1
|
Kesharwani S, Eeba, Tandi M, Agarwal N, Sundriyal S. Design and synthesis of non-hydroxamate lipophilic inhibitors of 1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR): in silico, in vitro and antibacterial studies. RSC Adv 2024; 14:27530-27554. [PMID: 39221132 PMCID: PMC11362829 DOI: 10.1039/d4ra05083e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2024] [Accepted: 08/13/2024] [Indexed: 09/04/2024] Open
Abstract
1-Deoxy-d-xylulose 5-phosphate reductoisomerase (DXR) is a key enzyme of the 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway operating in several pathogens, including Mycobacterium and Plasmodium. Since a DXR homologue is not present in humans, it is an important antimicrobial target. Fosmidomycin (FSM) and its analogues inhibit DXR function by chelating the divalent metal (Mn2+ or Mg2+) in its active site via a hydroxamate metal binding group (MBG). The latter, however, enhances the polarity of molecules and is known to display metabolic instability and toxicity issues. While attempts have been made to increase the lipophilicity of FSM by substituting the linker chain and prodrug approach, very few efforts have been made to replace the hydroxamate group with other lipophilic MBGs. We report a systematic in silico and experimental investigation to identify novel MBGs for designing non-hydroxamate lipophilic DXR inhibitors. The SAR studies with selected MBG fragments identified novel inhibitors of E. Coli DXR with IC50 values ranging from 0.29 to 106 μM. The promising inhibitors were also screened against ESKAPE pathogens and M. tuberculosis.
Collapse
Affiliation(s)
- Sharyu Kesharwani
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani (BITS) Pilani Campus, Vidya Vihar, Pilani Rajasthan 333 031 India
| | - Eeba
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster 3rd Mile Stone, Gurugram-Faridabad Expressway Faridabad 121001 Haryana India
| | - Mukesh Tandi
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani (BITS) Pilani Campus, Vidya Vihar, Pilani Rajasthan 333 031 India
| | - Nisheeth Agarwal
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster 3rd Mile Stone, Gurugram-Faridabad Expressway Faridabad 121001 Haryana India
| | - Sandeep Sundriyal
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani (BITS) Pilani Campus, Vidya Vihar, Pilani Rajasthan 333 031 India
| |
Collapse
|
2
|
Kwak SH, Cochrane CS, Cho J, Dome PA, Ennis AF, Kim JH, Zhou P, Hong J. Development of LpxH Inhibitors Chelating the Active Site Dimanganese Metal Cluster of LpxH. ChemMedChem 2023; 18:e202300023. [PMID: 37014664 PMCID: PMC10239344 DOI: 10.1002/cmdc.202300023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/07/2023] [Accepted: 03/31/2023] [Indexed: 04/05/2023]
Abstract
Despite the widespread emergence of multidrug-resistant nosocomial Gram-negative bacterial infections and the major public health threat it brings, no new class of antibiotics for Gram-negative pathogens has been approved over the past five decades. Therefore, there is an urgent medical need for developing effective novel antibiotics against multidrug-resistant Gram-negative pathogens by targeting previously unexploited pathways in these bacteria. To fulfill this crucial need, we have been investigating a series of sulfonyl piperazine compounds targeting LpxH, a dimanganese-containing UDP-2,3-diacylglucosamine hydrolase in the lipid A biosynthetic pathway, as novel antibiotics against clinically important Gram-negative pathogens. Inspired by a detailed structural analysis of our previous LpxH inhibitors in complex with K. pneumoniae LpxH (KpLpxH), here we report the development and structural validation of the first-in-class sulfonyl piperazine LpxH inhibitors, JH-LPH-45 (8) and JH-LPH-50 (13), that achieve chelation of the active site dimanganese cluster of KpLpxH. The chelation of the dimanganese cluster significantly improves the potency of JH-LPH-45 (8) and JH-LPH-50 (13). We expect that further optimization of these proof-of-concept dimanganese-chelating LpxH inhibitors will ultimately lead to the development of more potent LpxH inhibitors for targeting multidrug-resistant Gram-negative pathogens.
Collapse
Affiliation(s)
- Seung-Hwa Kwak
- Department of Chemistry, Duke University, Durham, NC 27708, United States
| | - C. Skyler Cochrane
- Department of Chemistry, Duke University, Durham, NC 27708, United States
| | - Jae Cho
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, United States
| | - Patrick A. Dome
- Department of Chemistry, Duke University, Durham, NC 27708, United States
| | - Amanda F. Ennis
- Department of Chemistry, Duke University, Durham, NC 27708, United States
| | - Jea Hyun Kim
- Department of Chemistry, Duke University, Durham, NC 27708, United States
| | - Pei Zhou
- Department of Chemistry, Duke University, Durham, NC 27708, United States
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, United States
| | - Jiyong Hong
- Department of Chemistry, Duke University, Durham, NC 27708, United States
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, United States
| |
Collapse
|
3
|
Tiede ER, Heckman MT, Brennessel WW, Kraft BM. Chelation Equilibria and π-Electron Delocalization in Neutral Hypercoordinate Organosilicon Complexes of Pyrithione. Organometallics 2022. [DOI: 10.1021/acs.organomet.2c00342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Erin R. Tiede
- Department of Chemistry, St. John Fisher University, Rochester, New York 14618, United States
| | - Matthew T. Heckman
- Department of Chemistry, St. John Fisher University, Rochester, New York 14618, United States
| | - William W. Brennessel
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Bradley M. Kraft
- Department of Chemistry, St. John Fisher University, Rochester, New York 14618, United States
| |
Collapse
|
4
|
Arshad JZ, Hanif M. Hydroxypyrone derivatives in drug discovery: from chelation therapy to rational design of metalloenzyme inhibitors. RSC Med Chem 2022; 13:1127-1149. [PMID: 36325396 PMCID: PMC9579940 DOI: 10.1039/d2md00175f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 07/28/2022] [Indexed: 07/31/2023] Open
Abstract
The versatile structural motif of hydroxypyrone is found in natural products and can be easily converted into hydroxypyridone and hydroxythiopyridone analogues. The favourable toxicity profile and ease of functionalization to access a vast library of compounds make them an ideal structural scaffold for drug design and discovery. This versatile scaffold possesses excellent metal chelating properties that can be exploited for chelation therapy in clinics. Deferiprone [1,2-dimethyl-3-hydroxy-4(1H)-one] was the first orally active chelator to treat iron overload in thalassemia major. Metal complexes of hydroxy-(thio)pyr(id)ones have been investigated as magnetic resonance imaging contrast agents, and anticancer and antidiabetic agents. In recent years, this compound class has demonstrated potential in discovering and developing metalloenzyme inhibitors. This review article summarizes recent literature on hydroxy-(thio)pyr(id)ones as inhibitors for metalloenzymes such as histone deacetylases, tyrosinase and metallo-β-lactamase. Different approaches to the design of hydroxy-(thio)pyr(id)ones and their biological properties against selected metalloenzymes are discussed.
