1
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Szél V, Zsidó BZ, Jeszenői N, Hetényi C. Target-ligand binding affinity from single point enthalpy calculation and elemental composition. Phys Chem Chem Phys 2023; 25:31714-31725. [PMID: 37964670 DOI: 10.1039/d3cp04483a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Reliable target-ligand binding thermodynamics data are essential for successful drug design and molecular engineering projects. Besides experimental methods, a number of theoretical approaches have been introduced for the generation of binding thermodynamics data. However, available approaches often neglect electronic effects or explicit water molecules influencing target-ligand interactions. To handle electronic effects within a reasonable time frame, we introduce a fast calculator QMH-L using a single target-ligand complex structure pre-optimized at the molecular mechanics level. QMH-L is composed of the semi-empirical quantum mechanics calculation of binding enthalpy with predicted explicit water molecules at the complex interface, and a simple descriptor based on the elemental composition of the ligand. QMH-L estimates the target-ligand binding free energy with a root mean square error (RMSE) of 0.94 kcal mol-1. The calculations also provide binding enthalpy values and they were compared with experimental binding thermodynamics data collected from the most reliable isothermal titration calorimetry studies of systems including various protein targets and challenging, large peptide ligands with a molecular weight of up to 2-3 thousand. The single point enthalpy calculations of QMH-L require modest computational resources and are based on short runs with open source and/or free software like Gromacs, Mopac, MobyWat, and Fragmenter. QMH-L can be applied for fast, automated scoring of drug candidates during a virtual screen, enthalpic engineering of new ligands or thermodynamic explanation of complex interactions.
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Affiliation(s)
- Viktor Szél
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary.
| | - Balázs Zoltán Zsidó
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary.
| | - Norbert Jeszenői
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary.
| | - Csaba Hetényi
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary.
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2
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Burgalassi S, Fragai M, Francesconi O, Cerofolini L, Monti D, Leone G, Lamponi S, Greco G, Magnani A, Nativi C. Functionalized Hyaluronic Acid for “ In Situ” Matrix Metalloproteinase Inhibition: A Bioactive Material to Treat the Dry Eye Sydrome. ACS Macro Lett 2022; 11:1190-1194. [PMID: 36103254 PMCID: PMC9583614 DOI: 10.1021/acsmacrolett.2c00455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Hyaluronic acid (HA)
is a naturally occurring polysaccharide
with
many molecular functions, including maintaining the structure and
physiology of the tissues, tissue remodeling, and inflammation. HA
is found naturally in physiological tear fluid, possesses excellent
mucus-layer-adhesive properties, and is successfully employed in the
treatment of dry eye syndrome (DES). However, HA has as major drawback:
its rapid in vivo degradation by hyaluronidase. We
report on a unique material, namely, HA-3, obtained by
the functionalization of HA with the metalloproteinase inhibitor 3 (MMPI). This material is characterized by an increased resistance
to hyaluronidase degradation, associated with MMP inhibition properties.
The ability of HA-3 to prevent dehydration of human corneal
epithelial cells in vitro and in vivo may accelerate the development of more efficient DES treatment and
broaden the application of HA in human diseases.
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Affiliation(s)
- Susi Burgalassi
- Department of Pharmacy, University of Pisa, via Bonanno 6, 56126 Pisa, Italy
| | - Marco Fragai
- Department of Chemistry (DICUS), University of Florence, Sesto Fiorentino 50019, Italy
- CeRM, via Sacconi 6, Sesto Fiorentino 50019, Italy
| | - Oscar Francesconi
- Department of Chemistry (DICUS), University of Florence, Sesto Fiorentino 50019, Italy
| | - Linda Cerofolini
- CIRMMP, University of Florence, via Sacconi, 6 Sesto Fiorentino 50019, Italy
| | - Daniela Monti
- Department of Pharmacy, University of Pisa, via Bonanno 6, 56126 Pisa, Italy
| | - Gemma Leone
- Department of Biotechnology, Chemistry and Pharmacy, via A. Moro, 2 53100 Siena, Italy
| | - Stefania Lamponi
- Department of Biotechnology, Chemistry and Pharmacy, via A. Moro, 2 53100 Siena, Italy
| | - Giuseppe Greco
- Rugani Hospital, SR222 Chiantigiana, 53035 Colombaio (Siena), Italy
| | - Agnese Magnani
- Department of Biotechnology, Chemistry and Pharmacy, via A. Moro, 2 53100 Siena, Italy
- INSTM, via G. Giusti,
9, 50121 Firenze, Italy
| | - Cristina Nativi
- Department of Chemistry (DICUS), University of Florence, Sesto Fiorentino 50019, Italy
- INSTM, via G. Giusti,
9, 50121 Firenze, Italy
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3
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López R, Díaz N, Francisco E, Martín-Pendás A, Suárez D. QM/MM Energy Decomposition Using the Interacting Quantum Atoms Approach. J Chem Inf Model 2022; 62:1510-1524. [PMID: 35212531 PMCID: PMC8965874 DOI: 10.1021/acs.jcim.1c01372] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The interacting quantum atoms (IQA) method decomposes the quantum mechanical (QM) energy of a molecular system in terms of one- and two-center (atomic) contributions within the context of the quantum theory of atoms in molecules. Here, we demonstrate that IQA, enhanced with molecular mechanics (MM) and Poisson-Boltzmann surface-area (PBSA) solvation methods, is naturally extended to the realm of hybrid QM/MM methodologies, yielding intra- and inter-residue energy terms that characterize all kinds of covalent and noncovalent bonding interactions. To test the robustness of this approach, both metal-water interactions and QM/MM boundary artifacts are characterized in terms of the IQA descriptors derived from QM regions of varying size in Zn(II)- and Mg(II)-water clusters. In addition, we analyze a homologous series of inhibitors in complex with a matrix metalloproteinase (MMP-12) by carrying out QM/MM-PBSA calculations on their crystallographic structures followed by IQA energy decomposition. Overall, these applications not only show the advantages of the IQA QM/MM approach but also address some of the challenges lying ahead for expanding the QM/MM methodology.
