51
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Fischer T, Riedl R. Inhibitory Antibodies Designed for Matrix Metalloproteinase Modulation. Molecules 2019; 24:molecules24122265. [PMID: 31216704 PMCID: PMC6631688 DOI: 10.3390/molecules24122265] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 06/13/2019] [Accepted: 06/14/2019] [Indexed: 01/20/2023] Open
Abstract
The family of matrix metalloproteinases (MMPs) consists of a set of biological targets that are involved in a multitude of severe pathogenic events such as different forms of cancers or arthritis. Modulation of the target class with small molecule drugs has not led to the anticipated success until present, as all clinical trials failed due to unacceptable side effects or a lack of therapeutic outcome. Monoclonal antibodies offer a tremendous therapeutic potential given their high target selectivity and good pharmacokinetic profiles. For the treatment of a variety of diseases there are already antibody therapies available and the number is increasing. Recently, several antibodies were developed for the selective inhibition of single MMPs that showed high potency and were therefore investigated in in vivo studies with promising results. In this review, we highlight the progress that has been achieved toward the design of inhibitory antibodies that successfully modulate MMP-9 and MMP-14.
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Affiliation(s)
- Thomas Fischer
- Institute of Chemistry and Biotechnology, Center of Organic and Medicinal Chemistry, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland.
| | - Rainer Riedl
- Institute of Chemistry and Biotechnology, Center of Organic and Medicinal Chemistry, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland.
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52
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Fields GB. Mechanisms of Action of Novel Drugs Targeting Angiogenesis-Promoting Matrix Metalloproteinases. Front Immunol 2019; 10:1278. [PMID: 31214203 PMCID: PMC6558196 DOI: 10.3389/fimmu.2019.01278] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 05/20/2019] [Indexed: 12/16/2022] Open
Abstract
Angiogenesis is facilitated by the proteolytic activities of members of the matrix metalloproteinase (MMP) family. More specifically, MMP-9 and MT1-MMP directly regulate angiogenesis, while several studies indicate a role for MMP-2 as well. The correlation of MMP activity to tumor angiogenesis has instigated numerous drug development programs. However, broad-based and Zn2+-chelating MMP inhibitors have fared poorly in the clinic. Selective MMP inhibition by antibodies, biologicals, and small molecules has utilized unique modes of action, such as (a) binding to protease secondary binding sites (exosites), (b) allosterically blocking the protease active site, or (c) preventing proMMP activation. Clinical trials have been undertaken with several of these inhibitors, while others are in advanced pre-clinical stages. The mechanistically non-traditional MMP inhibitors offer treatment strategies for tumor angiogenesis that avoid the off-target toxicities and lack of specificity that plagued Zn2+-chelating inhibitors.
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Affiliation(s)
- Gregg B Fields
- Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, FL, United States.,Department of Chemistry, The Scripps Research Institute/Scripps Florida, Jupiter, FL, United States
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53
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Cramer J, Sager CP, Ernst B. Hydroxyl Groups in Synthetic and Natural-Product-Derived Therapeutics: A Perspective on a Common Functional Group. J Med Chem 2019; 62:8915-8930. [DOI: 10.1021/acs.jmedchem.9b00179] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Jonathan Cramer
- Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Christoph P. Sager
- Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Beat Ernst
- Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
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54
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Pulsipher KW, Bulos JA, Villegas JA, Saven JG, Dmochowski IJ. A protein-protein host-guest complex: Thermostable ferritin encapsulating positively supercharged green fluorescent protein. Protein Sci 2019; 27:1755-1766. [PMID: 30051936 DOI: 10.1002/pro.3483] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 07/10/2018] [Accepted: 07/12/2018] [Indexed: 01/14/2023]
Abstract
We characterize the encapsulation of supercharged green fluorescent protein, GFP(+36), by thermophilic ferritin from Archaeoglobus fulgidus (AfFtn). The AfFtn-GFP(+36) assembly is rapid, nearly stoichiometric, and robust. Using a more stably assembled mutant AfFtn, we show that encapsulation can occur in the presence of mostly assembled cages, in addition to encapsulation starting from AfFtn individual subunits. Assembly and encapsulation do not occur with non-supercharged GFP or the alternately supercharged GFP(-30), highlighting the role of complementary electrostatic interactions between the cargo and AfFtn cage interior. We also present a method for verifying protein-protein encapsulation, using nickel nitrilotriacetic acid agarose resin. AfFtn-supercharged protein host-guest complexes could find applications in enzyme studies, protein separations, and in vivo protein stabilization and targeted delivery.
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Affiliation(s)
- Katherine W Pulsipher
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, 19104
| | - Joshua A Bulos
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, 19104
| | - José A Villegas
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, 19104
| | - Jeffery G Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, 19104
| | - Ivan J Dmochowski
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, 19104
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55
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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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56
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Basciu A, Malloci G, Pietrucci F, Bonvin AMJJ, Vargiu AV. Holo-like and Druggable Protein Conformations from Enhanced Sampling of Binding Pocket Volume and Shape. J Chem Inf Model 2019; 59:1515-1528. [PMID: 30883122 DOI: 10.1021/acs.jcim.8b00730] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Understanding molecular recognition of small molecules by proteins in atomistic detail is key for drug design. Molecular docking is a widely used computational method to mimic ligand-protein association in silico. However, predicting conformational changes occurring in proteins upon ligand binding is still a major challenge. Ensemble docking approaches address this issue by considering a set of different conformations of the protein obtained either experimentally or from computer simulations, e.g., molecular dynamics. However, holo structures prone to host (the correct) ligands are generally poorly sampled by standard molecular dynamics simulations of the apo protein. In order to address this limitation, we introduce a computational approach based on metadynamics simulations called ensemble docking with enhanced sampling of pocket shape (EDES) that allows holo-like conformations of proteins to be generated by exploiting only their apo structures. This is achieved by defining a set of collective variables that effectively sample different shapes of the binding site, ultimately mimicking the steric effect due to the ligand. We assessed the method on three challenging proteins undergoing different extents of conformational changes upon ligand binding. In all cases our protocol generates a significant fraction of structures featuring a low RMSD from the experimental holo geometry. Moreover, ensemble docking calculations using those conformations yielded in all cases native-like poses among the top-ranked ones.
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Affiliation(s)
- Andrea Basciu
- Dipartimento di Fisica , Università di Cagliari, Cittadella Universitaria , I- 09042 Monserrato (CA) , Italy
| | - Giuliano Malloci
- Dipartimento di Fisica , Università di Cagliari, Cittadella Universitaria , I- 09042 Monserrato (CA) , Italy
| | - Fabio Pietrucci
- Sorbonne Université , Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC , F-75005 Paris , France
| | - Alexandre M J J Bonvin
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry , Utrecht University , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - Attilio V Vargiu
- Dipartimento di Fisica , Università di Cagliari, Cittadella Universitaria , I- 09042 Monserrato (CA) , Italy.,Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry , Utrecht University , Padualaan 8 , 3584 CH Utrecht , The Netherlands
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57
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Fields GB. Methods for the Construction of Collagen-Based Triple-Helical Peptides Designed as Matrix Metalloproteinase Inhibitors. Methods Mol Biol 2019; 1944:229-252. [PMID: 30840247 DOI: 10.1007/978-1-4939-9095-5_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The triple-helical structure of collagen has been accurately reproduced in numerous chemical and recombinant model systems. Triple-helical peptides have found application for dissecting collagen-stabilizing forces, isolating receptor and protein binding sites in collagen, evaluating collagen-mediated cell signaling activities, mechanistic examination of collagenolytic proteases, and developing novel biomaterials and drug delivery vehicles. Due to their inherent stability to general proteolysis, triple-helical peptides present an opportunity as in vivo inhibitory agents. The present chapter provides methods for the construction of collagen-based triple-helical peptides designed as matrix metalloproteinase inhibitors.
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Affiliation(s)
- Gregg B Fields
- Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, FL, USA.
- Department of Chemistry, Scripps Research, Jupiter, FL, USA.
