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Rabuffetti M, Rinaldi F, Lo Bianco A, Speranza G, Ubiali D, de Moraes MC, Rodrigues Pereira da Silva LC, Massolini G, Calleri E, Lavecchia A. Discovery of a Novel Inhibitor of Human Purine Nucleoside Phosphorylase by a Simple Hydrophilic Interaction Liquid Chromatography Enzymatic Assay. ChemMedChem 2021; 16:1325-1334. [PMID: 33405358 DOI: 10.1002/cmdc.202000874] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Indexed: 11/10/2022]
Abstract
Human purine nucleoside phosphorylase (HsPNP) belongs to the purine salvage pathway of nucleic acids. Genetic deficiency of this enzyme triggers apoptosis of activated T-cells due to the accumulation of deoxyguanosine triphosphate (dGTP). Therefore, potential chemotherapeutic applications of human PNP inhibitors include the treatment of T-cell leukemia, autoimmune diseases and transplant tissue rejection. In this report, we present the discovery of novel HsPNP inhibitors by coupling experimental and computational tools. A simple, inexpensive, direct and non-radioactive enzymatic assay coupled to hydrophilic interaction liquid chromatography and UV detection (LC-UV using HILIC as elution mode) was developed for screening HsPNP inhibitors. Enzymatic activity was assessed by monitoring the phosphorolysis of inosine (Ino) to hypoxanthine (Hpx) by LC-UV. A small library of 6- and 8-substituted nucleosides was synthesized and screened. The inhibition potency of the most promising compound, 8-aminoinosine (4), was quantified through Ki and IC50 determinations. The effect of HsPNP inhibition was also evaluated in vitro through the study of cytotoxicity on human T-cell leukemia cells (CCRF-CEM). Docking studies were also carried out for the most potent compound, allowing further insights into the inhibitor interaction at the HsPNP active site. This study provides both new tools and a new lead for developing novel HsPNP inhibitors.
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Affiliation(s)
- Marco Rabuffetti
- Department of Chemistry, University of Milan, Via Golgi 21, 20133, Milan, Italy
| | - Francesca Rinaldi
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100, Pavia, Italy
| | - Alessandra Lo Bianco
- Department of Pharmacy, "Drug Discovery" Laboratory, University of Napoli Federico II, Via D. Montesano 49, 80131, Napoli, Italy
| | - Giovanna Speranza
- Department of Chemistry, University of Milan, Via Golgi 21, 20133, Milan, Italy
| | - Daniela Ubiali
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100, Pavia, Italy
| | - Marcela Cristina de Moraes
- Departamento de Química Orgânica, Instituto de Química, Universidade Federal Fluminense, Niterói, RJ 24210-141, Brazil
| | | | - Gabriella Massolini
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100, Pavia, Italy
| | - Enrica Calleri
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100, Pavia, Italy
| | - Antonio Lavecchia
- Department of Pharmacy, "Drug Discovery" Laboratory, University of Napoli Federico II, Via D. Montesano 49, 80131, Napoli, Italy
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2
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Fjelbye K, Marigo M, Clausen RP, Juhl K. Diastereodivergent Access to Syn and Anti 3,4-Substituted β-Fluoropyrrolidines: Enhancing or Reversing Substrate Preference. Org Lett 2016; 18:1170-3. [DOI: 10.1021/acs.orglett.6b00293] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kasper Fjelbye
- Discovery Chemistry
and DMPK, H. Lundbeck A/S, Ottiliavej
9, 2500 Valby, Denmark
- Department
of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Mauro Marigo
- Discovery Chemistry
and DMPK, H. Lundbeck A/S, Ottiliavej
9, 2500 Valby, Denmark
| | - Rasmus Prætorius Clausen
- Department
of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Karsten Juhl
- Discovery Chemistry
and DMPK, H. Lundbeck A/S, Ottiliavej
9, 2500 Valby, Denmark
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3
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Evans GB, Cameron SA, Luxenburger A, Guan R, Suarez J, Thomas K, Schramm VL, Tyler PC. Tight binding enantiomers of pre-clinical drug candidates. Bioorg Med Chem 2015; 23:5326-33. [PMID: 26260335 PMCID: PMC4567382 DOI: 10.1016/j.bmc.2015.07.059] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 07/26/2015] [Accepted: 07/27/2015] [Indexed: 11/30/2022]
Abstract
MTDIA is a picomolar transition state analogue inhibitor of human methylthioadenosine phosphorylase and a femtomolar inhibitor of Escherichia coli methylthioadenosine nucleosidase. MTDIA has proven to be a non-toxic, orally available pre-clinical drug candidate with remarkable anti-tumour activity against a variety of human cancers in mouse xenografts. The structurally similar compound MTDIH is a potent inhibitor of human and malarial purine nucleoside phosphorylase (PNP) as well as the newly discovered enzyme, methylthioinosine phosphorylase, isolated from Pseudomonas aeruginosa. Since the enantiomers of some pharmaceuticals have revealed surprising biological activities, the enantiomers of MTDIH and MTDIA, compounds 1 and 2, respectively, were prepared and their enzyme binding properties studied. Despite binding less tightly to their target enzymes than their enantiomers compounds 1 and 2 are nanomolar inhibitors.