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Affiliation(s)
- Roberto López
- Departamento de Química y Física Aplicadas, Universidad de León, Facultad de Biología, Campus de Vegazana s/n, 24071 León (Castilla y León), Spain
| | - Natalia Díaz
- Departamento de Química Física y Analítica, Universidad de Oviedo, Facultad de Química, Julián Clavería 8, 33006 Oviedo (Asturias), Spain
| | - Evelio Francisco
- Departamento de Química Física y Analítica, Universidad de Oviedo, Facultad de Química, Julián Clavería 8, 33006 Oviedo (Asturias), Spain
| | - Angel Martín-Pendás
- Departamento de Química Física y Analítica, Universidad de Oviedo, Facultad de Química, Julián Clavería 8, 33006 Oviedo (Asturias), Spain
| | - Dimas Suárez
- Departamento de Química Física y Analítica, Universidad de Oviedo, Facultad de Química, Julián Clavería 8, 33006 Oviedo (Asturias), Spain
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4
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Leone G, Pepi S, Consumi M, Lamponi S, Fragai M, Martinucci M, Baldoneschi V, Francesconi O, Nativi C, Magnani A. Sodium hyaluronate-g-2-((N-(6-aminohexyl)-4-methoxyphenyl)sulfonamido)-N-hydroxyacetamide with enhanced affinity towards MMP12 catalytic domain to be used as visco-supplement with increased degradation resistance. Carbohydr Polym 2021; 271:118452. [PMID: 34364546 DOI: 10.1016/j.carbpol.2021.118452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/13/2021] [Accepted: 07/14/2021] [Indexed: 01/16/2023]
Abstract
The present paper describes the functionalization of sodium hyaluronate (NaHA) with a small molecule (2-((N-(6-aminohexyl)-4-methoxyphenyl)sulfonamido)-N-hydroxyacetamide) (MMPI) having proven inhibitory activity against membrane metalloproteins involved in inflammatory processes (i.e. MMP12). The obtained derivative (HA-MMPI) demonstrated an increased resistance to the in-vitro degradation by hyaluronidase, viscoelastic properties close to those of healthy human synovial fluid, cytocompatibility towards human chondrocytes and nanomolar affinity towards MMP 12. Thus, HA-MMPI can be considered a good candidate as viscosupplement in the treatment of knee osteoarticular disease.
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Affiliation(s)
- Gemma Leone
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy; National Interuniversity Consortium of Materials Science and Technology (INSTM), Via Giusti 9, 50121 Firenze, Italy
| | - Simone Pepi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy; National Interuniversity Consortium of Materials Science and Technology (INSTM), Via Giusti 9, 50121 Firenze, Italy
| | - Marco Consumi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy; National Interuniversity Consortium of Materials Science and Technology (INSTM), Via Giusti 9, 50121 Firenze, Italy
| | - Stefania Lamponi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy; National Interuniversity Consortium of Materials Science and Technology (INSTM), Via Giusti 9, 50121 Firenze, Italy
| | - Marco Fragai
- Department of Chemistry, "Ugo Schiff" - University of Florence - Via della Lastruccia 13, 50019 Sesto Fiorentino, FI, Italy; Cerm, University of Florence, via L. Sacconi 6, 50019 Sesto Fiorentino, FI, Italy
| | - Marco Martinucci
- Department of Chemistry, "Ugo Schiff" - University of Florence - Via della Lastruccia 13, 50019 Sesto Fiorentino, FI, Italy
| | - Veronica Baldoneschi
- Department of Chemistry, "Ugo Schiff" - University of Florence - Via della Lastruccia 13, 50019 Sesto Fiorentino, FI, Italy; National Interuniversity Consortium of Materials Science and Technology (INSTM), Via Giusti 9, 50121 Firenze, Italy
| | - Oscar Francesconi
- Department of Chemistry, "Ugo Schiff" - University of Florence - Via della Lastruccia 13, 50019 Sesto Fiorentino, FI, Italy; National Interuniversity Consortium of Materials Science and Technology (INSTM), Via Giusti 9, 50121 Firenze, Italy
| | - Cristina Nativi
- Department of Chemistry, "Ugo Schiff" - University of Florence - Via della Lastruccia 13, 50019 Sesto Fiorentino, FI, Italy; National Interuniversity Consortium of Materials Science and Technology (INSTM), Via Giusti 9, 50121 Firenze, Italy
| | - Agnese Magnani
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy; National Interuniversity Consortium of Materials Science and Technology (INSTM), Via Giusti 9, 50121 Firenze, Italy.
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5
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Liebeschuetz JW. The Good, the Bad, and the Twisted Revisited: An Analysis of Ligand Geometry in Highly Resolved Protein-Ligand X-ray Structures. J Med Chem 2021; 64:7533-7543. [PMID: 34060310 DOI: 10.1021/acs.jmedchem.1c00228] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An analysis of the rotatable bond geometry of drug-like ligand models is reported for high-resolution (<1.1 Å) crystallographic protein-ligand complexes. In cases where the ligand fit to the electron density is very good, unusual torsional geometry is rare and, most often, though not exclusively, associated with strong polar, metal, or covalent ligand-protein interactions. It is rarely associated with a torsional strain of greater than 2 kcal mol-1 by calculation. An unusual torsional geometry is more prevalent where the fit to electron density is not perfect. Multiple low-strain conformer bindings were observed in 21% of the set and, it is suggested, may also lie behind many of the 35% of single-occupancy cases, where a poor fit to the e-density was found. It is concluded that multiple conformer ligand binding is an under-recognized phenomenon in structure-based drug design and that there is a need for more robust crystallographic refinement methods to better handle such cases.
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Affiliation(s)
- John W Liebeschuetz
- Skilos Chemoinformatics, 159 Water Street, Cambridge CB4 1PB, United Kingdom.,Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Milton, Cambridge CB4 0QA, United Kingdom
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6
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Prediction of an MMP-1 inhibitor activity cliff using the SAR matrix approach and its experimental validation. Sci Rep 2020; 10:14710. [PMID: 32895466 PMCID: PMC7477548 DOI: 10.1038/s41598-020-71696-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 08/19/2020] [Indexed: 11/30/2022] Open
Abstract
A matrix metalloproteinase 1 (MMP-1) inhibitor activity cliff was predicted using the SAR Matrix method. Compound 4 was predicted as a highly potent activity cliff partner and found to possess 60 times higher inhibitory activity against MMP-1 than the structurally related compound 3. Furthermore, pharmacophore fitting of synthesized compounds indicated that the correctly predicted activity cliff was caused by interactions between the trifluoromethyl group at para position in compound 4 and residue ARG214 of MMP-1.
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7
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Raeeszadeh-Sarmazdeh M, Do LD, Hritz BG. Metalloproteinases and Their Inhibitors: Potential for the Development of New Therapeutics. Cells 2020; 9:E1313. [PMID: 32466129 PMCID: PMC7290391 DOI: 10.3390/cells9051313] [Citation(s) in RCA: 152] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 02/06/2023] Open
Abstract
The metalloproteinase (MP) family of zinc-dependent proteases, including matrix metalloproteinases (MMPs), a disintegrin and metalloproteases (ADAMs), and a disintegrin and metalloproteinase with thrombospondin motifs (ADAMTSs) plays a crucial role in the extracellular matrix (ECM) remodeling and degradation activities. A wide range of substrates of the MP family includes ECM components, chemokines, cell receptors, and growth factors. Metalloproteinases activities are tightly regulated by proteolytic activation and inhibition via their natural inhibitors, tissue inhibitors of metalloproteinases (TIMPs), and the imbalance of the activation and inhibition is responsible in progression or inhibition of several diseases, e.g., cancer, neurological disorders, and cardiovascular diseases. We provide an overview of the structure, function, and the multifaceted role of MMPs, ADAMs, and TIMPs in several diseases via their cellular functions such as proteolysis of other cell signaling factors, degradation and remodeling of the ECM, and other essential protease-independent interactions in the ECM. The significance of MP inhibitors targeting specific MMP or ADAMs with high selectivity is also discussed. Recent advances and techniques used in developing novel MP inhibitors and MP responsive drug delivery tools are also reviewed.
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Affiliation(s)
- Maryam Raeeszadeh-Sarmazdeh
- Chemical and Materials Engineering Department, University of Nevada, Reno, NV 89557, USA; (L.D.D.); (B.G.H.)