Collapse
Affiliation(s)
- Jahan Zaib Arshad
- Department of Chemistry, Government College Women University Sialkot Sialkot Pakistan
| | - Muhammad Hanif
- School of Chemical Sciences, University of Auckland Private Bag 92019 Auckland 1142 New Zealand (+64) 9 373 7599 ext. 87422
- MacDiarmid Institute for Advanced Materials and Nanotechnology Wellington New Zealand
| |
Collapse
|
5
|
Gervasoni S, Spencer J, Hinchliffe P, Pedretti A, Vairoletti F, Mahler G, Mulholland AJ. A multiscale approach to predict the binding mode of metallo beta-lactamase inhibitors. Proteins 2022; 90:372-384. [PMID: 34455628 PMCID: PMC8944931 DOI: 10.1002/prot.26227] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/09/2021] [Accepted: 08/18/2021] [Indexed: 02/03/2023]
Abstract
Antibiotic resistance is a major threat to global public health. β-lactamases, which catalyze breakdown of β-lactam antibiotics, are a principal cause. Metallo β-lactamases (MBLs) represent a particular challenge because they hydrolyze almost all β-lactams and to date no MBL inhibitor has been approved for clinical use. Molecular simulations can aid drug discovery, for example, predicting inhibitor complexes, but empirical molecular mechanics (MM) methods often perform poorly for metalloproteins. Here we present a multiscale approach to model thiol inhibitor binding to IMP-1, a clinically important MBL containing two catalytic zinc ions, and predict the binding mode of a 2-mercaptomethyl thiazolidine (MMTZ) inhibitor. Inhibitors were first docked into the IMP-1 active site, testing different docking programs and scoring functions on multiple crystal structures. Complexes were then subjected to molecular dynamics (MD) simulations and subsequently refined through QM/MM optimization with a density functional theory (DFT) method, B3LYP/6-31G(d), increasing the accuracy of the method with successive steps. This workflow was tested on two IMP-1:MMTZ complexes, for which it reproduced crystallographically observed binding, and applied to predict the binding mode of a third MMTZ inhibitor for which a complex structure was crystallographically intractable. We also tested a 12-6-4 nonbonded interaction model in MD simulations and optimization with a SCC-DFTB QM/MM approach. The results show the limitations of empirical models for treating these systems and indicate the need for higher level calculations, for example, DFT/MM, for reliable structural predictions. This study demonstrates a reliable computational pipeline that can be applied to inhibitor design for MBLs and other zinc-metalloenzyme systems.
Collapse
Affiliation(s)
- Silvia Gervasoni
- Department of Pharmaceutical Sciences, University of Milan, Milan, Italy
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | | | - Franco Vairoletti
- Laboratorio de Química Farmacéutica, Departamento de Química Orgánica, Facultad de Química, Universidad de la República (UdelaR), Avda. General Flores 2124, Montevideo, Uruguay
| | - Graciela Mahler
- Laboratorio de Química Farmacéutica, Departamento de Química Orgánica, Facultad de Química, Universidad de la República (UdelaR), Avda. General Flores 2124, Montevideo, Uruguay
| | | |
Collapse
|
6
|
Kladnik J, Coverdale JPC, Kljun J, Burmeister H, Lippman P, Ellis FG, Jones AM, Ott I, Romero-Canelón I, Turel I. Organoruthenium Complexes with Benzo-Fused Pyrithiones Overcome Platinum Resistance in Ovarian Cancer Cells. Cancers (Basel) 2021; 13:2493. [PMID: 34065335 PMCID: PMC8160969 DOI: 10.3390/cancers13102493] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/07/2021] [Accepted: 05/14/2021] [Indexed: 02/07/2023] Open
Abstract
Drug resistance to existing anticancer agents is a growing clinical concern, with many first line treatments showing poor efficacy in treatment plans of some cancers. Resistance to platinum agents, such as cisplatin, is particularly prevalent in the treatment of ovarian cancer, one of the most common cancers amongst women in the developing world. Therefore, there is an urgent need to develop next generation of anticancer agents which can overcome resistance to existing therapies. We report a new series of organoruthenium(II) complexes bearing structurally modified pyrithione ligands with extended aromatic scaffold, which overcome platinum and adriamycin resistance in human ovarian cancer cells. The mechanism of action of such complexes appears to be unique from that of cisplatin, involving G1 cell cycle arrest without generation of cellular ROS, as is typically associated with similar ruthenium complexes. The complexes inhibit the enzyme thioredoxin reductase (TrxR) in a model system and reduce cell motility towards wound healing. Importantly, this work highlights further development in our understanding of the multi-targeting mechanism of action exhibited by transition metal complexes.
