, we investigate
the effects of ionic strength and mutagenesis on the association of
C3d:CR2 through Brownian dynamics simulations. We demonstrate that
the formation of the C3d:CR2 complex is ionic strength-dependent,
suggesting the presence of long-range electrostatic steering that
accelerates the complex formation. Electrostatic steering occurs through
the interaction of an acidic surface patch in C3d and the positively
charged CR2 and is supported by the effects of mutations within the
acidic patch of C3d that slow or diminish association. Our data are
in agreement with previous experimental mutagenesis and binding studies
and computational studies. Although the C3d acidic patch may be locally
destabilizing because of unfavorable Coulombic interactions of like
charges, it contributes to the acceleration of association. Therefore,
acceleration of function through electrostatic steering takes precedence
to stability. The site of interaction between C3d and CR2 has been
the target for delivery of CR2-bound nanoparticle, antibody, and small
molecule biomarkers, as well as potential therapeutics. A detailed
knowledge of the physicochemical basis of C3d:CR2 association may
be necessary to accelerate biomarker and drug discovery efforts.
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Affiliation(s)
- Rohith R Mohan
- Department of Bioengineering, University of California , Riverside, California 92521, United States
| | - Gary A Huber
- Department of Chemistry and Biochemistry, University of California , San Diego, California 92093, United States
| | - Dimitrios Morikis
- Department of Bioengineering, University of California , Riverside, California 92521, United States
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18
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Garg D, Skouloubris S, Briffotaux J, Myllykallio H, Wade RC. Conservation and Role of Electrostatics in Thymidylate Synthase. Sci Rep 2015; 5:17356. [PMID: 26612036 PMCID: PMC4661567 DOI: 10.1038/srep17356] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 10/28/2015] [Indexed: 11/17/2022] Open
Abstract
Conservation of function across families of orthologous enzymes is generally accompanied by conservation of their active site electrostatic potentials. To study the electrostatic conservation in the highly conserved essential enzyme, thymidylate synthase (TS), we conducted a systematic species-based comparison of the electrostatic potential in the vicinity of its active site. Whereas the electrostatics of the active site of TS are generally well conserved, the TSs from minimal organisms do not conform to the overall trend. Since the genomes of minimal organisms have a high thymidine content compared to other organisms, the observation of non-conserved electrostatics was surprising. Analysis of the symbiotic relationship between minimal organisms and their hosts, and the genetic completeness of the thymidine synthesis pathway suggested that TS from the minimal organism Wigglesworthia glossinidia (W.g.b.) must be active. Four residues in the vicinity of the active site of Escherichia coli TS were mutated individually and simultaneously to mimic the electrostatics of W.g.b TS. The measured activities of the E. coli TS mutants imply that conservation of electrostatics in the region of the active site is important for the activity of TS, and suggest that the W.g.b. TS has the minimal activity necessary to support replication of its reduced genome.
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Affiliation(s)
- Divita Garg
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany.,Munich Center for Integrated Protein Science, Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Stephane Skouloubris
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS UMR7645, INSERM U1182, Université Paris-Saclay, 91128, Palaiseau, France.,Université Paris-Sud, 91405, Orsay, France
| | - Julien Briffotaux
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS UMR7645, INSERM U1182, Université Paris-Saclay, 91128, Palaiseau, France
| | - Hannu Myllykallio
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS UMR7645, INSERM U1182, Université Paris-Saclay, 91128, Palaiseau, France
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, 69120 Heidelberg, Germany.,Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Baden-Württemberg, Germany
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19
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Huang YMM, Huber G, McCammon JA. Electrostatic steering enhances the rate of cAMP binding to phosphodiesterase: Brownian dynamics modeling. Protein Sci 2015; 24:1884-9. [PMID: 26346301 DOI: 10.1002/pro.2794] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 08/20/2015] [Accepted: 08/24/2015] [Indexed: 01/18/2023]
Abstract
Signaling in cells often involves co-localization of the signaling molecules. Most experimental evidence has shown that intracellular compartmentalization restricts the range of action of the second messenger, 3'-5'-cyclic adenosine monophosphate (cAMP), which is degraded by phosphodiesterases (PDEs). The objective of this study is to understand the details of molecular encounter that may play a role in efficient operation of the cAMP signaling apparatus. The results from electrostatic potential calculations and Brownian dynamics simulations suggest that positive potential of the active site from PDE enhances capture of diffusing cAMP molecules. This electrostatic steering between cAMP and the active site of a PDE plays a major role in the enzyme-substrate encounter, an effect that may be of significance in sequestering cAMP released from a nearby binding site or in attracting more freely diffusing cAMP molecules.
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Affiliation(s)
- Yu-ming M Huang
- Department of Pharmacology, University of California, San Diego, La Jolla, California, 92093
| | - Gary Huber
- Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California, 92093
| | - J Andrew McCammon
- Department of Pharmacology, University of California, San Diego, La Jolla, California, 92093.,Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California, 92093.,Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, 92093
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20
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Wang N, McCammon JA. Substrate channeling between the human dihydrofolate reductase and thymidylate synthase. Protein Sci 2015; 25:79-86. [PMID: 26096018 DOI: 10.1002/pro.2720] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 06/02/2015] [Accepted: 06/05/2015] [Indexed: 12/17/2022]
Abstract
In vivo, as an advanced catalytic strategy, transient non-covalently bound multi-enzyme complexes can be formed to facilitate the relay of substrates, i. e. substrate channeling, between sequential enzymatic reactions and to enhance the throughput of multi-step enzymatic pathways. The human thymidylate synthase and dihydrofolate reductase catalyze two consecutive reactions in the folate metabolism pathway, and experiments have shown that they are very likely to bind in the same multi-enzyme complex in vivo. While reports on the protozoa thymidylate synthase-dihydrofolate reductase bifunctional enzyme give substantial evidences of substrate channeling along a surface "electrostatic highway," attention has not been paid to whether the human thymidylate synthase and dihydrofolate reductase, if they are in contact with each other in the multi-enzyme complex, are capable of substrate channeling employing surface electrostatics. This work utilizes protein-protein docking, electrostatics calculations, and Brownian dynamics to explore the existence and mechanism of the substrate channeling between the human thymidylate synthase and dihydrofolate reductase. The results show that the bound human thymidylate synthase and dihydrofolate reductase are capable of substrate channeling and the formation of the surface "electrostatic highway." The substrate channeling efficiency between the two can be reasonably high and comparable to that of the protozoa.
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Affiliation(s)
- Nuo Wang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, 92037
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, 92037.,Department of Pharmacology, University of California San Diego, La Jolla, California, 92037.,Howard Hughes Medical Institute, University of California San Diego, La Jolla, California, 92037
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