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8
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Ferenczy GG, Keserű GM. Thermodynamic profiling for fragment-based lead discovery and optimization. Expert Opin Drug Discov 2019; 15:117-129. [PMID: 31741402 DOI: 10.1080/17460441.2020.1691166] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Introduction: The enthalpic and entropic components of the ligand-protein binding free energy reflect the type and quality of the interactions and relate to the physicochemical properties of the ligands. These findings have significance in medicinal chemistry optimizations since they suggest that the thermodynamic profiling of the binding may help monitor and control the unfavorable size and hydrophobicity increase typically accompanying affinity improvements and leading to suboptimal pharmacokinetic properties.Areas covered: This review describes the ligand-protein binding event in terms of elementary steps, their associated interactions, and their enthalpic and entropic consequences. The relationships among the breaking and forming interactions, the binding thermodynamic profile, and the physicochemical properties of the ligands are also discussed.Expert opinion: Analysis of the size dependence of available affinity and favorable enthalpy highlights the limitation of the simultaneous optimization of these quantities. Indeed, moderate, rather than very high affinities can be conciliated with favorable physicochemical and pharmacokinetic profiles as it is supported by the affinity range of historical oral drugs. Although thermodynamic quantities are not suitable endpoints for medicinal chemistry optimizations owing to the complexity of the binding thermodynamics, thermodynamic profiling together with structural studies can be advantageously used to understand the details of the binding process and to optimize it.
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Affiliation(s)
- György G Ferenczy
- Medicinal Chemistry Research Group, Research Center for Natural Sciences, Budapest, Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Center for Natural Sciences, Budapest, Hungary
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9
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Cerofolini L, Fragai M, Luchinat C. Mechanism and Inhibition of Matrix Metalloproteinases. Curr Med Chem 2019; 26:2609-2633. [PMID: 29589527 DOI: 10.2174/0929867325666180326163523] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 03/06/2018] [Accepted: 03/06/2018] [Indexed: 01/02/2023]
Abstract
Matrix metalloproteinases hydrolyze proteins and glycoproteins forming the extracellular matrix, cytokines and growth factors released in the extracellular space, and membrane-bound receptors on the outer cell membrane. The pathological relevance of MMPs has prompted the structural and functional characterization of these enzymes and the development of synthetic inhibitors as possible drug candidates. Recent studies have provided a better understanding of the substrate preference of the different members of the family, and structural data on the mechanism by which these enzymes hydrolyze the substrates. Here, we report the recent advancements in the understanding of the mechanism of collagenolysis and elastolysis, and we discuss the perspectives of new therapeutic strategies for targeting MMPs.
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Affiliation(s)
- Linda Cerofolini
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Italy
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10
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Fischer T, Senn N, Riedl R. Design and Structural Evolution of Matrix Metalloproteinase Inhibitors. Chemistry 2019; 25:7960-7980. [DOI: 10.1002/chem.201805361] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 01/09/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Thomas Fischer
- Center of Organic and Medicinal Chemistry, Institute of Chemistry, and BiotechnologyZurich University of Applied Sciences (ZHAW) Einsiedlerstrasse 31 8820 Wädenswil Switzerland
| | - Nicole Senn
- Center of Organic and Medicinal Chemistry, Institute of Chemistry, and BiotechnologyZurich University of Applied Sciences (ZHAW) Einsiedlerstrasse 31 8820 Wädenswil Switzerland
| | - Rainer Riedl
- Center of Organic and Medicinal Chemistry, Institute of Chemistry, and BiotechnologyZurich University of Applied Sciences (ZHAW) Einsiedlerstrasse 31 8820 Wädenswil Switzerland
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11
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Yokoyama H, Sawada JI, Sato K, Ogo N, Kamei N, Ishikawa Y, Hara K, Asai A, Hashimoto H. Structural and Thermodynamic Basis of the Enhanced Interaction between Kinesin Spindle Protein Eg5 and STLC-type Inhibitors. ACS OMEGA 2018; 3:12284-12294. [PMID: 31459302 PMCID: PMC6644766 DOI: 10.1021/acsomega.8b00778] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 08/22/2018] [Indexed: 06/10/2023]
Abstract
For a better understanding of protein-inhibitor interactions, we report structural, thermodynamic, and biological analyses of the interactions between S-trityl-l-cysteine (STLC) derivatives and the motor domain of kinesin spindle protein Eg5. Binding of STLC-type inhibitors to Eg5 was enthalpically driven and entropically unfavorable. The introduction of a para-methoxy substituent in one phenyl ring of STLC enhances its inhibitory activity resulting from a larger enthalpy gain possibly due to the increased shape complementarity. The substituent fits to a recess in the binding pocket. To avoid steric hindrance, the substituted STLC is nudged toward the side opposite to the recess, which enhances the interaction of Eg5 with the remaining part of the inhibitor. Further introduction of an ethylene linkage between two phenyl rings enhances Eg5 inhibitory activity by reducing the loss of entropy in forming the complex. This study provides valuable examples of enhancing protein-inhibitor interactions without forming additional hydrogen bonds.