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Affiliation(s)
- Gary B Evans
- Ferrier Research Institute, Victoria University of Wellington, 69 Gracefield Rd, Lower Hutt 5010, New Zealand
| | - Scott A Cameron
- Ferrier Research Institute, Victoria University of Wellington, 69 Gracefield Rd, Lower Hutt 5010, New Zealand; Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Andreas Luxenburger
- Ferrier Research Institute, Victoria University of Wellington, 69 Gracefield Rd, Lower Hutt 5010, New Zealand
| | - Rong Guan
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Javier Suarez
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Keisha Thomas
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Peter C Tyler
- Ferrier Research Institute, Victoria University of Wellington, 69 Gracefield Rd, Lower Hutt 5010, New Zealand
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4
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Roman G. Mannich bases in medicinal chemistry and drug design. Eur J Med Chem 2015; 89:743-816. [PMID: 25462280 PMCID: PMC7115492 DOI: 10.1016/j.ejmech.2014.10.076] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 10/22/2014] [Accepted: 10/23/2014] [Indexed: 01/18/2023]
Abstract
The biological activity of Mannich bases, a structurally heterogeneous class of chemical compounds that are generated from various substrates through the introduction of an aminomethyl function by means of the Mannich reaction, is surveyed, with emphasis on the relationship between structure and biological activity. The review covers extensively the literature reports that have disclosed Mannich bases as anticancer and cytotoxic agents, or compounds with potential antibacterial and antifungal activity in the last decade. The most relevant studies on the activity of Mannich bases as antimycobacterial agents, antimalarials, or antiviral candidates have been included as well. The review contains also a thorough coverage of anticonvulsant, anti-inflammatory, analgesic and antioxidant activities of Mannich bases. In addition, several minor biological activities of Mannich bases, such as their ability to regulate blood pressure or inhibit platelet aggregation, their antiparasitic and anti-ulcer effects, as well as their use as agents for the treatment of mental disorders have been presented. The review gives in the end a brief overview of the potential of Mannich bases as inhibitors of various enzymes or ligands for several receptors.
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Affiliation(s)
- Gheorghe Roman
- Petru Poni Institute of Macromolecular Chemistry, Department of Inorganic Polymers, 41A Aleea Gr. Ghica Vodă, Iaşi 700487, Romania.