Collapse
Affiliation(s)
- Jerneja Kladnik
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia; (J.K.); (J.K.)
| | - James P. C. Coverdale
- School of Pharmacy, Institute of Clinical Sciences, University of Birmingham, Birmingham B15 2TT, UK; (J.P.C.C.); (F.G.E.); (A.M.J.)
| | - Jakob Kljun
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia; (J.K.); (J.K.)
| | - Hilke Burmeister
- Institute of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, 38106 Braunschweig, Germany; (H.B.); (P.L.); (I.O.)
| | - Petra Lippman
- Institute of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, 38106 Braunschweig, Germany; (H.B.); (P.L.); (I.O.)
| | - Francesca G. Ellis
- School of Pharmacy, Institute of Clinical Sciences, University of Birmingham, Birmingham B15 2TT, UK; (J.P.C.C.); (F.G.E.); (A.M.J.)
| | - Alan M. Jones
- School of Pharmacy, Institute of Clinical Sciences, University of Birmingham, Birmingham B15 2TT, UK; (J.P.C.C.); (F.G.E.); (A.M.J.)
| | - Ingo Ott
- Institute of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, 38106 Braunschweig, Germany; (H.B.); (P.L.); (I.O.)
| | - Isolda Romero-Canelón
- School of Pharmacy, Institute of Clinical Sciences, University of Birmingham, Birmingham B15 2TT, UK; (J.P.C.C.); (F.G.E.); (A.M.J.)
| | - Iztok Turel
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia; (J.K.); (J.K.)
| |
Collapse
|
7
|
Non-hydroxamate inhibitors of 1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR): A critical review and future perspective. Eur J Med Chem 2020; 213:113055. [PMID: 33303239 DOI: 10.1016/j.ejmech.2020.113055] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/18/2020] [Accepted: 11/21/2020] [Indexed: 12/22/2022]
Abstract
1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR) catalyzes the second step of the non-mevalonate (or MEP) pathway that functions in several organisms and plants for the synthesis of isoprenoids. DXR is essential for the survival of multiple pathogenic bacteria/parasites, including those that cause tuberculosis and malaria in humans. DXR function is inhibited by fosmidomycin (1), a natural product, which forms a chelate with the active site divalent metal (Mg2+/Mn2+) through its hydroxamate metal-binding group (MBG). Most of the potent DXR inhibitors are structurally similar to 1 and retain hydroxamate despite the unfavourable pharmacokinetic and toxicity profile of the latter. We provide our perspective on the lack of non-hydroxamate DXR inhibitors. We also highlight the fundamental flaws in the design of MBG in these molecules, primarily responsible for their failure to inhibit DXR. We also suggest that for designing next-generation non-hydroxamate DXR inhibitors, approaches followed for other metalloenzymes targets may be exploited.
Collapse
|
8
|
Structural Isomerism and Enhanced Lipophilicity of Pyrithione Ligands of Organoruthenium(II) Complexes Increase Inhibition on AChE and BuChE. Int J Mol Sci 2020; 21:ijms21165628. [PMID: 32781544 PMCID: PMC7460603 DOI: 10.3390/ijms21165628] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/25/2020] [Accepted: 08/01/2020] [Indexed: 01/13/2023] Open
Abstract
The increasing number of Alzheimer’s disease (AD) cases requires the development of new improved drug candidates, possessing the ability of more efficient treatment as well as less unwanted side effects. Cholinesterase enzymes are highly associated with the development of AD and thus represent important druggable targets. Therefore, we have synthesized eight organoruthenium(II) chlorido complexes 1a–h with pyrithione-type ligands (pyrithione = 1-hydroxypyridine-2(1H)-thione, a), bearing either pyrithione a, its methyl (b-e) or bicyclic aromatic analogues (f–h) and tested them for their inhibition towards electric eel acetylcholinesterase (eeAChE) and horse serum butyrylcholinesterase (hsBuChE). The experimental results have shown that the novel complex 1g with the ligand 1-hydroxyquinoline-2-(1H)-thione (g) improves the inhibition towards eeAChE (IC50 = 4.9 μM) and even more potently towards hsBuChE (IC50 = 0.2 μM) in comparison with the referenced 1a. Moreover, computational studies on Torpedo californica AChE have supported the experimental outcomes for 1g, possessing the lowest energy value among all tested complexes and have also predicted several interactions of 1g with the target protein. Consequently, we have shown that the aromatic ring extension of the ligand a, though only at the appropriate position, is a viable strategy to enhance the activity against cholinesterases.
Collapse
|
9
|
Paul TK, Taraphder S. Coordination Dynamics of Zinc Triggers the Rate Determining Proton Transfer in Human Carbonic Anhydrase II. Chemphyschem 2020; 21:1455-1473. [DOI: 10.1002/cphc.202000177] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/17/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Tanmoy Kumar Paul
- Department of Chemistry Indian Institute of Technology Kharagpur 721302 India
| | - Srabani Taraphder
- Department of Chemistry Indian Institute of Technology Kharagpur 721302 India
| |
Collapse
|
10
|
Guo H, Cheng K, Gao Y, Bai W, Wu C, He W, Li C, Li Z. A novel potent metal-binding NDM-1 inhibitor was identified by fragment virtual, SPR and NMR screening. Bioorg Med Chem 2020; 28:115437. [DOI: 10.1016/j.bmc.2020.115437] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 03/05/2020] [Accepted: 03/10/2020] [Indexed: 01/25/2023]
|
11
|
Kladnik J, Kljun J, Burmeister H, Ott I, Romero-Canelón I, Turel I. Towards Identification of Essential Structural Elements of Organoruthenium(II)-Pyrithionato Complexes for Anticancer Activity. Chemistry 2019; 25:14169-14182. [PMID: 31461189 DOI: 10.1002/chem.201903109] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 08/14/2019] [Indexed: 12/25/2022]
Abstract
An organoruthenium(II) complex with pyrithione (2-mercaptopyridine N-oxide) 1 a has previously been identified by our group as a compound with promising anticancer potential without cytotoxicity towards non-cancerous cells. To expand the rather limited research on compounds of this type, an array of novel chlorido and 1,3,5-triaza-7-phosphaadamantane (pta) organoruthenium(II) complexes with methyl-substituted pyrithiones has been prepared. After thorough investigation of the aqueous stability of these complexes, their modes of action have been elucidated at the cellular level. Minor structural alterations in the ruthenium-pyrithionato compounds resulted in fine-tuning of their cytotoxicities. The best performing compounds, 1 b and 2 b, with a chlorido or pta ligand bound to ruthenium, respectively, and a methyl group at the 3-position of the pyrithione scaffold, have been further investigated. Both compounds trigger early apoptosis, induce the generation of reactive oxygen species and G1 arrest in A549 cancer cells, and show no strong interaction with DNA. However, only 1 b also inhibits thioredoxin reductase. Wound healing assays and mitochondrial function evaluation have revealed differences between these two compounds at the cellular level.