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58
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Pernas M, Blanco B, Lence E, Thompson P, Hawkins AR, González-Bello C. Synthesis of rigidified shikimic acid derivatives by ring-closing metathesis to imprint inhibitor efficacy against shikimate kinase enzyme. Org Chem Front 2019. [DOI: 10.1039/c9qo00562e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The rigidification of the high-energy conformation of shikimic acid was used to enhance inhibitor efficacy against shikimate kinase enzyme, an attractive target for antibiotic drug discovery.
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Affiliation(s)
- Marina Pernas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS)
- Departamento de Química Orgánica
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - Beatriz Blanco
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS)
- Departamento de Química Orgánica
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - Emilio Lence
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS)
- Departamento de Química Orgánica
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - Paul Thompson
- Institute of Cell and Molecular Biosciences
- Medical School
- University of Newcastle upon Tyne
- Newcastle upon Tyne NE2 4HH
- UK
| | - Alastair R. Hawkins
- Institute of Cell and Molecular Biosciences
- Medical School
- University of Newcastle upon Tyne
- Newcastle upon Tyne NE2 4HH
- UK
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS)
- Departamento de Química Orgánica
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
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59
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Kaysser L. Built to bind: biosynthetic strategies for the formation of small-molecule protease inhibitors. Nat Prod Rep 2019; 36:1654-1686. [DOI: 10.1039/c8np00095f] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The discovery and characterization of natural product protease inhibitors has inspired the development of numerous pharmaceutical agents.
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Affiliation(s)
- Leonard Kaysser
- Department of Pharmaceutical Biology
- University of Tübingen
- 72076 Tübingen
- Germany
- German Centre for Infection Research (DZIF)
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60
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Rathee D, Lather V, Grewal AS, Dureja H. Enzymatic inhibitory activity of iridoid glycosides from Picrorrhiza kurroa against matrix metalloproteinases: Correlating in vitro targeted screening and docking. Comput Biol Chem 2018; 78:28-36. [PMID: 30497018 DOI: 10.1016/j.compbiolchem.2018.10.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 10/29/2018] [Accepted: 10/31/2018] [Indexed: 11/25/2022]
Abstract
One specific group of MMPs; gelatinases A (MMP-2) and B (MMP-9) are of precise interest in view of the development and progression of cancer. In the current work, an attempt was made to investigate the enzymatic inhibitory activity of Kutkin (KT), Kutkoside (KS), and Picroside I (PS) by inhibition assay and to further check the downregulation of the expression of mRNA levels of MMP-2 and -9. Further in silico docking studies were performed to investigate the interaction of KT, KS and PS with MMP-2 and MMP-9. The results revealed a dose dependent cytotoxic activity of the compounds under investigation and showed a significant inhibition of MMP-9 in comparison to the activity against MMP-2. In addition, a considerable decrease in expression of mRNA levels (MMP-9) was observed in KT, KS, and PS-treated MDA-MB-231 and MDA-MB-435 cancer cells as was detected by reverse transcriptase polymerase chain reaction (semi-quantitative RT-PCR). The molecular docking studies between KT, KS, PS with MMPs revealed that KT, KS, PS occupied the active site of MMP-9 and showed better binding interactions in comparison to MMP-2. The binding energies of the complexes were -7.4, -7.1 and -7.2 kJ/mol for KT, KS and PS with MMP-9, respectively and -8.9, -8.0 and -8.0 kJ/mol for KT, KS and PS with MMP-2, respectively. The findings from the in vitro studies revealed that KT, KS and PS exhibited significant anti-proliferative effects on both MDA-MB-231 and MDA-MB-435 breast cancer cells. In addition, the results of inhibition assay showed that MMP-9 activity was significantly inhibited by KT, KS and PS and the results were consistent with in silico assay.
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Affiliation(s)
- Dharmender Rathee
- Department of Pharmaceutical Sciences, MaharshiDayanand University, Rohtak, Haryana, 124001, India
| | - Viney Lather
- Amity Institute of Pharmacy, Amity University, Sector-125, Noida, 201313, U.P., India
| | - Ajmer Singh Grewal
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Patiala, Punjab, 140401, India
| | - Harish Dureja
- Department of Pharmaceutical Sciences, MaharshiDayanand University, Rohtak, Haryana, 124001, India.
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61
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Zhang D, Lv P, Zhou C, Zhao Y, Liao X, Yang B. Cyclodextrin-based delivery systems for cancer treatment. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2018; 96:872-886. [PMID: 30606602 DOI: 10.1016/j.msec.2018.11.031] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 10/09/2018] [Accepted: 11/22/2018] [Indexed: 02/07/2023]
Abstract
Cyclodextrins, one of safe excipients, are able to form host-guest complexes with fitted molecules given the unique nature imparted by their structure in result of a number of pharmaceutical applications. On the other hand, targeted or responsive materials are appealing therapeutic platforms for the development of next-generation precision medications. Meanwhile, cyclodextrin-based polymers or assemblies can condense DNA and RNA in result to be used as genetic therapeutic agents. Armed with a better understanding of various pharmaceutical mechanisms, especially for cancer treatment, researchers have made lots of works about cyclodextrin-based drug delivery systems in materials chemistry and pharmaceutical science. This Review highlights recent advances in cyclodextrin-based delivery systems for cancer treatment capable of targeting or responding to the physiological environment. Key design principles, challenges and future directions, including clinical translation, of cyclodextrin-based delivery systems are also discussed.
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Affiliation(s)
- Dongjing Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, PR China
| | - Pin Lv
- Industrial Crop Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, PR China
| | - Cheng Zhou
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, PR China
| | - Yulin Zhao
- Faculty of Chemical Engineering, Kunming University of Science and Technology, Kunming 650500, PR China
| | - Xiali Liao
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, PR China
| | - Bo Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, PR China.
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Zanobini C, Bozovic O, Jankovic B, Koziol KL, Johnson PJM, Hamm P, Gulzar A, Wolf S, Stock G. Azidohomoalanine: A Minimally Invasive, Versatile, and Sensitive Infrared Label in Proteins To Study Ligand Binding. J Phys Chem B 2018; 122:10118-10125. [DOI: 10.1021/acs.jpcb.8b08368] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Claudio Zanobini
- Department of Chemistry, University of Zurich, Zurich 8057, Switzerland
| | - Olga Bozovic
- Department of Chemistry, University of Zurich, Zurich 8057, Switzerland
| | - Brankica Jankovic
- Department of Chemistry, University of Zurich, Zurich 8057, Switzerland
| | - Klemens L. Koziol
- Department of Chemistry, University of Zurich, Zurich 8057, Switzerland
| | | | - Peter Hamm
- Department of Chemistry, University of Zurich, Zurich 8057, Switzerland
| | - Adnan Gulzar
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, Freiburg 79104, Germany
| | - Steffen Wolf
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, Freiburg 79104, Germany
| | - Gerhard Stock
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, Freiburg 79104, Germany
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63
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A Hybrid Cuckoo Search and Differential Evolution Approach to Protein⁻Ligand Docking. Int J Mol Sci 2018; 19:ijms19103181. [PMID: 30326669 PMCID: PMC6214097 DOI: 10.3390/ijms19103181] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 10/11/2018] [Accepted: 10/12/2018] [Indexed: 11/16/2022] Open
Abstract
Protein⁻ligand docking is a molecular modeling technique that is used to predict the conformation of a small molecular ligand at the binding pocket of a protein receptor. There are many protein⁻ligand docking tools, among which AutoDock Vina is the most popular open-source docking software. In recent years, there have been numerous attempts to optimize the search process in AutoDock Vina by means of heuristic optimization methods, such as genetic and particle swarm optimization algorithms. This study, for the first time, explores the use of cuckoo search (CS) to solve the protein⁻ligand docking problem. The result of this study is CuckooVina, an enhanced conformational search algorithm that hybridizes cuckoo search with differential evolution (DE). Extensive tests using two benchmark datasets, PDBbind 2012 and Astex Diverse set, show that CuckooVina improves the docking performances in terms of RMSD, binding affinity, and success rate compared to Vina though it requires about 9⁻15% more time to complete a run than Vina. CuckooVina predicts more accurate docking poses with higher binding affinities than PSOVina with similar success rates. CuckooVina's slower convergence but higher accuracy suggest that it is better able to escape from local energy minima and improves the problem of premature convergence. As a summary, our results assure that the hybrid CS⁻DE process to continuously generate diverse solutions is a good strategy to maintain the proper balance between global and local exploitation required for the ligand conformational search.