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Affiliation(s)
- Hideshi Yokoyama
- Faculty
of Pharmaceutical Sciences, Tokyo University
of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Jun-ichi Sawada
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Kohei Sato
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Naohisa Ogo
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Nanami Kamei
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Yoshinobu Ishikawa
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Kodai Hara
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Akira Asai
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Hiroshi Hashimoto
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
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12
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Wienen-Schmidt B, Jonker HRA, Wulsdorf T, Gerber HD, Saxena K, Kudlinzki D, Sreeramulu S, Parigi G, Luchinat C, Heine A, Schwalbe H, Klebe G. Paradoxically, Most Flexible Ligand Binds Most Entropy-Favored: Intriguing Impact of Ligand Flexibility and Solvation on Drug–Kinase Binding. J Med Chem 2018; 61:5922-5933. [DOI: 10.1021/acs.jmedchem.8b00105] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Barbara Wienen-Schmidt
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Hendrik R. A. Jonker
- Institut für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Straße 7, N160-3.14, 60438 Frankfurt am Main, Germany
| | - Tobias Wulsdorf
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Hans-Dieter Gerber
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Krishna Saxena
- Institut für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Straße 7, N160-3.14, 60438 Frankfurt am Main, Germany
| | - Denis Kudlinzki
- Institut für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Straße 7, N160-3.14, 60438 Frankfurt am Main, Germany
| | - Sridhar Sreeramulu
- Institut für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Straße 7, N160-3.14, 60438 Frankfurt am Main, Germany
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM/CIRMMP) and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM/CIRMMP) and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Harald Schwalbe
- Institut für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Straße 7, N160-3.14, 60438 Frankfurt am Main, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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13
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Claveria-Gimeno R, Vega S, Abian O, Velazquez-Campoy A. A look at ligand binding thermodynamics in drug discovery. Expert Opin Drug Discov 2017; 12:363-377. [DOI: 10.1080/17460441.2017.1297418] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Rafael Claveria-Gimeno
- Institute of Biocomputation and Physics of Complex Systems (BIFI), IQFR-CSIC-BIFI and GBsC-CSIC-BIFI Joint Units, Universidad de Zaragoza, Zaragoza, Spain
- Instituto Aragonés de Ciencias de la Salud (IACS), Zaragoza, Spain
- Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain
| | - Sonia Vega
- Institute of Biocomputation and Physics of Complex Systems (BIFI), IQFR-CSIC-BIFI and GBsC-CSIC-BIFI Joint Units, Universidad de Zaragoza, Zaragoza, Spain
| | - Olga Abian
- Institute of Biocomputation and Physics of Complex Systems (BIFI), IQFR-CSIC-BIFI and GBsC-CSIC-BIFI Joint Units, Universidad de Zaragoza, Zaragoza, Spain
- Instituto Aragonés de Ciencias de la Salud (IACS), Zaragoza, Spain
- Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain
- Department of Biochemistry and Molecular and Cell Biology, Universidad de Zaragoza, Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), IQFR-CSIC-BIFI and GBsC-CSIC-BIFI Joint Units, Universidad de Zaragoza, Zaragoza, Spain
- Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain
- Department of Biochemistry and Molecular and Cell Biology, Universidad de Zaragoza, Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
- Fundación ARAID, Government of Aragon, Zaragoza, Spain
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14
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Arylsulfonamides and selectivity of matrix metalloproteinase-2: An overview. Eur J Med Chem 2017; 129:72-109. [DOI: 10.1016/j.ejmech.2017.02.014] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 02/02/2017] [Accepted: 02/06/2017] [Indexed: 12/14/2022]
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15
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Synthesis and binding monitoring of a new nanomolar PAMAM-based matrix metalloproteinases inhibitor (MMPIs). Bioorg Med Chem 2017; 25:523-527. [DOI: 10.1016/j.bmc.2016.11.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 11/10/2016] [Accepted: 11/11/2016] [Indexed: 11/18/2022]
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16
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Schneider HJ. Spatial mismatch, non-additive binding energies and selectivity in supramolecular complexes. Org Biomol Chem 2017; 15:2146-2151. [DOI: 10.1039/c6ob02755e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A geometric mismatch in supramolecular complexes often leads to deviations from the additivity of binding energies with the consequence of large changes in selectivity and binding mode.
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Affiliation(s)
- Hans-Jörg Schneider
- FR Organische Chemie der Universität des Saarlandes
- D 66123 Saarbrücken
- Germany
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17
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Rouanet-Mehouas C, Czarny B, Beau F, Cassar-Lajeunesse E, Stura EA, Dive V, Devel L. Zinc–Metalloproteinase Inhibitors: Evaluation of the Complex Role Played by the Zinc-Binding Group on Potency and Selectivity. J Med Chem 2016; 60:403-414. [DOI: 10.1021/acs.jmedchem.6b01420] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Cecile Rouanet-Mehouas
- Service d’Ingénierie
Moléculaire des Protéines (SIMOPRO), IBITECS, CEA, Université Paris-Saclay, Gif/Yvette F-91191, France
| | - Bertrand Czarny
- Service d’Ingénierie
Moléculaire des Protéines (SIMOPRO), IBITECS, CEA, Université Paris-Saclay, Gif/Yvette F-91191, France
| | - Fabrice Beau
- Service d’Ingénierie
Moléculaire des Protéines (SIMOPRO), IBITECS, CEA, Université Paris-Saclay, Gif/Yvette F-91191, France
| | - Evelyne Cassar-Lajeunesse
- Service d’Ingénierie
Moléculaire des Protéines (SIMOPRO), IBITECS, CEA, Université Paris-Saclay, Gif/Yvette F-91191, France
| | - Enrico A. Stura
- Service d’Ingénierie
Moléculaire des Protéines (SIMOPRO), IBITECS, CEA, Université Paris-Saclay, Gif/Yvette F-91191, France
| | - Vincent Dive
- Service d’Ingénierie
Moléculaire des Protéines (SIMOPRO), IBITECS, CEA, Université Paris-Saclay, Gif/Yvette F-91191, France
| | - Laurent Devel
- Service d’Ingénierie
Moléculaire des Protéines (SIMOPRO), IBITECS, CEA, Université Paris-Saclay, Gif/Yvette F-91191, France
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18
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Baldoneschi V, Cerofolini L, Dragoni E, Storai A, Luchinat C, Fragai M, Richichi B, Nativi C. Active-Site Targeting Paramagnetic Probe for Matrix Metalloproteinases. Chempluschem 2016; 81:1333-1338. [DOI: 10.1002/cplu.201600375] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 09/23/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Veronica Baldoneschi
- Department of Chemistry “Ugo Schiff”; University of Florence; Via della Lastruccia 3-13 50019 Sesto Fiorentino Italy
| | - Linda Cerofolini
- Department of Chemistry “Ugo Schiff”; University of Florence; Via della Lastruccia 3-13 50019 Sesto Fiorentino Italy
- CERM; Univeristy of Florence; Via Sacconi 6 50019 Sesto Fiorentino Italy
| | - Elisa Dragoni
- Department of Chemistry “Ugo Schiff”; University of Florence; Via della Lastruccia 3-13 50019 Sesto Fiorentino Italy
| | - Andrea Storai
- Department of Chemistry “Ugo Schiff”; University of Florence; Via della Lastruccia 3-13 50019 Sesto Fiorentino Italy
| | - Claudio Luchinat
- Department of Chemistry “Ugo Schiff”; University of Florence; Via della Lastruccia 3-13 50019 Sesto Fiorentino Italy
- CERM; Univeristy of Florence; Via Sacconi 6 50019 Sesto Fiorentino Italy
| | - Marco Fragai
- Department of Chemistry “Ugo Schiff”; University of Florence; Via della Lastruccia 3-13 50019 Sesto Fiorentino Italy
- CERM; Univeristy of Florence; Via Sacconi 6 50019 Sesto Fiorentino Italy
| | - Barbara Richichi
- Department of Chemistry “Ugo Schiff”; University of Florence; Via della Lastruccia 3-13 50019 Sesto Fiorentino Italy
| | - Cristina Nativi
- Department of Chemistry “Ugo Schiff”; University of Florence; Via della Lastruccia 3-13 50019 Sesto Fiorentino Italy
- CERM; Univeristy of Florence; Via Sacconi 6 50019 Sesto Fiorentino Italy
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19
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Yuan XM, Lin DQ, Zhang QL, Gao D, Yao SJ. A microcalorimetric study of molecular interactions between immunoglobulin G and hydrophobic charge-induction ligand. J Chromatogr A 2016; 1443:145-51. [DOI: 10.1016/j.chroma.2016.03.041] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 03/14/2016] [Accepted: 03/14/2016] [Indexed: 10/22/2022]
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20
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Abstract
Detailed thermodynamic analysis of fragment binding revealed that unlike drug-like compounds, fragments bind with significant enthalpic preference.