Collapse
Affiliation(s)
- Jerneja Kladnik
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, 1000, Ljubljana, Slovenia
| | - Jakob Kljun
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, 1000, Ljubljana, Slovenia
| | - Hilke Burmeister
- Institute of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, 38106, Braunschweig, Germany
| | - Ingo Ott
- Institute of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, 38106, Braunschweig, Germany
| | - Isolda Romero-Canelón
- School of Pharmacy, Institute of Clinical Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Iztok Turel
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, 1000, Ljubljana, Slovenia
| |
Collapse
|
12
|
Thermodynamic, kinetic, and structural parameterization of human carbonic anhydrase interactions toward enhanced inhibitor design. Q Rev Biophys 2019; 51:e10. [PMID: 30912486 DOI: 10.1017/s0033583518000082] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The aim of rational drug design is to develop small molecules using a quantitative approach to optimize affinity. This should enhance the development of chemical compounds that would specifically, selectively, reversibly, and with high affinity interact with a target protein. It is not yet possible to develop such compounds using computational (i.e., in silico) approach and instead the lead molecules are discovered in high-throughput screening searches of large compound libraries. The main reason why in silico methods are not capable to deliver is our poor understanding of the compound structure-thermodynamics and structure-kinetics correlations. There is a need for databases of intrinsic binding parameters (e.g., the change upon binding in standard Gibbs energy (ΔGint), enthalpy (ΔHint), entropy (ΔSint), volume (ΔVintr), heat capacity (ΔCp,int), association rate (ka,int), and dissociation rate (kd,int)) between a series of closely related proteins and a chemically diverse, but pharmacophoric group-guided library of compounds together with the co-crystal structures that could help explain the structure-energetics correlations and rationally design novel compounds. Assembly of these data will facilitate attempts to provide correlations and train data for modeling of compound binding. Here, we report large datasets of the intrinsic thermodynamic and kinetic data including over 400 primary sulfonamide compound binding to a family of 12 catalytically active human carbonic anhydrases (CA). Thermodynamic parameters have been determined by the fluorescent thermal shift assay, isothermal titration calorimetry, and by the stopped-flow assay of the inhibition of enzymatic activity. Kinetic measurements were performed using surface plasmon resonance. Intrinsic thermodynamic and kinetic parameters of binding were determined by dissecting the binding-linked protonation reactions of the protein and sulfonamide. The compound structure-thermodynamics and kinetics correlations reported here helped to discover compounds that exhibited picomolar affinities, hour-long residence times, and million-fold selectivities over non-target CA isoforms. Drug-lead compounds are suggested for anticancer target CA IX and CA XII, antiglaucoma CA IV, antiobesity CA VA and CA VB, and other isoforms. Together with 85 X-ray crystallographic structures of 60 compounds bound to six CA isoforms, the database should be of help to continue developing the principles of rational target-based drug design.
Collapse
|
13
|
Credille CV, Dick BL, Morrison CN, Stokes RW, Adamek RN, Wu NC, Wilson IA, Cohen SM. Structure-Activity Relationships in Metal-Binding Pharmacophores for Influenza Endonuclease. J Med Chem 2018; 61:10206-10217. [PMID: 30351002 DOI: 10.1021/acs.jmedchem.8b01363] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Metalloenzymes represent an important target space for drug discovery. A limitation to the early development of metalloenzyme inhibitors has been the lack of established structure-activity relationships (SARs) for molecules that bind the metal ion cofactor(s) of a metalloenzyme. Herein, we employed a bioinorganic perspective to develop an SAR for inhibition of the metalloenzyme influenza RNA polymerase PAN endonuclease. The identified trends highlight the importance of the electronics of the metal-binding pharmacophore (MBP), in addition to MBP sterics, for achieving improved inhibition and selectivity. By optimization of the MBPs for PAN endonuclease, a class of highly active and selective fragments was developed that displays IC50 values <50 nM. This SAR led to structurally distinct molecules that also displayed IC50 values of ∼10 nM, illustrating the utility of a metal-centric development campaign in generating highly active and selective metalloenzyme inhibitors.
Collapse
Affiliation(s)
- Cy V Credille
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Benjamin L Dick
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Christine N Morrison
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Ryjul W Stokes
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Rebecca N Adamek
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Nicholas C Wu
- Department of Integrative Structural and Computational Biology , The Scripps Research Institute , La Jolla , California 92037 , United States
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology , The Scripps Research Institute , La Jolla , California 92037 , United States.,The Skaggs Institute for Chemical Biology , The Scripps Research Institute , La Jolla , California 92037 , United States
| | - Seth M Cohen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| |
Collapse
|
14
|
Adamek RN, Credille CV, Dick BL, Cohen SM. Isosteres of hydroxypyridinethione as drug-like pharmacophores for metalloenzyme inhibition. J Biol Inorg Chem 2018; 23:1129-1138. [PMID: 30003339 DOI: 10.1007/s00775-018-1593-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 06/28/2018] [Indexed: 12/18/2022]
Abstract
Hydroxypyridinethiones (HOPTOs) are strong ligands for metal ions and potentially useful pharmacophores for inhibiting metalloenzymes relevant to human disease. However, HOPTOs have been sparingly used in drug discovery efforts due, in part, to concerns that this scaffold will act as a promiscuous, non-selective metalloenzyme inhibitor, as well as possess poor pharmacokinetics (PK), which may undermine drug candidates containing this functional group. To advance HOPTOs as a useful pharmacophore for metalloenzyme inhibitors, a library of 22 HOPTO isostere compounds has been synthesized and investigated. This library demonstrates that it is possible to maintain the core metal-binding pharmacophore (MBP) while generating diversity in structure, electronics, and PK properties. This HOPTO library has been screened against a set of four different metalloenzymes, demonstrating that while the same metal-binding donor atoms are maintained, there is a wide range of activity between metalloenzyme targets. Overall, this work shows that HOPTO isosteres are useful MBPs and valuable scaffolds for metalloenzyme inhibitors.