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64
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Chen G, Huang BX, Guo M. Current advances in screening for bioactive components from medicinal plants by affinity ultrafiltration mass spectrometry. PHYTOCHEMICAL ANALYSIS : PCA 2018; 29:375-386. [PMID: 29785715 DOI: 10.1002/pca.2769] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 03/08/2018] [Accepted: 03/08/2018] [Indexed: 06/08/2023]
Abstract
INTRODUCTION Medicinal plants have played an important role in maintaining human health for thousands of years. However, the interactions between the active components in medicinal plants and some certain biological targets during a disease are still unclear in most cases. OBJECTIVE To conduct the high-throughput screening for small active molecules that can interact with biological targets, which is of great theoretical significance and practical value. METHODOLOGY The ultrafiltration mass spectrometry (UF-LC/MS) is a powerful bio-analytical method by combining affinity ultrafiltration and liquid chromatography-mass spectrometry (LC/MS), which could rapidly screen and identify small active molecules that bind to biological targets of interest at the same time. Compared with other analytical methods, affinity UF-LC/MS has the characteristics of fast, sensitive and high throughput, and is especially suitable for the complicated extracts of medicinal plants. RESULTS In this review, the basic principle, characteristics and some most recent challenges in UF-LC/MS have been demonstrated. Meanwhile, the progress and applications of affinity UF-LC/MS in the discovery of the active components from natural medicinal plants and the interactions between small molecules and biological target proteins are also briefly summarised. In addition, the future directions for UF-LC/MS are also prospected. CONCLUSION Affinity UF-LC/MS is a powerful tool in studies on the interactions between small active molecules and biological protein targets, especially in the high-throughput screening of active components from the natural medicinal plants.
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Affiliation(s)
- Guilin Chen
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, 430074, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, 430074, Wuhan, China
| | - Bill X Huang
- Laboratory of Molecular Signaling, National Institute of Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland, USA
| | - Mingquan Guo
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, 430074, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, 430074, Wuhan, China
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65
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Rathee D, Lather V, Grewal AS, Dureja H. Targeting matrix metalloproteinases with novel diazepine substituted cinnamic acid derivatives: design, synthesis, in vitro and in silico studies. Chem Cent J 2018; 12:41. [PMID: 29679218 PMCID: PMC5910448 DOI: 10.1186/s13065-018-0411-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 04/13/2018] [Indexed: 11/21/2022] Open
Abstract
Lung cancer is the notable cause of cancer associated deaths worldwide. Recent studies revealed that the expression of matrix metalloproteinases (MMPs) is extremely high in lung tumors compared with non-malignant lung tissue. MMPs (-2 and -9) play an important part in tumor development and angiogenesis, which suggests that creating potent MMP-2 and -9 inhibitors, should be an important goal in lung cancer therapy. In the present study, an effort has been made to develop new anti-metastatic and anti-invasive agents, wherein a series of novel diazepine substituted cinnamic acid derivatives were designed, synthesized and assayed for their inhibitory activities on MMP-2 and MMP-9. These derivatives were prepared via microwave assisted reaction of tert-butyl (3-cinnamamidopropyl)carbamate derivatives mixed with 2,3-dibromopropanoic acid and potassium carbonate was added to obtain 4-(tert-butoxycarbonyl)-1-cinnamoyl-1,4-diazepane-2-carboxylic acid derivatives. The newly synthesized compounds were characterized by IR, NMR and mass spectroscopy. All the tested compounds showed good to excellent cytotoxic potential against A549 human lung cancer cells. The active compounds displaying good activity were further examined for the inhibitory activity against MMPs (-2 and -9). In addition, the structure and anticancer activity relationship were further supported by in silico docking studies of the active compounds against MMP-2 and MMP-9.![]()
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Affiliation(s)
- Dharmender Rathee
- Department of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Viney Lather
- Department of Pharmaceutical Chemistry, JCDM College of Pharmacy, Sirsa, Haryana, 125055, India
| | - Ajmer Singh Grewal
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Patiala, Punjab, 140401, India
| | - Harish Dureja
- Department of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak, Haryana, 124001, India.
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66
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Dewar JC, Thakur AS, Brennessel WW, Cafiero M, Peterson LW, Eckenhoff WT. Simple zinc complex to model substrate binding to zinc enzymes. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2017.12.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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67
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Heravi MM, Lashaki TB, Fattahi B, Zadsirjan V. Application of asymmetric Sharpless aminohydroxylation in total synthesis of natural products and some synthetic complex bio-active molecules. RSC Adv 2018; 8:6634-6659. [PMID: 35559209 PMCID: PMC9092437 DOI: 10.1039/c7ra12625e] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 01/30/2018] [Indexed: 01/23/2023] Open
Abstract
This report illustrates the applications of Asymmetric Sharpless Aminohydroxylation (ASAH) in the stereoselective synthesis of vicinal amino alcohols as important intermediates in the total synthesis of complex molecules and natural products with significant biological activities. The ASHA allows the regio- syn-selective synthesis of 1,2-amino alcohols via reaction of alkenes with salts of N-halosulfonamides, -amides and -carbamates employing osmium tetroxide (OsO4) as an efficient catalyst. In this reaction, chirality is induced via the addition of dihydroquinine- and dihydroquinidine as derived chiral ligands.
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Affiliation(s)
- Majid M Heravi
- Department of Chemistry, School of Science, Alzahra University Vanak Tehran Iran
| | | | - Bahareh Fattahi
- Department of Chemistry, School of Science, Alzahra University Vanak Tehran Iran
| | - Vahideh Zadsirjan
- Department of Chemistry, School of Science, Alzahra University Vanak Tehran Iran
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Abstract
A key challenge in chemical biology is to identify small molecule regulators for every single protein. However, protein surfaces are notoriously difficult to recognise with synthetic molecules, often having large flat surfaces that are poorly matched to traditional small molecules. In the surface mimetic approach, a supramolecular scaffold is used to project recognition groups in such a manner as to make multivalent non-covalent contacts over a large area of protein surface. Metal based supramolecular scaffolds offer unique advantages over conventional organic molecules for protein binding, including greater stereochemical and geometrical diversity conferred through the metal centre and the potential for direct assessment of binding properties and even visualisation in cells without recourse to further functionalisation. This feature article will highlight the current state of the art in protein surface recognition using metal complexes as surface mimetics.
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Affiliation(s)
- Sarah H Hewitt
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK. and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Andrew J Wilson
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK. and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
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69
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Wei B, Zhang J, Ou X, Lou X, Xia F, Vallée-Bélisle A. Engineering Biosensors with Dual Programmable Dynamic Ranges. Anal Chem 2018; 90:1506-1510. [PMID: 29300471 DOI: 10.1021/acs.analchem.7b04852] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Although extensively used in all fields of chemistry, molecular recognition still suffers from a significant limitation: host-guest binding displays a fixed, hyperbolic dose-response curve, which limits its usefulness in many applications. Here we take advantage of the high programmability of DNA chemistry and propose a universal strategy to engineer biorecognition-based sensors with dual programmable dynamic ranges. Using DNA aptamers as our model recognition element and electrochemistry as our readout signal, we first designed a dual signaling "signal-on" and "signal-off" adenosine triphosphate (ATP) sensor composed of a ferrocene-labeled ATP aptamer in complex to a complementary, electrode-bound, methylene-blue labeled DNA. Using this simple "dimeric" sensor, we show that we can easily (1) tune the dynamic range of this dual-signaling sensor through base mutations on the electrode-bound DNA, (2) extend the dynamic range of this sensor by 2 orders of magnitude by using a combination of electrode-bound strands with varying affinity for the aptamers, (3) create an ultrasensitive dual signaling sensor by employing a sequestration strategy in which a nonsignaling, high affinity "depletant" DNA aptamer is added to the sensor surface, and (4) engineer a sensor that simultaneously provides extended and ultrasensitive readouts. These strategies, applicable to a wide range of biosensors and chemical systems, should broaden the application of molecular recognition in various fields of chemistry.