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Affiliation(s)
- György G. Ferenczy
- Medicinal Chemistry Research Group
- Research Centre for Natural Sciences
- Hungarian Academy of Sciences
- Budapest 1117
- Hungary
| | - György M. Keserű
- Medicinal Chemistry Research Group
- Research Centre for Natural Sciences
- Hungarian Academy of Sciences
- Budapest 1117
- Hungary
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21
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The impact of binding thermodynamics on medicinal chemistry optimizations. Future Med Chem 2015; 7:1285-303. [DOI: 10.4155/fmc.15.63] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Ligand binding thermodynamics has been attracted considerable interest in the past decade owing to the recognized relation between binding thermodynamic profile and the physicochemical and druglike properties of compounds. In this review, the relation between optimization strategies and ligand properties is presented based on the structural and thermodynamic analysis of ligand–protein complex formation. The control of the binding thermodynamic profile is beneficial for the balanced affinity and physicochemical properties of drug candidates, and early phase optimization gives more opportunity to this control.
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22
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Radisky ES, Radisky DC. Matrix metalloproteinases as breast cancer drivers and therapeutic targets. Front Biosci (Landmark Ed) 2015; 20:1144-63. [PMID: 25961550 DOI: 10.2741/4364] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Members of the matrix metalloproteinase (MMP) family have been identified as poor prognosis markers for breast cancer patients and as drivers of many facets of the tumor phenotype in experimental models. Early enthusiasm for MMPs as therapeutic targets was tempered following disappointing clinical trials that utilized broad spectrum, small molecule catalytic site inhibitors. However, subsequent research has continued to define key roles for MMPs as breast cancer promoters, to elucidate the complex roles that that these proteins play in breast cancer development and progression, and to identify how these roles are linked to specific and unique biochemical features of individual members of the MMP family. Here, we provide an overview of the structural features of the MMPs, then discuss clinical studies identifying which MMP family members are linked with breast cancer development and new experimental studies that reveal how these specific MMPs may play unique roles in the breast cancer microenvironment. We conclude with a discussion of the most promising avenues for development of therapeutic agents capable of targeting the tumor-promoting properties of MMPs.
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Affiliation(s)
- Evette S Radisky
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida 32224,
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23
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2-Benzisothiazolylimino-5-benzylidene-4-thiazolidinones as protective agents against cartilage destruction. Bioorg Med Chem 2015; 23:1551-6. [DOI: 10.1016/j.bmc.2015.02.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 02/02/2015] [Accepted: 02/04/2015] [Indexed: 11/17/2022]
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24
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Is there a link between selectivity and binding thermodynamics profiles? Drug Discov Today 2015; 20:86-94. [DOI: 10.1016/j.drudis.2014.09.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 09/02/2014] [Accepted: 09/17/2014] [Indexed: 01/29/2023]
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25
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Panico A, Maccari R, Cardile V, Avondo S, Crascì L, Ottanà R. Evaluation of the anti-inflammatory/chondroprotective activity of aldose reductase inhibitors in human chondrocyte cultures. MEDCHEMCOMM 2015. [DOI: 10.1039/c4md00556b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
2-Thioxo-4-thiazolidinone derivatives active as aldose reductase inhibitors were able to control key inflammatory/degenerative events induced by IL-1β in human chondrocytes, appearing to be promising candidates in the search for novel anti-inflammatory agents.
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Affiliation(s)
- Annamaria Panico
- Department of Drug Sciences
- University of Catania
- 95125 Catania
- Italy
| | - Rosanna Maccari
- Department of Scienze del Farmaco e dei Prodotti per la Salute
- University of Messina
- Polo Universitario dell'Annunziata
- 98168 Messina
- Italy
| | - Venera Cardile
- Department of Biomedical Sciences
- University of Catania
- 95125 Catania
- Italy
| | - Sergio Avondo
- Department of Surgery
- University of Catania
- 95125 Catania
- Italy
| | - Lucia Crascì
- Department of Drug Sciences
- University of Catania
- 95125 Catania
- Italy
| | - Rosaria Ottanà
- Department of Scienze del Farmaco e dei Prodotti per la Salute
- University of Messina
- Polo Universitario dell'Annunziata
- 98168 Messina
- Italy
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26
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Hitaoka S, Chuman H, Yoshizawa K. A QSAR study on the inhibition mechanism of matrix metalloproteinase-12 by arylsulfone analogs based on molecular orbital calculations. Org Biomol Chem 2015; 13:793-806. [DOI: 10.1039/c4ob01843e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The inhibition mechanism of matrix metalloproteinase-12 by arylsulfone analogs is revealed using a comprehensive computational approach including docking simulations, molecular orbital calculations, and QSAR.
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Affiliation(s)
- Seiji Hitaoka
- Institute for Materials Chemistry and Engineering and International Research Center for Molecular System
- Kyushu University
- Fukuoka 819-0395
- Japan
| | - Hiroshi Chuman
- Institute of Health Biosciences
- The University of Tokushima Graduate School
- Tokushima 770-8505
- Japan
| | - Kazunari Yoshizawa
- Institute for Materials Chemistry and Engineering and International Research Center for Molecular System
- Kyushu University
- Fukuoka 819-0395
- Japan
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27
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Fabre B, Filipiak K, Díaz N, Zapico JM, Suárez D, Ramos A, de Pascual-Teresa B. An Integrated Computational and Experimental Approach to Gaining Selectivity for MMP-2 within the Gelatinase Subfamily. Chembiochem 2014; 15:399-412. [DOI: 10.1002/cbic.201300698] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Indexed: 12/27/2022]
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28
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Fragai M, Luchinat C, Martelli T, Ravera E, Sagi I, Solomonov I, Udi Y. SSNMR of biosilica-entrapped enzymes permits an easy assessment of preservation of native conformation in atomic detail. Chem Commun (Camb) 2014; 50:421-3. [DOI: 10.1039/c3cc46896h] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Kreituss I, Rozenberga E, Zemītis J, Trapencieris P, Romanchikova N, Turks M. Discovery of aziridine-triazole conjugates as selective MMP-2 inhibitors. Chem Heterocycl Compd (N Y) 2013. [DOI: 10.1007/s10593-013-1351-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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30
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Turcu I, Mic M. Size Dependence of Molecular Self-Assembling in Stacked Aggregates. 2. Heat Exchange Effects. J Phys Chem B 2013; 117:9083-93. [DOI: 10.1021/jp403768x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ioan Turcu
- Department of Molecular and Biomolecular Physics, National Institute of Isotopic and Molecular Technology, 400293 Cluj-Napoca, Romania
| | - Mihaela Mic
- Department of Molecular and Biomolecular Physics, National Institute of Isotopic and Molecular Technology, 400293 Cluj-Napoca, Romania
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31
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Mori M, Massaro A, Calderone V, Fragai M, Luchinat C, Mordini A. Discovery of a New Class of Potent MMP Inhibitors by Structure-Based Optimization of the Arylsulfonamide Scaffold. ACS Med Chem Lett 2013; 4:565-9. [PMID: 24900710 DOI: 10.1021/ml300446a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 03/13/2013] [Indexed: 01/29/2023] Open
Abstract
A new class of potent matrix metalloproteinase (MMP) inhibitors designed by structure-based optimization of the well-known arylsulfonamide scaffold is presented. Molecules show an ethylene linker connecting the sulfonamide group with the P1' aromatic portion and a d-proline residue bearing the zinc-binding group. The affinity improvement provided by these modifications led us to discover a nanomolar MMP inhibitor bearing a carboxylate moiety as zinc-binding group, which might be a promising lead molecule. Notably, a significant selectivity for MMP-8, MMP-12, and MMP-13 was observed with respect to MMP-1 and MMP-7.