Collapse
Affiliation(s)
- Rebecca N Adamek
- Department of Chemistry and Biochemistry, University of California, La Jolla, San Diego, CA, 92093, USA
| | - Cy V Credille
- Department of Chemistry and Biochemistry, University of California, La Jolla, San Diego, CA, 92093, USA
| | - Benjamin L Dick
- Department of Chemistry and Biochemistry, University of California, La Jolla, San Diego, CA, 92093, USA
| | - Seth M Cohen
- Department of Chemistry and Biochemistry, University of California, La Jolla, San Diego, CA, 92093, USA.
| |
Collapse
|
15
|
|
16
|
Zuo X, Huo Z, Kang D, Wu G, Zhou Z, Liu X, Zhan P. Current insights into anti-HIV drug discovery and development: a review of recent patent literature (2014-2017). Expert Opin Ther Pat 2018; 28:299-316. [PMID: 29411697 DOI: 10.1080/13543776.2018.1438410] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
INTRODUCTION To deal with the rapid emergence of drug resistance challenges, together with the difficulty to eradicate the virus, off-target effects and significant cumulative drug toxicities, it is still imperative to develop next-generation anti-HIV agents with novel chemical classes or new mechanisms of action. AREAS COVERED We primarily focused on current strategies to discover novel anti-HIV agents. Moreover, examples of anti-HIV lead compounds were mainly selected from recently patented publications (reported between 2014 and 2017). In particular, 'privileged structure'-focused substituents decorating approach, scaffold hopping, natural-product diversification and prodrug are focused on. Furthermore, exploitation of new compounds with unexplored mechanisms of action and medicinal chemistry strategies to deplete the HIV reservoir were also described. Perspectives that could inspire future anti-HIV drug discovery are delineated. EXPERT OPINION Even if a large number of patents have been disclosed recently, additional HIV inhibitors are still required, especially novel chemical skeletons displaying a unexploited mechanism of action. Current medicinal chemistry strategies are inadequate, and appropriate and new methodologies and technologies should be exploited to identify novel anti-HIV drug candidates in a time- and cost- effective manner.
Collapse
Affiliation(s)
- Xiaofang Zuo
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Ji'nan , PR China
| | - Zhipeng Huo
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Ji'nan , PR China
| | - Dongwei Kang
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Ji'nan , PR China
| | - Gaochan Wu
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Ji'nan , PR China
| | - Zhongxia Zhou
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Ji'nan , PR China
| | - Xinyong Liu
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Ji'nan , PR China
| | - Peng Zhan
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Ji'nan , PR China
| |
Collapse
|
17
|
Chrysanthopoulos PK, Mujumdar P, Woods LA, Dolezal O, Ren B, Peat TS, Poulsen SA. Identification of a New Zinc Binding Chemotype by Fragment Screening. J Med Chem 2017; 60:7333-7349. [PMID: 28817930 DOI: 10.1021/acs.jmedchem.7b00606] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The discovery of a new zinc binding chemotype from screening a nonbiased fragment library is reported. Using the orthogonal fragment screening methods of native state mass spectrometry and surface plasmon resonance a 3-unsubstituted 2,4-oxazolidinedione fragment was found to have low micromolar binding affinity to the zinc metalloenzyme carbonic anhydrase II (CA II). This affinity approached that of fragment sized primary benzenesulfonamides, the classical zinc binding group found in most CA II inhibitors. Protein X-ray crystallography established that 3-unsubstituted 2,4-oxazolidinediones bound to CA II via an interaction of the acidic ring nitrogen with the CA II active site zinc, as well as two hydrogen bonds between the oxazolidinedione ring oxygen and the CA II protein backbone. Furthermore, 3-unsubstituted 2,4-oxazolidinediones appear to be a viable starting point for the development of an alternative class of CA inhibitor, wherein the medicinal chemistry pedigree of primary sulfonamides has dominated for several decades.
Collapse
Affiliation(s)
| | - Prashant Mujumdar
- Griffith University , Griffith Institute for Drug Discovery, Nathan, Brisbane, Queensland 4111, Australia
| | - Lucy A Woods
- Griffith University , Griffith Institute for Drug Discovery, Nathan, Brisbane, Queensland 4111, Australia
| | - Olan Dolezal
- CSIRO , Biomedical Manufacturing Program, 343 Royal Parade, Parkville, Melbourne, Victoria 3052, Australia
| | - Bin Ren
- CSIRO , Biomedical Manufacturing Program, 343 Royal Parade, Parkville, Melbourne, Victoria 3052, Australia
| | - Thomas S Peat
- CSIRO , Biomedical Manufacturing Program, 343 Royal Parade, Parkville, Melbourne, Victoria 3052, Australia
| | - Sally-Ann Poulsen
- Griffith University , Griffith Institute for Drug Discovery, Nathan, Brisbane, Queensland 4111, Australia
| |
Collapse
|
18
|
Cohen SM. A Bioinorganic Approach to Fragment-Based Drug Discovery Targeting Metalloenzymes. Acc Chem Res 2017; 50:2007-2016. [PMID: 28715203 DOI: 10.1021/acs.accounts.7b00242] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Metal-dependent enzymes (i.e., metalloenzymes) make up a large fraction of all enzymes and are critically important in a wide range of biological processes, including DNA modification, protein homeostasis, antibiotic resistance, and many others. Consequently, metalloenzymes represent a vast and largely untapped space for drug development. The discovery of effective therapeutics that target metalloenzymes lies squarely at the interface of bioinorganic and medicinal chemistry and requires expertise, methods, and strategies from both fields to mount an effective campaign. In this Account, our research program that brings together the principles and methods of bioinorganic and medicinal chemistry are described, in an effort to bridge the gap between these fields and address an important class of medicinal targets. Fragment-based drug discovery (FBDD) is an important drug discovery approach that is particularly well suited for metalloenzyme inhibitor development. FBDD uses relatively small but diverse chemical structures that allow for the assembly of privileged molecular collections that focus on a specific feature of the target enzyme. For metalloenzyme inhibition, the specific feature is rather obvious, namely, a metal-dependent active site. Surprisingly, prior to our work, the exploration of diverse molecular fragments for binding the metal active sites of metalloenzymes was largely unexplored. By assembling a modest library of metal-binding pharmacophores (MBPs), we have been able to find lead hits for many metalloenzymes and, from these hits, develop inhibitors that act via novel mechanisms of action. A specific case study on the use of this strategy to identify a first-in-class inhibitor of zinc-dependent Rpn11 (a component of the proteasome) is highlighted. The application of FBDD for the development of metalloenzyme inhibitors has raised several other compelling questions, such as how the metalloenzyme active site influences the coordination chemistry of bound fragments, how one can identify the best fragments for a given metalloenzyme, and many others. Among the most significant, and concerning, questions for metalloenzyme inhibition are those that reside around issues of specificity and whether metalloenzyme inhibitors can be as selective and specific as other small molecule inhibitors (i.e., compounds that inhibit enzymes that do not utilize a metal at their active site). This also leads to the question of whether metalloenzyme inhibitors might interfere more broadly with the metallome. Efforts to address these and related questions are discussed, with the expectation that our findings will illuminate some of these topics, alleviate some of these concerns, and encourage greater interest in this important, undervalued class of drug targets.