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Affiliation(s)
- Benmei Wei
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology , Wuhan 430074, P. R. China
| | - Juntao Zhang
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology , Wuhan 430074, P. R. China
| | - Xiaowen Ou
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology , Wuhan 430074, P. R. China
| | - Xiaoding Lou
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology , Wuhan 430074, P. R. China
| | - Fan Xia
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology , Wuhan 430074, P. R. China
| | - Alexis Vallée-Bélisle
- Laboratory Biosensors & Nanomachines, Département de Chimie, Université de Montréal , Montréal, Québec H3T 1J4, Canada
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70
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Mohan B, Modi K, Bhatia P, Sharma HK, Mishra D, Jain VK, Arora LS. An ionic receptor for Zn2+ metal ion using synthesised bis-formylpyrazole calix[4]arene and its computational study. Supramol Chem 2017. [DOI: 10.1080/10610278.2017.1415437] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Brij Mohan
- Department of Chemistry, Kurukshetra University, Kurukshetra, India
| | - Krunal Modi
- J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Pankaj Bhatia
- Department of Chemistry, Kurukshetra University, Kurukshetra, India
| | - H. K. Sharma
- Department of Chemistry, Kurukshetra University, Kurukshetra, India
| | - Divya Mishra
- Department of Chemistry, University School of Sciences, Gujarat University, Ahmedabad, India
| | - Vinod K. Jain
- Department of Chemistry, University School of Sciences, Gujarat University, Ahmedabad, India
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71
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Aarthy M, Panwar U, Selvaraj C, Singh SK. Advantages of Structure-Based Drug Design Approaches in Neurological Disorders. Curr Neuropharmacol 2017; 15:1136-1155. [PMID: 28042767 PMCID: PMC5725545 DOI: 10.2174/1570159x15666170102145257] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 11/05/2016] [Accepted: 11/03/2016] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVE The purpose of the review is to portray the theoretical concept on neurological disorders from research data. BACKGROUND The freak changes in chemical response of nerve impulse causes neurological disorders. The research evidence of the effort done in the older history suggests that the biological drug targets and their effective feature with responsive drugs could be valuable in promoting the future development of health statistics structure for improved treatment for curing the nervous disorders. METHODS In this review, we summarized the most iterative theoretical concept of structure based drug design approaches in various neurological disorders to unfathomable understanding of reported information for future drug design and development. RESULTS On the premise of reported information we analyzed the model of theoretical drug designing process for understanding the mechanism and pathology of the neurological diseases which covers the development of potentially effective inhibitors against the biological drug targets. Finally, it also suggests the management and implementation of the current treatment in improving the human health system behaviors. CONCLUSION With the survey of reported information we concluded the development strategies of diagnosis and treatment against neurological diseases which leads to supportive progress in the drug discovery.
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Affiliation(s)
- Murali Aarthy
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630004, Tamil Nadu, India
| | - Umesh Panwar
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630004, Tamil Nadu, India
| | - Chandrabose Selvaraj
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Postal Code: 143-701, Seoul, Korea
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630004, Tamil Nadu, India
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72
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Affiliation(s)
- Hope A. Flaxman
- Department of Chemistry and
Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Christina M. Woo
- Department of Chemistry and
Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
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73
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Beema Shafreen R, Dymerski T, Namieśnik J, Jastrzębski Z, Vearasilp S, Gorinstein S. Interaction of human serum albumin with volatiles and polyphenols from some berries. Food Hydrocoll 2017. [DOI: 10.1016/j.foodhyd.2017.06.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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74
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Kitayama Y, Yoshikawa K, Takeuchi T. Post-Cross-Linked Molecular Imprinting with Functional Polymers as a Universal Building Block for Artificial Polymeric Receptors. Macromolecules 2017. [DOI: 10.1021/acs.macromol.7b01233] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Yukiya Kitayama
- Graduate School of Engineering, Kobe University, 1-1
Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Kazuki Yoshikawa
- Graduate School of Engineering, Kobe University, 1-1
Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Toshifumi Takeuchi
- Graduate School of Engineering, Kobe University, 1-1
Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
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75
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Development of a Non-Hydroxamate Dual Matrix Metalloproteinase (MMP)-7/-13 Inhibitor. Molecules 2017; 22:molecules22091548. [PMID: 32961647 PMCID: PMC6151531 DOI: 10.3390/molecules22091548] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 09/08/2017] [Accepted: 09/08/2017] [Indexed: 12/12/2022] Open
Abstract
Matrix metalloproteinase 7 (MMP-7) is a member of the MMP superfamily and is able to degrade extracellular matrix proteins such as casein, gelatin, fibronectin and proteoglycan. MMP-7 is a validated target for the development of small molecule drugs against cancer. MMP-13 is within the enzyme class the most efficient contributor to type II collagen degeneration and is a validated target in arthritis and cancer. We have developed the dual MMP-7/-13 inhibitor ZHAWOC6941 with IC50-values of 2.2 μM (MMP-7) and 1.2 μM (MMP-13) that is selective over a broad range of MMP isoforms. It spares MMP-1, -2, -3, -8, -9, -12 and -14, making it a valuable modulator for targeted polypharmacology approaches.
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76
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Arodola OA, Soliman MES. Quantum mechanics implementation in drug-design workflows: does it really help? Drug Des Devel Ther 2017; 11:2551-2564. [PMID: 28919707 PMCID: PMC5587087 DOI: 10.2147/dddt.s126344] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The pharmaceutical industry is progressively operating in an era where development costs are constantly under pressure, higher percentages of drugs are demanded, and the drug-discovery process is a trial-and-error run. The profit that flows in with the discovery of new drugs has always been the motivation for the industry to keep up the pace and keep abreast with the endless demand for medicines. The process of finding a molecule that binds to the target protein using in silico tools has made computational chemistry a valuable tool in drug discovery in both academic research and pharmaceutical industry. However, the complexity of many protein-ligand interactions challenges the accuracy and efficiency of the commonly used empirical methods. The usefulness of quantum mechanics (QM) in drug-protein interaction cannot be overemphasized; however, this approach has little significance in some empirical methods. In this review, we discuss recent developments in, and application of, QM to medically relevant biomolecules. We critically discuss the different types of QM-based methods and their proposed application to incorporating them into drug-design and -discovery workflows while trying to answer a critical question: are QM-based methods of real help in drug-design and -discovery research and industry?