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5
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Hernández D, Boto A. Nucleoside Analogues: Synthesis and Biological Properties of Azanucleoside Derivatives. European J Org Chem 2014. [DOI: 10.1002/ejoc.201301731] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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6
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Clinch K, Evans GB, Fröhlich RFG, Gulab SA, Gutierrez JA, Mason JM, Schramm VL, Tyler PC, Woolhouse AD. Transition state analogue inhibitors of human methylthioadenosine phosphorylase and bacterial methylthioadenosine/S-adenosylhomocysteine nucleosidase incorporating acyclic ribooxacarbenium ion mimics. Bioorg Med Chem 2012; 20:5181-7. [PMID: 22854195 DOI: 10.1016/j.bmc.2012.07.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 06/28/2012] [Accepted: 07/04/2012] [Indexed: 11/24/2022]
Abstract
Several acyclic hydroxy-methylthio-amines with 3-5 carbon atoms were prepared and coupled via a methylene link to 9-deazaadenine. The products were tested for inhibition against human MTAP and Escherichia coli and Neisseria meningitidis MTANs and gave K(i) values as low as 0.23 nM. These results were compared to those obtained with 1st and 2nd generation inhibitors (1S)-1-(9-deazaadenin-9-yl)-1,4-dideoxy-1,4-imino-5-methylthio-D-ribitol (MT-Immucillin-A, 3) and (3R,4S)-1-[9-deazaadenin-9-yl)methyl]3-hydroxy-4-methylthiomethylpyrrolidine (MT-DADMe-Immucillin-A, 4). The best inhibitors were found to exhibit binding affinities of approximately 2- to 4-fold those of 3 but were significantly weaker than 4. Cleavage of the 2,3 carbon-carbon bond in MT-Immucillin-A (3) gave an acyclic product (79) with a 21,500 fold loss of activity against E. coli MTAN. In another case, N-methylation of a side chain secondary amine resulted in a 250-fold loss of activity against the same enzyme [(±)-65 vs (±)-68]. The inhibition results were also contrasted with those acyclic derivatives previously prepared as inhibitors for a related enzyme, purine nucleoside phosphorylase (PNP), where some inhibitors in the latter case were found to be more potent than their cyclic counterparts.
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Affiliation(s)
- Keith Clinch
- Carbohydrate Chemistry, Industrial Research Limited, PO Box 31310, Lower Hutt 5040, New Zealand.
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7
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Guan R, Ho MC, Almo SC, Schramm VL. Methylthioinosine phosphorylase from Pseudomonas aeruginosa. Structure and annotation of a novel enzyme in quorum sensing. Biochemistry 2011; 50:1247-54. [PMID: 21197954 DOI: 10.1021/bi101642d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The PA3004 gene of Pseudomonas aeruginosa PAO1 was originally annotated as a 5'-methylthioadenosine phosphorylase (MTAP). However, the PA3004 encoded protein uses 5'-methylthioinosine (MTI) as a preferred substrate and represents the only known example of a specific MTI phosphorylase (MTIP). MTIP does not utilize 5'-methylthioadenosine (MTA). Inosine is a weak substrate with a k(cat)/K(m) value 290-fold less than MTI and is the second best substrate identified. The crystal structure of P. aeruginosa MTIP (PaMTIP) in complex with hypoxanthine was determined to 2.8 Å resolution and revealed a 3-fold symmetric homotrimer. The methylthioribose and phosphate binding regions of PaMTIP are similar to MTAPs, and the purine binding region is similar to that of purine nucleoside phosphorylases (PNPs). The catabolism of MTA in P. aeruginosa involves deamination to MTI and phosphorolysis to hypoxanthine (MTA → MTI → hypoxanthine). This pathway also exists in Plasmodium falciparum, where the purine nucleoside phosphorylase (PfPNP) acts on both inosine and MTI. Three tight-binding transition state analogue inhibitors of PaMTIP are identified with dissociation constants in the picomolar range. Inhibitor specificity suggests an early dissociative transition state for PaMTIP. Quorum sensing molecules are associated with MTA metabolism in bacterial pathogens suggesting PaMTIP as a potential therapeutic target.
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Affiliation(s)
- Rong Guan
- Department of Biochemistry, Albert Einstein College of Medicine, Yeshiva University, 1300 Morris Park Avenue, Bronx, New York 10461, United States
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Boto A, Hernández D, Hernández R. One-Pot Conversion of Proline Derivatives into Iodinated Iminosugar-Based Nucleosides, Useful Precursors of Highly Functionalized Nucleoside Analogues. European J Org Chem 2010. [DOI: 10.1002/ejoc.201000997] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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9
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Boto A, Hernández D, Hernández R. One-Pot Synthesis of Azanucleosides from Proline Derivatives - Stereoselectivity in Sequential Processes. European J Org Chem 2010. [DOI: 10.1002/ejoc.201000360] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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10
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Machleder SQ, Pineda ET, Schwartz SD. On the Origin of the Chemical Barrier and Tunneling in Enzymes. J PHYS ORG CHEM 2010; 23:690-695. [PMID: 20582160 DOI: 10.1002/poc.1688] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This paper presents both a review of some recent results from our group and experimental groups, and some new theoretical results all of which are helping to form a more physically rigorous picture of the process of enzymatic catalysis. A common classical picture of enzymatic catalysis is the transition state tight binding model. Schwartz and Schramm1 have recently argued from both theoretical and experimental results that this picture is incorrect. We now investigate what the nature of barriers might be in enzymatic reactions, and what this viewpoint might imply for tunneling in a hydrogen transfer enzyme. For lactate dehydrogenase we conclude that the enzymes role in catalysis is at least partially to hunt through configuration space for those configurations that minimize chemical free energy barriers. Those configurations do not seem to be stable basins on the free energy surface, and in fact the overall free energy barrier to reaction may well largely be due to this stochastic hunt - both probabilistically and energetically. We suggest further computations to test this hypothesis.