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Affiliation(s)
- Mattia Mori
- ProtEra Srl, Scientific Campus, University of Florence, viale delle idee 22, I-50019
Sesto Fiorentino, Italy
- Magnetic Resonance Center (CERM), University of Florence, via L. Sacconi 6, I-50019 Sesto
Fiorentino, Italy
| | - Assunta Massaro
- ProtEra Srl, Scientific Campus, University of Florence, viale delle idee 22, I-50019
Sesto Fiorentino, Italy
| | - Vito Calderone
- Magnetic Resonance Center (CERM), University of Florence, via L. Sacconi 6, I-50019 Sesto
Fiorentino, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, via L. Sacconi 6, I-50019 Sesto
Fiorentino, Italy
- Department
of Chemistry “Ugo
Shiff”, University of Florence,
via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, via L. Sacconi 6, I-50019 Sesto
Fiorentino, Italy
- Department
of Chemistry “Ugo
Shiff”, University of Florence,
via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Alessandro Mordini
- ICCOM-CNR, Dipartimento
di Chimica “U. Schiff”, via della Lastruccia
13, I-50019 Sesto Fiorentino, Italy
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32
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Czarny B, Stura EA, Devel L, Vera L, Cassar-Lajeunesse E, Beau F, Calderone V, Fragai M, Luchinat C, Dive V. Molecular Determinants of a Selective Matrix Metalloprotease-12 Inhibitor: Insights from Crystallography and Thermodynamic Studies. J Med Chem 2013; 56:1149-59. [DOI: 10.1021/jm301574d] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bertrand Czarny
- CEA, Service
d’Ingénierie
Moléculaire des Protéines (SIMOPRO), Gif/Yvette 91191
Cedex, France
| | - Enrico A. Stura
- CEA, Service
d’Ingénierie
Moléculaire des Protéines (SIMOPRO), Gif/Yvette 91191
Cedex, France
| | - Laurent Devel
- CEA, Service
d’Ingénierie
Moléculaire des Protéines (SIMOPRO), Gif/Yvette 91191
Cedex, France
| | - Laura Vera
- CEA, Service
d’Ingénierie
Moléculaire des Protéines (SIMOPRO), Gif/Yvette 91191
Cedex, France
| | | | - Fabrice Beau
- CEA, Service
d’Ingénierie
Moléculaire des Protéines (SIMOPRO), Gif/Yvette 91191
Cedex, France
| | - Vito Calderone
- Magnetic
Resonance Center (CERM),
University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino,
Italy
| | - Marco Fragai
- Magnetic
Resonance Center (CERM),
University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino,
Italy
| | - Claudio Luchinat
- Magnetic
Resonance Center (CERM),
University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino,
Italy
| | - Vincent Dive
- CEA, Service
d’Ingénierie
Moléculaire des Protéines (SIMOPRO), Gif/Yvette 91191
Cedex, France
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33
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Crascì L, Panico A. Protective Effects of Many <i>Citrus</i> Flavonoids on Cartilage Degradation Process. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/jbnb.2013.43035] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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34
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Bartoloni M, Domínguez BE, Dragoni E, Richichi B, Fragai M, André S, Gabius HJ, Ardá A, Luchinat C, Jiménez-Barbero J, Nativi C. Targeting Matrix Metalloproteinases: Design of a Bifunctional Inhibitor for Presentation by Tumour-Associated Galectins. Chemistry 2012; 19:1896-902. [DOI: 10.1002/chem.201203794] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Indexed: 12/18/2022]
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35
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Jain P, Saravanan C, Singh SK. Sulphonamides: Deserving class as MMP inhibitors? Eur J Med Chem 2012; 60:89-100. [PMID: 23287054 DOI: 10.1016/j.ejmech.2012.10.016] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Revised: 09/26/2012] [Accepted: 10/02/2012] [Indexed: 12/14/2022]
Abstract
The importance of sulphonamide moiety in medicinal chemistry cannot be ignored as it constitutes an important class of extensively used drugs. Recently, sulphonamides have also been reported for their matrix metalloproteinase (MMP) inhibitory activity. MMPs are calcium- and zinc-dependent endopeptidases, involved in both inter- and intra-cellular activity. This review documents the emergence of sulphonamides as matrix metalloproteinase inhibitors (MMPIs) from the first generation to the recent third generation MMPIs, their mode of action - how sulphonamides act on MMPs? as well as the structure activity relationship along with their therapeutic uses in chronic obstructive pulmonary disease (COPD), ulcer, asthma, arthritis and cancer. From this review, readers can get answer for the question- is sulphonamides a potential class of MMPIs?
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Affiliation(s)
- Pranjali Jain
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutics, Indian Institute of Technology (BHU), Varanasi 221005, India
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36
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Kovacs H, Agback T, Isaksson J. Probing water-protein contacts in a MMP-12/CGS27023A complex by nuclear magnetic resonance spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2012; 53:85-92. [PMID: 22528292 DOI: 10.1007/s10858-012-9624-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Accepted: 03/28/2012] [Indexed: 05/31/2023]
Abstract
Using the case of the catalytic domain of MMP-12 in complex with the known inhibitor CGS27023A, a recently assembled 3D (15)N-edited/(14)N,(12)C-filtered ROESY experiment is used to monitor and distinguish protein amide protons in fast exchange with bulk water from amide protons close to water molecules with longer residence times, the latter possibly reflecting water molecules of structural or functional importance. The (15)N-edited/(14)N,(12)C-filtered ROESY spectra were compared to the original (15)N-edited/(14)N,(12)C-filtered NOESY and the conventional amide-water exchange experiment, CLEANEX. Three protein backbone amide protons experiencing direct dipolar cross relaxation with water in the (15)N-edited/(14)N,(12)C-filtered ROESY spectrum were assigned. In an ensemble of six crystal structures, two conserved water molecules within 3 Å of the three amide protons were identified. These two water molecules are buried into cavities in the protein surface and thus sufficiently slowed down by the protein topology to account for the observed dipolar interaction. Structural analysis of an ensemble of six crystal structures ruled out any exchange-relayed contributions for the amide-water interactions of interest.