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Affiliation(s)
- Olayide A Arodola
- Department of Pharmaceutical Chemistry, University of KwaZulu-Natal, Durban, South Africa
| | - Mahmoud ES Soliman
- Department of Pharmaceutical Chemistry, University of KwaZulu-Natal, Durban, South Africa
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Zagazig University, Egypt
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77
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Steinman JB, Santarossa CC, Miller RM, Yu LS, Serpinskaya AS, Furukawa H, Morimoto S, Tanaka Y, Nishitani M, Asano M, Zalyte R, Ondrus AE, Johnson AG, Ye F, Nachury MV, Fukase Y, Aso K, Foley MA, Gelfand VI, Chen JK, Carter AP, Kapoor TM. Chemical structure-guided design of dynapyrazoles, cell-permeable dynein inhibitors with a unique mode of action. eLife 2017; 6. [PMID: 28524820 PMCID: PMC5478271 DOI: 10.7554/elife.25174] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 05/17/2017] [Indexed: 12/11/2022] Open
Abstract
Cytoplasmic dyneins are motor proteins in the AAA+ superfamily that transport cellular cargos toward microtubule minus-ends. Recently, ciliobrevins were reported as selective cell-permeable inhibitors of cytoplasmic dyneins. As is often true for first-in-class inhibitors, the use of ciliobrevins has in part been limited by low potency. Moreover, suboptimal chemical properties, such as the potential to isomerize, have hindered efforts to improve ciliobrevins. Here, we characterized the structure of ciliobrevins and designed conformationally constrained isosteres. These studies identified dynapyrazoles, inhibitors more potent than ciliobrevins. At single-digit micromolar concentrations dynapyrazoles block intraflagellar transport in the cilium and lysosome motility in the cytoplasm, processes that depend on cytoplasmic dyneins. Further, we find that while ciliobrevins inhibit both dynein's microtubule-stimulated and basal ATPase activity, dynapyrazoles strongly block only microtubule-stimulated activity. Together, our studies suggest that chemical-structure-based analyses can lead to inhibitors with improved properties and distinct modes of inhibition. DOI:http://dx.doi.org/10.7554/eLife.25174.001
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Affiliation(s)
- Jonathan B Steinman
- Laboratory of Chemistry and Cell Biology, Rockefeller University, New York, United States
| | - Cristina C Santarossa
- Laboratory of Chemistry and Cell Biology, Rockefeller University, New York, United States
| | - Rand M Miller
- Laboratory of Chemistry and Cell Biology, Rockefeller University, New York, United States
| | - Lola S Yu
- Laboratory of Chemistry and Cell Biology, Rockefeller University, New York, United States
| | - Anna S Serpinskaya
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, United States
| | - Hideki Furukawa
- Tri-Institutitional Therapeutics Discovery Institute, New York, United States
| | - Sachie Morimoto
- Tri-Institutitional Therapeutics Discovery Institute, New York, United States
| | - Yuta Tanaka
- Tri-Institutitional Therapeutics Discovery Institute, New York, United States
| | | | - Moriteru Asano
- Tri-Institutitional Therapeutics Discovery Institute, New York, United States
| | - Ruta Zalyte
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Alison E Ondrus
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States
| | - Alex G Johnson
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, United States
| | - Fan Ye
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States
| | - Maxence V Nachury
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States
| | - Yoshiyuki Fukase
- Tri-Institutitional Therapeutics Discovery Institute, New York, United States
| | - Kazuyoshi Aso
- Tri-Institutitional Therapeutics Discovery Institute, New York, United States
| | - Michael A Foley
- Tri-Institutitional Therapeutics Discovery Institute, New York, United States
| | - Vladimir I Gelfand
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, United States
| | - James K Chen
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, United States
| | - Andrew P Carter
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Tarun M Kapoor
- Laboratory of Chemistry and Cell Biology, Rockefeller University, New York, United States
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78
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Inhibition of Gelatinases (MMP-2 and MMP-9) by Withania somnifera Phytochemicals Confers Neuroprotection in Stroke: An In Silico Analysis. Interdiscip Sci 2017; 10:722-733. [PMID: 28488219 DOI: 10.1007/s12539-017-0231-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 01/25/2017] [Accepted: 04/01/2017] [Indexed: 01/24/2023]
Abstract
A stroke or cerebrovascular accident is a serious, life-threatening medical condition that occurs when the blood supply to part of the brain is severely reduced or cut off, depriving brain tissue of oxygen and nutrients. Studies suggested that level of gelatinases (MMP-2 and MMP-9) usually increases in the brain after stroke. The elevated activity of gelatinases plays the deleterious role in ischemic stroke, hemorrhagic stroke and perinatal hypoxic-ischemic brain injury. Therefore, matrix metalloproteinase (MMP)-2 and MMP-9 inhibition have therapeutic importance in stroke condition. Present in silico study investigates whether Withania somnifera (WS) phytochemicals inhibit the MMP-2 and MMP-9 by binding to the catalytic domain, as similar to their inhibitor or not. For that, we performed molecular docking study to evaluate the gelatinases-inhibitory potential of 36 WS phytochemicals, which compared with gelatinases inhibitors viz. hydroxamic acid, quercetin, doxycycline, minocycline and reverse hydroxamate. The results suggest that 28 out of 36 WS phytochemicals show higher affinity for MMP-2 owing to bind with active site residues of S1'-pocket with lower binding energy and smaller inhibition constant (Ki) than considered inhibitors. As well as, withanolide G and withafastuosin E show higher affinity for MMP-9 than reverse hydroxamate inhibitor. These phytochemicals have neuroprotective potential as an inherently useful oral drug to combat ischemic and hemorrhagic stroke mediated by gelatinases.
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79
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Limones-Herrero D, Pérez-Ruiz R, Lence E, González-Bello C, Miranda MA, Jiménez MC. Mapping a protein recognition centre with chiral photoactive ligands. An integrated approach combining photophysics, reactivity, proteomics and molecular dynamics simulation studies. Chem Sci 2017; 8:2621-2628. [PMID: 28553497 PMCID: PMC5431658 DOI: 10.1039/c6sc04900a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 12/30/2016] [Indexed: 01/10/2023] Open
Abstract
A multidisciplinary strategy to obtain structural information on the intraprotein region is described here. As probe ligands, (S)- and (R)-CPFMe (the methyl esters of the chiral drug carprofen) have been selected, while bovine α1-acid glycoprotein (BAAG) has been chosen as a biological host. The procedure involves the separate irradiation of the BAAG/(S)-CPFMe and BAAG/(R)-CPFMe complexes, coupled with fluorescence spectroscopy, laser flash photolysis, proteomic analysis, docking and molecular dynamics simulations. Thus, irradiation of the BAAG/CPFMe complexes at λ = 320 nm was followed by fluorescence spectroscopy. The intensity of the emission band obtained after irradiation indicated photodehalogenation, whereas its structureless shape suggested covalent binding of the resulting radical CBZMe˙ to the biopolymer. After gel filtration chromatography, the spectra still displayed emission, in agreement with covalent attachment of CBZMe˙ to BAAG. Stereodifferentiation was observed in this process. After trypsin digestion and ESI-MS/MS, the incorporation of CBZMe was detected at Phe68. Docking and molecular dynamics simulation studies, which were carried out using a homology model of BAAG, reveal that the closer proximity of the aromatic moiety of the (S)-enantiomer to the phenyl group of Phe68 would be responsible for the experimentally observed, more effective chemical modification of the protein. The proposed tridimensional structure of BAAG covalently modified by the two enantiomers is also provided. In principle, this approach can be extended to a variety of protein/ligand complexes.
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Affiliation(s)
- Daniel Limones-Herrero
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC , Universitat Politècnica de València , Camino de Vera s/n , 46022 , Valencia , Spain . ;
| | - Raúl Pérez-Ruiz
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC , Universitat Politècnica de València , Camino de Vera s/n , 46022 , Valencia , Spain . ;
| | - Emilio Lence
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) , Departamento de Química Orgánica , Universidade de Santiago de Compostela , C/ Jenaro de la Fuente s/n , 15782 Santiago de Compostela , Spain
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) , Departamento de Química Orgánica , Universidade de Santiago de Compostela , C/ Jenaro de la Fuente s/n , 15782 Santiago de Compostela , Spain
| | - Miguel A Miranda
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC , Universitat Politècnica de València , Camino de Vera s/n , 46022 , Valencia , Spain . ;
| | - M Consuelo Jiménez
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC , Universitat Politècnica de València , Camino de Vera s/n , 46022 , Valencia , Spain . ;
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80
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A Synopsis of the Properties and Applications of Heteroaromatic Rings in Medicinal Chemistry. ADVANCES IN HETEROCYCLIC CHEMISTRY 2017. [DOI: 10.1016/bs.aihch.2016.11.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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81
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Liu F, Zhang K, Liu Y, Chen S, Chen Y, Zhang D, Lin C, Wang B. Solvent-free one-pot oxidation of ethylarenes for the preparation of α-ketoamides under mild conditions. RSC Adv 2017. [DOI: 10.1039/c6ra26679g] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Here we developed a highly efficient solvent-free, one-pot procedure for synthesizing α-ketoamides from ethylarenes and amines, by oxidizing a C–H bond sp3 center.