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Affiliation(s)
- Sara Quaytman Machleder
- Dept. of Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bx, NY 10461
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11
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Schwartz SD, Schramm VL. Enzymatic transition states and dynamic motion in barrier crossing. Nat Chem Biol 2009; 5:551-8. [PMID: 19620996 DOI: 10.1038/nchembio.202] [Citation(s) in RCA: 203] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
What are the atomic motions at enzymatic catalytic sites on the timescale of chemical change? Combined experimental and computational chemistry approaches take advantage of transition-state analogs to reveal dynamic motions linked to transition-state formation. QM/MM transition path sampling from reactive complexes provides both temporal and dynamic information for barrier crossing. Fast (femtosecond to picosecond) dynamic motions provide essential links to enzymatic barrier crossing by local or promoting-mode dynamic searches through bond-vibrational space. Transition-state lifetimes are within the femtosecond timescales of bond vibrations and show no manifestations of stabilized, equilibrated complexes. The slow binding and protein conformational changes (microsecond to millisecond) also required for catalysis are temporally decoupled from the fast dynamic motions forming the transition state. According to this view of enzymatic catalysis, transition states are formed by fast, coincident dynamic excursions of catalytic site elements, while the binding of transition-state analogs is the conversion of the dynamic excursions to equilibrated states.
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Affiliation(s)
- Steven D Schwartz
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA
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12
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Edwards AA, Mason JM, Clinch K, Tyler PC, Evans GB, Schramm VL. Altered enthalpy-entropy compensation in picomolar transition state analogues of human purine nucleoside phosphorylase. Biochemistry 2009; 48:5226-38. [PMID: 19425594 DOI: 10.1021/bi9005896] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Human purine nucleoside phosphorylase (PNP) belongs to the trimeric class of PNPs and is essential for catabolism of deoxyguanosine. Genetic deficiency of PNP in humans causes a specific T-cell immune deficiency, and transition state analogue inhibitors of PNP are in development for treatment of T-cell cancers and autoimmune disorders. Four generations of Immucillins have been developed, each of which contains inhibitors binding with picomolar affinity to human PNP. Full inhibition of PNP occurs upon binding to the first of three subunits, and binding to subsequent sites occurs with negative cooperativity. In contrast, substrate analogue and product bind without cooperativity. Titrations of human PNP using isothermal calorimetry indicate that binding of a structurally rigid first-generation Immucillin (K(d) = 56 pM) is driven by large negative enthalpy values (DeltaH = -21.2 kcal/mol) with a substantial entropic (-TDeltaS) penalty. The tightest-binding inhibitors (K(d) = 5-9 pM) have increased conformational flexibility. Despite their conformational freedom in solution, flexible inhibitors bind with high affinity because of reduced entropic penalties. Entropic penalties are proposed to arise from conformational freezing of the PNP.inhibitor complex with the entropy term dominated by protein dynamics. The conformationally flexible Immucillins reduce the system entropic penalty. Disrupting the ribosyl 5'-hydroxyl interaction of transition state analogues with PNP causes favorable entropy of binding. Tight binding of the 17 Immucillins is characterized by large enthalpic contributions, emphasizing their similarity to the transition state. Via introduction of flexibility into the inhibitor structure, the enthalpy-entropy compensation pattern is altered to permit tighter binding.
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Affiliation(s)
- Achelle A Edwards
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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