Collapse
Affiliation(s)
- Seth M. Cohen
- Department of Chemistry and
Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| |
Collapse
|
19
|
Cheng X, Gao P, Sun L, Tian Y, Zhan P, Liu X. Identification of spirocyclic or phosphate substituted quinolizine derivatives as novel HIV-1 integrase inhibitors: a patent evaluation of WO2016094197A1, WO2016094198A1 and WO2016154527A1. Expert Opin Ther Pat 2017; 27:1277-1286. [PMID: 28749251 DOI: 10.1080/13543776.2017.1360283] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Highly active antiretroviral therapy (HAART) has been widely adopted to control the HIV-1 infection successfully. HIV-1 integrase (IN) inhibitors are primary drugs in HAART regimens targeting integration step in the HIV-1 life cycle. However, due to the emergence of viral resistance and cross-resistance amongst drugs, there is a pressing need for new and potent IN inhibitors. This review covers the three patents describing spirocyclic and phosphate substituted quinolizine derivatives as novel HIV-1 IN inhibitors for the discovery of new anti-HIV-1 drug candidates. Areas covered: This review is focused on spirocyclic and phosphate substituted quinolizine derivatives bearing the same metal chelation scaffold as novel HIV-1 IN inhibitors. Expert opinion: Generally, privileged structure-based optimizations have emerged as an effective approach to discover newly antiviral agents. More generally, due to the similar Mg2+ catalytic active centers of endoribonucleases, some divalent metal ion chelators were found to be versatile binders targeting multiple metalloenzymes. Therefore, privileged structure-based scaffold re-evolution is an important tactic to identify new chemotypes, to explore unknown biological activities, or to provide effective ligands for multiple targets by modifying the existing active compounds.
Collapse
Affiliation(s)
- Xiqiang Cheng
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , Shandong , P. R. China
| | - Ping Gao
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , Shandong , P. R. China
| | - Lin Sun
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , Shandong , P. R. China
| | - Ye Tian
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , Shandong , P. R. China
| | - Peng Zhan
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , Shandong , P. R. China
| | - Xinyong Liu
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , Shandong , P. R. China
| |
Collapse
|
20
|
Dick BL, Patel A, McCammon JA, Cohen SM. Effect of donor atom identity on metal-binding pharmacophore coordination. J Biol Inorg Chem 2017; 22:605-613. [PMID: 28389830 DOI: 10.1007/s00775-017-1454-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 03/28/2017] [Indexed: 01/03/2023]
Abstract
The inhibition and binding of three metal-binding pharmacophores (MBPs), 2-hydroxycyclohepta-2,4,6-trien-1-one (tropolone), 2-mercaptopyridine-N-oxide (1,2-HOPTO), and 2-hydroxycyclohepta-2,4,6-triene-1-thione (thiotropolone) to human carbonic anhydrase II (hCAII) and a mutant protein hCAII L198G were investigated. These MBPs displayed bidentate coordination to the active site Zn(II) metal ion, but the MBPs respond to the mutation of L198G differently, as characterized by inhibition activity assays and X-ray crystallography. The L198G mutation increases the active site volume thereby decreasing the steric pressure exerted on MBPs upon binding, allowing changes in MBP coordination to be observed. When comparing the binding mode of tropolone to thiotropolone or 1,2-HOPTO (O,O versus O,S donor sets), structural modifications of the hCAII active site were shown to have a stronger effect on MBPs with an O,O versus O,S donor set. These findings were corroborated with density functional theory (DFT) calculations of model coordination complexes. These results suggest that the MBP binding geometry is a malleable interaction, particularly for certain ligands, and that the identity of the donor atoms influences the response of the ligand to changes in the protein active site environment. Understanding underlying interactions between a MBP and a metalloenzyme active site may aid in the design and development of potent metalloenzyme inhibitors.
Collapse
Affiliation(s)
- Benjamin L Dick
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Ashay Patel
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA.,Department of Pharmacology, University of California San Diego, La Jolla, CA, USA.,Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA, USA.,National Biomedical Computation Resource, University of California San Diego, La Jolla, CA, USA
| | - Seth M Cohen
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA.
| |
Collapse
|
21
|
Ju H, Zhang J, Huang B, Kang D, Huang B, Liu X, Zhan P. Inhibitors of Influenza Virus Polymerase Acidic (PA) Endonuclease: Contemporary Developments and Perspectives. J Med Chem 2017; 60:3533-3551. [PMID: 28118010 DOI: 10.1021/acs.jmedchem.6b01227] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Influenza virus (IFV) causes periodic global influenza pandemics, resulting in substantial socioeconomic loss and burden on medical facilities. Yearly variation in the effectiveness of vaccines, slow responsiveness to vaccination in cases of pandemic IFV, and emerging resistance to available drugs highlight the need to develop additional small-molecular inhibitors that act on IFV proteins. One promising target is polymerase acidic (PA) endonuclease, which is a bridged dinuclear metalloenzyme that plays a crucial role in initiating IFV replication. During the past decade, intensive efforts have been made to develop small-molecular inhibitors of this endonuclease as candidate agents for treatment of IFV infection. Here, we review the current status of development of PA endonuclease inhibitors and we discuss the applicability of newer medicinal-chemistry strategies for the discovery more potent, selective, and safer inhibitors.