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Affiliation(s)
- Fuyan Liu
- State Key Lab of Marine Resource Utilisation in South China Sea
- Hainan University
- Haikou 570228
- PR China
| | - Kuan Zhang
- State Key Lab of Marine Resource Utilisation in South China Sea
- Hainan University
- Haikou 570228
- PR China
| | - Yanfeng Liu
- State Key Lab of Marine Resource Utilisation in South China Sea
- Hainan University
- Haikou 570228
- PR China
| | - Shan Chen
- Institute of Chemical Engineering
- College of Materials and Chemical Engineering
- Hainan University
- Haikou 570228
- PR China
| | - Yiping Chen
- State Key Lab of Marine Resource Utilisation in South China Sea
- Hainan University
- Haikou 570228
- PR China
| | - Dela Zhang
- State Key Lab of Marine Resource Utilisation in South China Sea
- Hainan University
- Haikou 570228
- PR China
| | - Chunfu Lin
- State Key Lab of Marine Resource Utilisation in South China Sea
- Hainan University
- Haikou 570228
- PR China
- Institute of Chemical Engineering
| | - Bo Wang
- State Key Lab of Marine Resource Utilisation in South China Sea
- Hainan University
- Haikou 570228
- PR China
- Institute of Chemical Engineering
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82
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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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83
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84
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Castro E, Martinez ZS, Seong CS, Cabrera-Espinoza A, Ruiz M, Hernandez Garcia A, Valdez F, Llano M, Echegoyen L. Characterization of New Cationic N,N-Dimethyl[70]fulleropyrrolidinium Iodide Derivatives as Potent HIV-1 Maturation Inhibitors. J Med Chem 2016; 59:10963-10973. [PMID: 28002960 DOI: 10.1021/acs.jmedchem.6b00994] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
HIV-1 maturation can be impaired by altering protease (PR) activity, the structure of the Gag-Pol substrate, or the molecular interactions of viral structural proteins. Here we report the synthesis and characterization of new cationic N,N-dimethyl[70]fulleropyrrolidinium iodide derivatives that inhibit more than 99% of HIV-1 infectivity at low micromolar concentrations. Analysis of the HIV-1 life cycle indicated that these compounds inhibit viral maturation by impairing Gag and Gag-Pol processing. Importantly, fullerene derivatives 2a-c did not inhibit in vitro PR activity and strongly interacted with HIV immature capsid protein in pull-down experiments. Furthermore, these compounds potently blocked infectivity of viruses harboring mutant PR that are resistant to multiple PR inhibitors or mutant Gag proteins that confer resistance to the maturation inhibitor Bevirimat. Collectively, our studies indicate fullerene derivatives 2a-c as potent and novel HIV-1 maturation inhibitors.
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Affiliation(s)
- Edison Castro
- Department of Chemistry, University of Texas at El Paso , 500 West University Avenue, CCSB #3.0302, El Paso, Texas 79968, United States
| | - Zachary S Martinez
- Department of Biological Sciences, University of Texas at El Paso , 500 West University Avenue, El Paso, Texas 79968, United States
| | - Chang-Soo Seong
- Department of Biological Sciences, University of Texas at El Paso , 500 West University Avenue, El Paso, Texas 79968, United States
| | - Andrea Cabrera-Espinoza
- Department of Chemistry, University of Texas at El Paso , 500 West University Avenue, CCSB #3.0302, El Paso, Texas 79968, United States
| | - Mauro Ruiz
- Department of Chemistry, University of Texas at El Paso , 500 West University Avenue, CCSB #3.0302, El Paso, Texas 79968, United States
| | - Andrea Hernandez Garcia
- Department of Chemistry, University of Texas at El Paso , 500 West University Avenue, CCSB #3.0302, El Paso, Texas 79968, United States
| | - Federico Valdez
- Department of Biological Sciences, University of Texas at El Paso , 500 West University Avenue, El Paso, Texas 79968, United States
| | - Manuel Llano
- Department of Biological Sciences, University of Texas at El Paso , 500 West University Avenue, El Paso, Texas 79968, United States
| | - Luis Echegoyen
- Department of Chemistry, University of Texas at El Paso , 500 West University Avenue, CCSB #3.0302, El Paso, Texas 79968, United States
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85
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Kuznetsova OV, Egorochkin AN, Khamaletdinova NM, Domratcheva-Lvova LG. Noncovalent interactions involving aromatic rings: correlation analysis via substituent constants. J PHYS ORG CHEM 2016. [DOI: 10.1002/poc.3662] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Olga V. Kuznetsova
- G.A. Razuvaev Institute of Organometallic Chemistry; Russian Academy of Sciences; Nizhny Novgorod Russian Federation
| | - Alexey N. Egorochkin
- G.A. Razuvaev Institute of Organometallic Chemistry; Russian Academy of Sciences; Nizhny Novgorod Russian Federation
| | - Nadiya M. Khamaletdinova
- G.A. Razuvaev Institute of Organometallic Chemistry; Russian Academy of Sciences; Nizhny Novgorod Russian Federation
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86
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An insight into the binding of an ester functionalized gemini surfactant to hemoglobin. Colloids Surf A Physicochem Eng Asp 2016. [DOI: 10.1016/j.colsurfa.2016.07.076] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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87
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Bagchi D, Ghosh A, Singh P, Dutta S, Polley N, Althagafi II, Jassas RS, Ahmed SA, Pal SK. Allosteric Inhibitory Molecular Recognition of a Photochromic Dye by a Digestive Enzyme: Dihydroindolizine makes α-chymotrypsin Photo-responsive. Sci Rep 2016; 6:34399. [PMID: 27677331 PMCID: PMC5039621 DOI: 10.1038/srep34399] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 09/13/2016] [Indexed: 11/10/2022] Open
Abstract
The structural-functional regulation of enzymes by the administration of an external stimulus such as light could create photo-switches that exhibit unique biotechnological applications. However, molecular recognition of small ligands is a central phenomenon involved in all biological processes. We demonstrate herein that the molecular recognition of a photochromic ligand, dihydroindolizine (DHI), by serine protease α-chymotrypsin (CHT) leads to the photo-control of enzymatic activity. We synthesized and optically characterized the photochromic DHI. Light-induced reversible pyrroline ring opening and a consequent thermal back reaction via 1,5-electrocyclization are responsible for the photochromic behavior. Furthermore, DHI inhibits the enzymatic activity of CHT in a photo-controlled manner. Simultaneous binding of the well-known inhibitors 4-nitrophenyl anthranilate (NPA) or proflavin (PF) in the presence of DHI displays spectral overlap between the emission of CHT-NPA or CHT-PF with the respective absorption of cis or trans DHI. The results suggest an opportunity to explore the binding site of DHI using Förster resonance energy transfer (FRET). Moreover, to more specifically evaluate the DHI binding interactions, we employed molecular docking calculations, which suggested binding near the hydrophobic site of Cys-1-Cys-122 residues. Variations in the electrostatic interactions of the two conformers of DHI adopt unfavorable conformations, leading to the allosteric inhibition of enzymatic activity.
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Affiliation(s)
- Damayanti Bagchi
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 106, India
| | - Abhijit Ghosh
- Computer Service Cell, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 106, India
| | - Priya Singh
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 106, India
| | - Shreyasi Dutta
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 106, India
| | - Nabarun Polley
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 106, India
| | - Ismail I Althagafi
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University, 21955 Makkah, Saudi Arabia
| | - Rabab S Jassas
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University, 21955 Makkah, Saudi Arabia
| | - Saleh A Ahmed
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University, 21955 Makkah, Saudi Arabia.,Chemistry Department, Faculty of Science, Assiut University, 71516 Assiut, Egypt
| | - Samir Kumar Pal
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 106, India
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88
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Pairas GN, Tsoungas PG. H-Bond: Τhe Chemistry-Biology H-Bridge. ChemistrySelect 2016; 1:4520-4532. [PMID: 32328512 PMCID: PMC7169486 DOI: 10.1002/slct.201600770] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 07/29/2016] [Indexed: 12/19/2022]
Abstract
H-bonding, as a non covalent stabilizing interaction of diverse nature, has a central role in the structure, function and dynamics of chemical and biological processes, pivotal to molecular recognition and eventually to drug design. Types of conventional and non conventional (H-H, dihydrogen, H- π, CH- π, anti- , proton coordination and H-S) H-bonding interactions are discussed as well as features emerging from their interplay, such as cooperativity (σ- and π-) effects and allostery. Its utility in many applications is described. Catalysis, proton and electron transfer processes in various materials or supramolecular architectures of preorganized hosts for guest binding, are front-line technology. The H-bond-related concept of proton transfer (PT) addresses energy issues or deciphering the mechanism of many natural and synthetic processes. PT is also of paramount importance in the functions of cells and is assisted by large complex proteins embedded in membranes. Both intermolecular and intramolecular PT in H-bonded systems has received attention, theoretically and experimentally, using prototype molecules. It is found in rearrangement reactions, protein functions, and enzyme reactions or across proton channels and pumps. Investigations on the competition between intra- and intermolecular H bonding are discussed. Of particular interest is the H-bond furcation, a common phenomenon in protein-ligand binding. Multiple H-bonding (H-bond furcation) is observed in supramolecular structures.