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37
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Mori M, De Lorenzo E, Torre E, Fragai M, Nativi C, Luchinat C, Arcangeli A. A Highly Soluble Matrix Metalloproteinase-9 Inhibitor for Potential Treatment of Dry Eye Syndrome. Basic Clin Pharmacol Toxicol 2012; 111:289-95. [DOI: 10.1111/j.1742-7843.2012.00896.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 04/07/2012] [Indexed: 12/13/2022]
Affiliation(s)
- Mattia Mori
- ProtEra Srl; Scientific Campus of the University of Florence; Florence; Italy
| | - Emanuele De Lorenzo
- ProtEra Srl; Scientific Campus of the University of Florence; Florence; Italy
| | - Eugenio Torre
- Department of Experimental Pathology and Oncology; University of Florence; Florence; Italy
| | - Marco Fragai
- Magnetic Resonance Centre and Department of Chemistry; University of Florence; Florence; Italy
| | | | | | - Annarosa Arcangeli
- Department of Experimental Pathology and Oncology; University of Florence; Florence; Italy
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38
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Benzisothiazolyliminothiazolidin-4-ones with Chondroprotective Properties: Searching for Potent and Selective Inhibitors of MMP-13. ChemMedChem 2011; 6:1199-202. [DOI: 10.1002/cmdc.201100223] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Indexed: 12/21/2022]
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Zapico JM, Serra P, García-Sanmartín J, Filipiak K, Carbajo RJ, Schott AK, Pineda-Lucena A, Martínez A, Martín-Santamaría S, de Pascual-Teresa B, Ramos A. Potent “Clicked” MMP2 Inhibitors: Synthesis, Molecular Modeling and Biological Exploration. Org Biomol Chem 2011; 9:4587-99. [DOI: 10.1039/c0ob00852d] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Panico AM, Vicini P, Geronikaki A, Incerti M, Cardile V, Crascì L, Messina R, Ronsisvalle S. Heteroarylimino-4-thiazolidinones as inhibitors of cartilage degradation. Bioorg Chem 2010; 39:48-52. [PMID: 21208635 DOI: 10.1016/j.bioorg.2010.11.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Revised: 11/23/2010] [Accepted: 11/24/2010] [Indexed: 02/03/2023]
Abstract
2-Benzo[d]thiazolyl- and 2-benzo[d]isothiazolyl-imino-5-benzylidene-4-thiazolidinone derivatives were investigated as potential metalloproteinases (MMPs) inhibitors and evaluated for their antidegenerative activity on human chondrocyte cultures stimulated by IL-1β, using an experimental model that reproduces the mechanisms involved in osteoarthritic (OA) diseases. Cell viability, the amount of glycosaminoglycans (GAGs) and the production of nitric oxide (NO) were measured. The most potent compound, 5-(4-methoxy-benzylidene)-2-(benzo[d]isothiazol-3-ylimino)-thiazolidin-4-one (4b), a MMP-13 inhibitor at nanomolar concentration (IC(50)=0.036 μM), could be considered as a lead compound for the development of novel clinical agents, inhibitors of cartilage degradation, for the treatment of OA.
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Affiliation(s)
- Anna Maria Panico
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Catania, Viale A. Doria 6, Catania, Italy.
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Attolino E, Calderone V, Dragoni E, Fragai M, Richichi B, Luchinat C, Nativi C. Structure-based approach to nanomolar, water soluble matrix metalloproteinases inhibitors (MMPIs). Eur J Med Chem 2010; 45:5919-25. [DOI: 10.1016/j.ejmech.2010.09.057] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Revised: 09/22/2010] [Accepted: 09/27/2010] [Indexed: 01/10/2023]
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Nuti E, Casalini F, Avramova SI, Santamaria S, Fabbi M, Ferrini S, Marinelli L, La Pietra V, Limongelli V, Novellino E, Cercignani G, Orlandini E, Nencetti S, Rossello A. Potent Arylsulfonamide Inhibitors of Tumor Necrosis Factor-α Converting Enzyme Able to Reduce Activated Leukocyte Cell Adhesion Molecule Shedding in Cancer Cell Models. J Med Chem 2010; 53:2622-35. [DOI: 10.1021/jm901868z] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Elisa Nuti
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, via Bonanno 6, 56126 Pisa, Italy
| | - Francesca Casalini
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, via Bonanno 6, 56126 Pisa, Italy
| | - Stanislava I. Avramova
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, via Bonanno 6, 56126 Pisa, Italy
| | - Salvatore Santamaria
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, via Bonanno 6, 56126 Pisa, Italy
| | - Marina Fabbi
- Istituto Nazionale per la Ricerca sul Cancro, Largo R. Benzi 10, 16132 Genova, Italy
| | - Silvano Ferrini
- Istituto Nazionale per la Ricerca sul Cancro, Largo R. Benzi 10, 16132 Genova, Italy
| | - Luciana Marinelli
- Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via Domenico Montesano 49, 80131 Napoli, Italy
| | - Valeria La Pietra
- Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via Domenico Montesano 49, 80131 Napoli, Italy
| | - Vittorio Limongelli
- Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via Domenico Montesano 49, 80131 Napoli, Italy
| | - Ettore Novellino
- Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via Domenico Montesano 49, 80131 Napoli, Italy
| | - Giovanni Cercignani
- Dipartimento di Biologia, Unità di Biochimica, Università di Pisa, Via San Zeno, 51, 56127 Pisa, Italy
| | - Elisabetta Orlandini
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, via Bonanno 6, 56126 Pisa, Italy
| | - Susanna Nencetti
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, via Bonanno 6, 56126 Pisa, Italy
| | - Armando Rossello
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, via Bonanno 6, 56126 Pisa, Italy
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Edink E, Jansen C, Leurs R, de Esch IJ. The heat is on: thermodynamic analysis in fragment-based drug discovery. DRUG DISCOVERY TODAY. TECHNOLOGIES 2010; 7:e147-e202. [PMID: 24103770 DOI: 10.1016/j.ddtec.2010.12.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
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Abstract
The recognition that the successful clinical use of MMP inhibitors will require quantitative correlation of MMP activity with disease type, and to disease progression, has stimulated intensive effort toward the development of sensitive assay methods, improved analytical methods for the determination of the structural profile for MMP-sub-type inhibition, and the development of new methods for the determination - in both quantitative and qualitative terms - of MMP activity. This chapter reviews recent progress toward these objectives, with particular emphasis on the quantitative and qualitative profiling of MMP activity in cells and tissues. Quantitative determination of MMP activity is made from the concentration of the MMP from the tissue, using immobilization of a broad-spectrum MMP inhibitor on a chromatography resin. Active MMP, to the exclusion of MMP zymogens and endogenous TIMP-inhibited MMPs, is retained on the column. Characterization of the MMP sub-type(s) follows from appropriate analysis of the active MMP eluted from the resin. Qualitative determination of MMP involvement in disease can be made using an MMP sub-type-selective inhibitor. The proof of principle, with respect to this qualitative determination of the disease involvement of the gelatinase MMP-2 and MMP-9 sub-types, is provided by the class of thiirane-based MMP mechanism-based inhibitors (SB-3CT as the prototype). Positive outcomes in animal models of disease having MMP-2 and/or -9 dependency follow administration of this MMP inhibitor, whereas this inhibitor is inactive in disease models where other MMPs (such as MMP-14) are involved.