Collapse
Affiliation(s)
- Han Ju
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University , 44, West Culture Road, 250012, Jinan, Shandong, P. R. China
| | - Jian Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University , 44, West Culture Road, 250012, Jinan, Shandong, P. R. China
| | - Boshi Huang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University , 44, West Culture Road, 250012, Jinan, Shandong, P. R. China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University , 44, West Culture Road, 250012, Jinan, Shandong, P. R. China
| | - Bing Huang
- Poultry Institute, Shandong Academy of Agricultural Sciences , 1, Jiaoxiao Road, 250023, Jinan, Shandong, P. R. China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University , 44, West Culture Road, 250012, Jinan, Shandong, P. R. China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University , 44, West Culture Road, 250012, Jinan, Shandong, P. R. China
| |
Collapse
|
22
|
Cave-Ayland C, Skylaris CK, Essex JW. A Monte Carlo Resampling Approach for the Calculation of Hybrid Classical and Quantum Free Energies. J Chem Theory Comput 2017; 13:415-424. [DOI: 10.1021/acs.jctc.6b00506] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
| | | | - Jonathan W. Essex
- School of Chemistry, University of Southampton, Hampshire, SO17 1BJ, United Kingdom
| |
Collapse
|
23
|
Kljun J, Anko M, Traven K, Sinreih M, Pavlič R, Peršič Š, Ude Ž, Codina EE, Stojan J, Lanišnik Rižner T, Turel I. Pyrithione-based ruthenium complexes as inhibitors of aldo-keto reductase 1C enzymes and anticancer agents. Dalton Trans 2016; 45:11791-800. [PMID: 27357845 DOI: 10.1039/c6dt00668j] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Four ruthenium complexes of clinically used zinc ionophore pyrithione and its oxygen analog 2-hydroxypyridine N-oxide were prepared and evaluated as inhibitors of enzymes of the aldo-keto reductase subfamily 1C (AKR1C). A kinetic study assisted with docking simulations showed a mixed type of inhibition consisting of a fast reversible and a slow irreversible step in the case of both organometallic compounds 1A and 1B. Both compounds also showed a remarkable selectivity towards AKR1C1 and AKR1C3 which are targets for breast cancer drug design. The organoruthenium complex of ligand pyrithione as well as pyrithione itself also displayed toxicity on the hormone-dependent MCF-7 breast cancer cell line with EC50 values in the low micromolar range.
Collapse
Affiliation(s)
- Jakob Kljun
- Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Annunziato G, Angeli A, D'Alba F, Bruno A, Pieroni M, Vullo D, De Luca V, Capasso C, Supuran CT, Costantino G. Discovery of New Potential Anti-Infective Compounds Based on Carbonic Anhydrase Inhibitors by Rational Target-Focused Repurposing Approaches. ChemMedChem 2016; 11:1904-14. [PMID: 27304878 DOI: 10.1002/cmdc.201600180] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 05/16/2016] [Indexed: 12/31/2022]
Abstract
In academia, compound recycling represents an alternative drug discovery strategy to identify new pharmaceutical targets from a library of chemical compounds available in house. Herein we report the application of a rational target-based drug-repurposing approach to find diverse applications for our in-house collection of compounds. The carbonic anhydrase (CA, EC 4.2.1.1) metalloenzyme superfamily was identified as a potential target of our compounds. The combination of a thoroughly validated docking screening protocol, together with in vitro assays against various CA families and isoforms, allowed us to identify two unprecedented chemotypes as CA inhibitors. The identified compounds have the capacity to preferentially bind pathogenic (bacterial/protozoan) CAs over human isoforms and represent excellent hits for further optimization in hit-to-lead campaigns.
Collapse
Affiliation(s)
- Giannamaria Annunziato
- Università degli Studi di Parma, Dipartimento di Farmacia, P4T group, Parco Area delle Scienze, Via G.P. Usberti 27A, 43121, Parma, Italy
| | - Andrea Angeli
- Università degli Studi di Firenze, Neurofarba Dept., Section of Pharmaceutical and Nutriceutical Sciences, Via U. Schiff 6, 50019, Sesto Fiorentino, Florence, Italy
| | - Francesca D'Alba
- Università degli Studi di Parma, Dipartimento di Farmacia, P4T group, Parco Area delle Scienze, Via G.P. Usberti 27A, 43121, Parma, Italy
| | - Agostino Bruno
- Università degli Studi di Parma, Dipartimento di Farmacia, P4T group, Parco Area delle Scienze, Via G.P. Usberti 27A, 43121, Parma, Italy.
| | - Marco Pieroni
- Università degli Studi di Parma, Dipartimento di Farmacia, P4T group, Parco Area delle Scienze, Via G.P. Usberti 27A, 43121, Parma, Italy
| | - Daniela Vullo
- Università degli Studi di Firenze, Polo Scientifico, Laboratorio di Chimica Bioinorganica, Rm. 188, Via della Lastruccia 3, 50019, Sesto Fiorentino, Florence, Italy
| | - Viviana De Luca
- Istituto di Bioscienze e Biorisorse, CNR, Via Pietro Castellino 111, 80131, Napoli, Italy
| | - Clemente Capasso
- Istituto di Bioscienze e Biorisorse, CNR, Via Pietro Castellino 111, 80131, Napoli, Italy
| | - Claudiu T Supuran
- Università degli Studi di Firenze, Neurofarba Dept., Section of Pharmaceutical and Nutriceutical Sciences, Via U. Schiff 6, 50019, Sesto Fiorentino, Florence, Italy. .,Università degli Studi di Firenze, Polo Scientifico, Laboratorio di Chimica Bioinorganica, Rm. 188, Via della Lastruccia 3, 50019, Sesto Fiorentino, Florence, Italy.