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Affiliation(s)
- George N. Pairas
- Department of PharmacyLaboratory of Medicinal ChemistryUniversity of PatrasGR-265 04PatrasGreece
| | - Petros G. Tsoungas
- Laboratory of BiochemistryHellenic Pasteur Institute127 Vas. Sofias Ave.GR-115 21AthensGreece
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89
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In search of novel ligands using a structure-based approach: a case study on the adenosine A 2A receptor. J Comput Aided Mol Des 2016; 30:863-874. [PMID: 27629350 PMCID: PMC5083784 DOI: 10.1007/s10822-016-9963-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 09/02/2016] [Indexed: 12/03/2022]
Abstract
In this work, we present a case study to explore the challenges associated with finding novel molecules for a receptor that has been studied in depth and has a wealth of chemical information available. Specifically, we apply a previously described protocol that incorporates explicit water molecules in the ligand binding site to prospectively screen over 2.5 million drug-like and lead-like compounds from the commercially available eMolecules database in search of novel binders to the adenosine A2A receptor (A2AAR). A total of seventy-one compounds were selected for purchase and biochemical assaying based on high ligand efficiency and high novelty (Tanimoto coefficient ≤0.25 to any A2AAR tested compound). These molecules were then tested for their affinity to the adenosine A2A receptor in a radioligand binding assay. We identified two hits that fulfilled the criterion of ~50 % radioligand displacement at a concentration of 10 μM. Next we selected an additional eight novel molecules that were predicted to make a bidentate interaction with Asn2536.55, a key interacting residue in the binding pocket of the A2AAR. None of these eight molecules were found to be active. Based on these results we discuss the advantages of structure-based methods and the challenges associated with finding chemically novel molecules for well-explored targets.
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90
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Liu K, Jiang X, Hunziker P. Carbohydrate-based amphiphilic nano delivery systems for cancer therapy. NANOSCALE 2016; 8:16091-16156. [PMID: 27714108 DOI: 10.1039/c6nr04489a] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Nanoparticles (NPs) are novel drug delivery systems that have been attracting more and more attention in recent years, and have been used for the treatment of cancer, infection, inflammation and other diseases. Among the numerous classes of materials employed for constructing NPs, organic polymers are outstanding due to the flexibility of design and synthesis and the ease of modification and functionalization. In particular, NP based amphiphilic polymers make a great contribution to the delivery of poorly-water soluble drugs. For example, natural, biocompatible and biodegradable products like polysaccharides are widely used as building blocks for the preparation of such drug delivery vehicles. This review will detail carbohydrate based amphiphilic polymeric systems for cancer therapy. Specifically, it focuses on the nature of the polymer employed for the preparation of targeted nanocarriers, the synthetic methods, as well as strategies for the application and evaluation of biological activity. Applications of the amphiphilic polymer systems include drug delivery, gene delivery, photosensitizer delivery, diagnostic imaging and specific ligand-assisted cellular uptake. As a result, a thorough understanding of the relationship between chemical structure and biological properties facilitate the optimal design and rational clinical application of the resulting carbohydrate based nano delivery systems for cancer therapy.
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Affiliation(s)
- Kegang Liu
- Nanomedicine Research Lab CLINAM, University Hospital Basel, Bernoullistrasse 20, Basel, CH-4056, Switzerland.
| | - Xiaohua Jiang
- Institute of Molecular Pharmacy, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Patrick Hunziker
- Nanomedicine Research Lab CLINAM, University Hospital Basel, Bernoullistrasse 20, Basel, CH-4056, Switzerland. and CLINAM Foundation for Clinical Nanomedicine, Alemannengasse 12, Basel, CH-4016, Switzerland.
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91
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Furukawa A, Konuma T, Yanaka S, Sugase K. Quantitative analysis of protein-ligand interactions by NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 96:47-57. [PMID: 27573180 DOI: 10.1016/j.pnmrs.2016.02.002] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 02/21/2016] [Accepted: 02/21/2016] [Indexed: 06/06/2023]
Abstract
Protein-ligand interactions have been commonly studied through static structures of the protein-ligand complex. Recently, however, there has been increasing interest in investigating the dynamics of protein-ligand interactions both for fundamental understanding of the underlying mechanisms and for drug development. NMR is a versatile and powerful tool, especially because it provides site-specific quantitative information. NMR has widely been used to determine the dissociation constant (KD), in particular, for relatively weak interactions. The simplest NMR method is a chemical-shift titration experiment, in which the chemical-shift changes of a protein in response to ligand titration are measured. There are other quantitative NMR methods, but they mostly apply only to interactions in the fast-exchange regime. These methods derive the dissociation constant from population-averaged NMR quantities of the free and bound states of a protein or ligand. In contrast, the recent advent of new relaxation-based experiments, including R2 relaxation dispersion and ZZ-exchange, has enabled us to obtain kinetic information on protein-ligand interactions in the intermediate- and slow-exchange regimes. Based on R2 dispersion or ZZ-exchange, methods that can determine the association rate, kon, dissociation rate, koff, and KD have been developed. In these approaches, R2 dispersion or ZZ-exchange curves are measured for multiple samples with different protein and/or ligand concentration ratios, and the relaxation data are fitted to theoretical kinetic models. It is critical to choose an appropriate kinetic model, such as the two- or three-state exchange model, to derive the correct kinetic information. The R2 dispersion and ZZ-exchange methods are suitable for the analysis of protein-ligand interactions with a micromolar or sub-micromolar dissociation constant but not for very weak interactions, which are typical in very fast exchange. This contrasts with the NMR methods that are used to analyze population-averaged NMR quantities. Essentially, to apply NMR successfully, both the type of experiment and equation to fit the data must be carefully and specifically chosen for the protein-ligand interaction under analysis. In this review, we first explain the exchange regimes and kinetic models of protein-ligand interactions, and then describe the NMR methods that quantitatively analyze these specific interactions.
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Affiliation(s)
- Ayako Furukawa
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 1-1-1 Wakayamadai, Shimamoto, Mishima, Osaka 618-8503, Japan; Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Tsuyoshi Konuma
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 1-1-1 Wakayamadai, Shimamoto, Mishima, Osaka 618-8503, Japan; Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Saeko Yanaka
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 1-1-1 Wakayamadai, Shimamoto, Mishima, Osaka 618-8503, Japan; Department of Life and Coordination-Complex Molecular Science, Biomolecular Functions, Institute of Molecular Science, National Institute of Natural Sciences, Japan
| | - Kenji Sugase
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 1-1-1 Wakayamadai, Shimamoto, Mishima, Osaka 618-8503, Japan; Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto 615-8510, Japan.