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Affiliation(s)
- Jed F Fisher
- Department of Chemistry and Biochemistry, Walther Cancer Research Center, University of Notre Dame, Notre Dame, IN, USA
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Roselin LS, Lin MS, Lin PH, Chang Y, Chen WY. Recent trends and some applications of isothermal titration calorimetry in biotechnology. Biotechnol J 2010; 5:85-98. [DOI: 10.1002/biot.200900092] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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46
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Nuti E, Casalini F, Avramova SI, Santamaria S, Cercignani G, Marinelli L, La Pietra V, Novellino E, Orlandini E, Nencetti S, Tuccinardi T, Martinelli A, Lim NH, Visse R, Nagase H, Rossello A. N-O-isopropyl sulfonamido-based hydroxamates: design, synthesis and biological evaluation of selective matrix metalloproteinase-13 inhibitors as potential therapeutic agents for osteoarthritis. J Med Chem 2009; 52:4757-73. [PMID: 19606871 DOI: 10.1021/jm900261f] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Matrix metalloproteinase-13 (MMP-13) is a key enzyme implicated in the degradation of the extracellular matrix in osteoarthritis (OA). For this reason, MMP-13 synthetic inhibitors are being sought as potential therapeutic agents to prevent cartilage degradation and to halt the progression of OA. Herein, we report the synthesis and in vitro evaluation of a new series of selective MMP-13 inhibitors possessing an arylsulfonamidic scaffold. Among these potential inhibitors, a very promising compound was discovered exhibiting nanomolar activity for MMP-13 and was highly selective for this enzyme compared to MMP-1, -14, and TACE. This compound acted as a slow-binding inhibitor of MMP-13 and was demonstrated to be effective in an in vitro collagen assay and in a model of cartilage degradation. Furthermore, a docking study was conducted for this compound in order to investigate its binding interactions with MMP-13 and the reasons for its selectivity toward MMP-13 versus other MMPs.
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Affiliation(s)
- Elisa Nuti
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, via Bonanno 6, 56126 Pisa, Italy
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Dragoni E, Calderone V, Fragai M, Jaiswal R, Luchinat C, Nativi C. Biotin-tagged probes for MMP expression and activation: design, synthesis, and binding properties. Bioconjug Chem 2009; 20:719-27. [PMID: 19275207 DOI: 10.1021/bc8003827] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The design and synthesis of biotin chain-terminated inhibitors (BTI) showing high affinity for matrix metalloproteinases (MMPs) on one side and high affinity for avidin through the biotinylated tag on the other are reported. The affinity of the designed BTI toward five different MMPs has been evaluated and the simultaneous formation of a highly stable ternary system Avidin-BTI-MMP clearly assessed. This system will permit the development of new approaches to detect, quantify, or collect MMPs in biological samples, with potential applications in vivo.
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Affiliation(s)
- Elisa Dragoni
- Magnetic Resonance Center - University of Florence, Sesto Fiorentino, Italy
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Isaksson J, Nyström S, Derbyshire D, Wallberg H, Agback T, Kovacs H, Bertini I, Giachetti A, Luchinat C. Does a Fast Nuclear Magnetic Resonance Spectroscopy- and X-Ray Crystallography Hybrid Approach Provide Reliable Structural Information of Ligand-Protein Complexes? A Case Study of Metalloproteinases. J Med Chem 2009; 52:1712-22. [DOI: 10.1021/jm801388q] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Johan Isaksson
- Medivir AB, PO Box 1086, SE-141 22 Huddinge, Sweden, Bruker BioSpin AG, Industriestrasse 26, CH-8117 Fällanden, Switzerland, Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy, Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy, Department of Agricultural Biotechnology, University of Florence, Via Maragliano 75−77, 50144 Florence, Italy, ProtEra S.r.l., Via delle Idee 22, 50019 Sesto Fiorentino,
| | - Susanne Nyström
- Medivir AB, PO Box 1086, SE-141 22 Huddinge, Sweden, Bruker BioSpin AG, Industriestrasse 26, CH-8117 Fällanden, Switzerland, Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy, Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy, Department of Agricultural Biotechnology, University of Florence, Via Maragliano 75−77, 50144 Florence, Italy, ProtEra S.r.l., Via delle Idee 22, 50019 Sesto Fiorentino,
| | - Dean Derbyshire
- Medivir AB, PO Box 1086, SE-141 22 Huddinge, Sweden, Bruker BioSpin AG, Industriestrasse 26, CH-8117 Fällanden, Switzerland, Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy, Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy, Department of Agricultural Biotechnology, University of Florence, Via Maragliano 75−77, 50144 Florence, Italy, ProtEra S.r.l., Via delle Idee 22, 50019 Sesto Fiorentino,
| | - Hans Wallberg
- Medivir AB, PO Box 1086, SE-141 22 Huddinge, Sweden, Bruker BioSpin AG, Industriestrasse 26, CH-8117 Fällanden, Switzerland, Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy, Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy, Department of Agricultural Biotechnology, University of Florence, Via Maragliano 75−77, 50144 Florence, Italy, ProtEra S.r.l., Via delle Idee 22, 50019 Sesto Fiorentino,
| | - Tatiana Agback
- Medivir AB, PO Box 1086, SE-141 22 Huddinge, Sweden, Bruker BioSpin AG, Industriestrasse 26, CH-8117 Fällanden, Switzerland, Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy, Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy, Department of Agricultural Biotechnology, University of Florence, Via Maragliano 75−77, 50144 Florence, Italy, ProtEra S.r.l., Via delle Idee 22, 50019 Sesto Fiorentino,
| | - Helena Kovacs
- Medivir AB, PO Box 1086, SE-141 22 Huddinge, Sweden, Bruker BioSpin AG, Industriestrasse 26, CH-8117 Fällanden, Switzerland, Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy, Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy, Department of Agricultural Biotechnology, University of Florence, Via Maragliano 75−77, 50144 Florence, Italy, ProtEra S.r.l., Via delle Idee 22, 50019 Sesto Fiorentino,
| | - Ivano Bertini
- Medivir AB, PO Box 1086, SE-141 22 Huddinge, Sweden, Bruker BioSpin AG, Industriestrasse 26, CH-8117 Fällanden, Switzerland, Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy, Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy, Department of Agricultural Biotechnology, University of Florence, Via Maragliano 75−77, 50144 Florence, Italy, ProtEra S.r.l., Via delle Idee 22, 50019 Sesto Fiorentino,
| | - Andrea Giachetti
- Medivir AB, PO Box 1086, SE-141 22 Huddinge, Sweden, Bruker BioSpin AG, Industriestrasse 26, CH-8117 Fällanden, Switzerland, Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy, Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy, Department of Agricultural Biotechnology, University of Florence, Via Maragliano 75−77, 50144 Florence, Italy, ProtEra S.r.l., Via delle Idee 22, 50019 Sesto Fiorentino,
| | - Claudio Luchinat
- Medivir AB, PO Box 1086, SE-141 22 Huddinge, Sweden, Bruker BioSpin AG, Industriestrasse 26, CH-8117 Fällanden, Switzerland, Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy, Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy, Department of Agricultural Biotechnology, University of Florence, Via Maragliano 75−77, 50144 Florence, Italy, ProtEra S.r.l., Via delle Idee 22, 50019 Sesto Fiorentino,
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Abstract
In the past decade, the potential of harnessing the ability of nuclear magnetic resonance (NMR) spectroscopy to monitor intermolecular interactions as a tool for drug discovery has been increasingly appreciated in academia and industry. In this Perspective, we highlight some of the major applications of NMR in drug discovery, focusing on hit and lead generation, and provide a critical analysis of its current and potential utility.
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50
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Rouffet M, Denhez C, Bourguet E, Bohr F, Guillaume D. In silico study of MMP inhibition. Org Biomol Chem 2009; 7:3817-25. [DOI: 10.1039/b910543c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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