| | - Gabriele Costantino
- Università degli Studi di Parma, Dipartimento di Farmacia, P4T group, Parco Area delle Scienze, Via G.P. Usberti 27A, 43121, Parma, Italy
| |
Collapse
|
25
|
Kavanagh ME, Coyne AG, McLean KJ, James GG, Levy CW, Marino LB, de Carvalho LPS, Chan DSH, Hudson SA, Surade S, Leys D, Munro AW, Abell C. Fragment-Based Approaches to the Development of Mycobacterium tuberculosis CYP121 Inhibitors. J Med Chem 2016; 59:3272-302. [PMID: 27002486 PMCID: PMC4835159 DOI: 10.1021/acs.jmedchem.6b00007] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The essential enzyme CYP121 is a target for drug development against antibiotic resistant strains of Mycobacterium tuberculosis. A triazol-1-yl phenol fragment 1 was identified to bind to CYP121 using a cascade of biophysical assays. Synthetic merging and optimization of 1 produced a 100-fold improvement in binding affinity, yielding lead compound 2 (KD = 15 μM). Deconstruction of 2 into its component retrofragments allowed the group efficiency of structural motifs to be assessed, the identification of more LE scaffolds for optimization and highlighted binding affinity hotspots. Structure-guided addition of a metal-binding pharmacophore onto LE retrofragment scaffolds produced low nanomolar (KD = 15 nM) CYP121 ligands. Elaboration of these compounds to target binding hotspots in the distal active site afforded compounds with excellent selectivity against human drug-metabolizing P450s. Analysis of the factors governing ligand potency and selectivity using X-ray crystallography, UV-vis spectroscopy, and native mass spectrometry provides insight for subsequent drug development.
Collapse
Affiliation(s)
- Madeline E Kavanagh
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, U.K
| | - Anthony G Coyne
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, U.K
| | - Kirsty J McLean
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester , 131 Princess Street, Manchester M1 7DN, U.K
| | - Guy G James
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, U.K
| | - Colin W Levy
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester , 131 Princess Street, Manchester M1 7DN, U.K
| | - Leonardo B Marino
- Laboratory of Mycobacterial Metabolism and Antibiotic Research, Francis Crick Institute, The Mill Hill Laboratory , London NW7 1AA, U.K.,School of Pharmaceutical Sciences, São Paulo State University (UNESP) , 4801-902 Araraquara, SP, Brazil
| | - Luiz Pedro S de Carvalho
- Laboratory of Mycobacterial Metabolism and Antibiotic Research, Francis Crick Institute, The Mill Hill Laboratory , London NW7 1AA, U.K
| | - Daniel S H Chan
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, U.K
| | - Sean A Hudson
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, U.K
| | - Sachin Surade
- Department of Biochemistry, University of Cambridge , 80 Tennis Court Road, Cambridge CB2 1GA U.K
| | - David Leys
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester , 131 Princess Street, Manchester M1 7DN, U.K
| | - Andrew W Munro
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester , 131 Princess Street, Manchester M1 7DN, U.K
| | - Chris Abell
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, U.K
| |
Collapse
|
26
|
Choi J, Choi KE, Park SJ, Kim SY, Jee JG. Ensemble-Based Virtual Screening Led to the Discovery of New Classes of Potent Tyrosinase Inhibitors. J Chem Inf Model 2016; 56:354-67. [DOI: 10.1021/acs.jcim.5b00484] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Joonhyeok Choi
- Research
Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 702-701, Republic of Korea
| | - Kwang-Eun Choi
- Research
Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 702-701, Republic of Korea
| | - Sung Jean Park
- College
of Pharmacy, Gachon University, Incheon 406-799, Republic of Korea
| | - Sun Yeou Kim
- College
of Pharmacy, Gachon University, Incheon 406-799, Republic of Korea
| | - Jun-Goo Jee
- Research
Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 702-701, Republic of Korea
| |
Collapse
|
27
|
Rogolino D, Bacchi A, De Luca L, Rispoli G, Sechi M, Stevaert A, Naesens L, Carcelli M. Investigation of the salicylaldehyde thiosemicarbazone scaffold for inhibition of influenza virus PA endonuclease. J Biol Inorg Chem 2015; 20:1109-21. [PMID: 26323352 DOI: 10.1007/s00775-015-1292-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 08/04/2015] [Indexed: 01/10/2023]
Abstract
The influenza virus PA endonuclease is an attractive target for the development of novel anti-influenza virus therapeutics, which are urgently needed because of the emergence of drug-resistant viral strains. Reported PA inhibitors are assumed to chelate the divalent metal ion(s) (Mg²⁺ or Mn²⁺) in the enzyme's catalytic site, which is located in the N-terminal part of PA (PA-Nter). In the present work, a series of salicylaldehyde thiosemicarbazone derivatives have been synthesized and evaluated for their ability to inhibit the PA-Nter catalytic activity. Compounds 1-6 have been evaluated against influenza virus, both in enzymatic assays with influenza virus PA-Nter and in virus yield assays in MDCK cells. In order to establish a structure-activity relationship, the hydrazone analogue of the most active thiosemicarbazone has also been evaluated. Since chelation may represent a mode of action of such class of molecules, we studied the interaction of two of them, one with and one without biological activity versus the PA enzyme, towards Mg²⁺, the ion that is probably involved in the endonuclease activity of the heterotrimeric influenza polymerase complex. The crystal structure of the magnesium complex of the o-vanillin thiosemicarbazone ligand 1 is also described. Moreover, docking studies of PA endonuclease with compounds 1 and 2 were performed, to further analyse the possible mechanism of action of this class of inhibitors.
Collapse
Affiliation(s)
- Dominga Rogolino
- Dipartimento di Chimica, Università di Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy
| | - Alessia Bacchi
- Dipartimento di Chimica, Università di Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy
| | - Laura De Luca
- Dipartimento di Scienze del Farmaco e Prodotti per la Salute, Università di Messina, Polo Universitario SS. Annunziata, 98158, Messina, Italy
| | - Gabriele Rispoli
- Dipartimento di Chimica, Università di Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy
| | - Mario Sechi
- Dipartimento di Chimica e Farmacia, Università di Sassari, Via Vienna 2, 07100, Sassari, Italy
| | - Annelies Stevaert
- Rega Institute for Medical Research, KU Leuven, 3000, Louvain, Belgium
| | - Lieve Naesens
- Rega Institute for Medical Research, KU Leuven, 3000, Louvain, Belgium
| | - Mauro Carcelli
- Dipartimento di Chimica, Università di Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy.
| |
Collapse
|