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92
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Agamennone M, Belov DS, Laghezza A, Ivanov VN, Novoselov AM, Andreev IA, Ratmanova NK, Altieri A, Tortorella P, Kurkin AV. Fragment-Based Discovery of 5-Arylisatin-Based Inhibitors of Matrix Metalloproteinases 2 and 13. ChemMedChem 2016; 11:1892-8. [DOI: 10.1002/cmdc.201600266] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 06/21/2016] [Indexed: 01/03/2023]
Affiliation(s)
- Mariangela Agamennone
- Dipartimento di Farmacia; Università “G. d'Annunzio”; Chieti Via dei Vestini 31 66013 Chieti Italy
| | - Dmitry S. Belov
- EDASA Scientific srls; Via Stingi 37 66050 San Salvo Italy
- Chemistry Department; Lomonosov Moscow State University; 119991, GSP-2 Leninskie gory, 1/3 Moscow Russia
| | - Antonio Laghezza
- Dipartimento di Farmacia-Scienze del Farmaco; Università degli Studi “Aldo Moro” di Bari; Via Orabona 4 70126 Bari Italy
| | - Vladimir N. Ivanov
- Chemistry Department; Lomonosov Moscow State University; 119991, GSP-2 Leninskie gory, 1/3 Moscow Russia
| | - Anton M. Novoselov
- Chemistry Department; Lomonosov Moscow State University; 119991, GSP-2 Leninskie gory, 1/3 Moscow Russia
| | - Ivan A. Andreev
- EDASA Scientific srls; Via Stingi 37 66050 San Salvo Italy
- Chemistry Department; Lomonosov Moscow State University; 119991, GSP-2 Leninskie gory, 1/3 Moscow Russia
| | - Nina K. Ratmanova
- Chemistry Department; Lomonosov Moscow State University; 119991, GSP-2 Leninskie gory, 1/3 Moscow Russia
| | - Andrea Altieri
- EDASA Scientific srls; Via Stingi 37 66050 San Salvo Italy
| | - Paolo Tortorella
- Dipartimento di Farmacia-Scienze del Farmaco; Università degli Studi “Aldo Moro” di Bari; Via Orabona 4 70126 Bari Italy
| | - Alexander V. Kurkin
- Chemistry Department; Lomonosov Moscow State University; 119991, GSP-2 Leninskie gory, 1/3 Moscow Russia
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93
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Mittal R, Patel AP, Debs LH, Nguyen D, Patel K, Grati M, Mittal J, Yan D, Chapagain P, Liu XZ. Intricate Functions of Matrix Metalloproteinases in Physiological and Pathological Conditions. J Cell Physiol 2016; 231:2599-621. [DOI: 10.1002/jcp.25430] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 05/16/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Rahul Mittal
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - Amit P. Patel
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - Luca H. Debs
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - Desiree Nguyen
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - Kunal Patel
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - M'hamed Grati
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - Jeenu Mittal
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - Denise Yan
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - Prem Chapagain
- Department of Physics; Florida International University; Miami Florida
- Biomolecular Science Institute; Florida International University; Miami Florida
| | - Xue Zhong Liu
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
- Department of Biochemistry; University of Miami Miller School of Medicine; Miami Florida
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94
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Furukawa S, Takahashi K, Komatsu T. Well-structured bimetallic surface capable of molecular recognition for chemoselective nitroarene hydrogenation. Chem Sci 2016; 7:4476-4484. [PMID: 30009002 PMCID: PMC6014374 DOI: 10.1039/c6sc00817h] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 03/28/2016] [Indexed: 11/21/2022] Open
Abstract
Unprecedented molecular recognition ability governed by a simple bimetallic surface was demonstrated.
Unprecedented molecular recognition ability governed by a simple bimetallic surface is reported. A series of Rh-based ordered alloys supported on silica gel (RhxMy/SiO2, where M is Bi, Fe, Ga, Ge, In, Ni, Pb, Sb, Sn, or Zn) were tested in the hydrogenation of nitrostyrene to form aminostyrene. RhIn/SiO2 showed remarkably high catalytic activity and good selectivity under 1 atm H2 at room temperature. Moreover, various other nitroarenes containing carbonyl, cyano, or halo moieties were selectively hydrogenated into the corresponding amino derivatives using RhIn/SiO2. Kinetic study and density functional theory (DFT) calculations revealed that the high selectivity originates from RhIn/SiO2 adsorbing nitro groups much more favorably than vinyl groups. In addition, the DFT calculations indicated that the RhIn ordered alloy presents concave Rh rows and convex In rows on its surface, which are able to capture the nitro group with end-on geometry while effectively minimizing vinyl-π adsorption. Thus, the specific and highly ordered surface structure of RhIn enables the chemoselective molecular recognition of nitro groups over vinyl groups through geometric and chemical effects.
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Affiliation(s)
- Shinya Furukawa
- Department of Chemistry , Tokyo Institute of Technology , 2-12-1-E1-10 Ookayama, Meguro-ku , Tokyo 152-8551 , Japan . ; ; ; ; Tel: +81-3-5734-2602 ; Tel: +81-3-5734-3532
| | - Katsuya Takahashi
- Department of Chemistry , Tokyo Institute of Technology , 2-12-1-E1-10 Ookayama, Meguro-ku , Tokyo 152-8551 , Japan . ; ; ; ; Tel: +81-3-5734-2602 ; Tel: +81-3-5734-3532
| | - Takayuki Komatsu
- Department of Chemistry , Tokyo Institute of Technology , 2-12-1-E1-10 Ookayama, Meguro-ku , Tokyo 152-8551 , Japan . ; ; ; ; Tel: +81-3-5734-2602 ; Tel: +81-3-5734-3532
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95
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Azadi S, Cohen RE. Chemical accuracy from quantum Monte Carlo for the benzene dimer. J Chem Phys 2016; 143:104301. [PMID: 26374029 DOI: 10.1063/1.4930137] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report an accurate study of interactions between benzene molecules using variational quantum Monte Carlo (VMC) and diffusion quantum Monte Carlo (DMC) methods. We compare these results with density functional theory using different van der Waals functionals. In our quantum Monte Carlo (QMC) calculations, we use accurate correlated trial wave functions including three-body Jastrow factors and backflow transformations. We consider two benzene molecules in the parallel displaced geometry, and find that by highly optimizing the wave function and introducing more dynamical correlation into the wave function, we compute the weak chemical binding energy between aromatic rings accurately. We find optimal VMC and DMC binding energies of -2.3(4) and -2.7(3) kcal/mol, respectively. The best estimate of the coupled-cluster theory through perturbative triplets/complete basis set limit is -2.65(2) kcal/mol [Miliordos et al., J. Phys. Chem. A 118, 7568 (2014)]. Our results indicate that QMC methods give chemical accuracy for weakly bound van der Waals molecular interactions, comparable to results from the best quantum chemistry methods.
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Affiliation(s)
- Sam Azadi
- Department of Earth Science and Thomas Young Centre, University College London, London WC1E 6BT, United Kingdom
| | - R E Cohen
- London Centre for Nanotechnology, University College London, London WC1E 6BT, United Kingdom and Extreme Materials Initiative, Geophysical Laboratory, Carnegie Institution of Washington, Washington, D.C. 20015, USA
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96
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Trost BM, Ryan MC, Rao M. Chiral cyclopentadienylruthenium sulfoxide catalysts for asymmetric redox bicycloisomerization. Beilstein J Org Chem 2016; 12:1136-52. [PMID: 27559366 PMCID: PMC4979649 DOI: 10.3762/bjoc.12.110] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 05/03/2016] [Indexed: 01/19/2023] Open
Abstract
A full account of our efforts toward an asymmetric redox bicycloisomerization reaction is presented in this article. Cyclopentadienylruthenium (CpRu) complexes containing tethered chiral sulfoxides were synthesized via an oxidative [3 + 2] cycloaddition reaction between an alkyne and an allylruthenium complex. Sulfoxide complex 1 containing a p-anisole moiety on its sulfoxide proved to be the most efficient and selective catalyst for the asymmetric redox bicycloisomerization of 1,6- and 1,7-enynes. This complex was used to synthesize a broad array of [3.1.0] and [4.1.0] bicycles. Sulfonamide- and phosphoramidate-containing products could be deprotected under reducing conditions. Catalysis performed with enantiomerically enriched propargyl alcohols revealed a matched/mismatched effect that was strongly dependent on the nature of the solvent.
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Affiliation(s)
- Barry M Trost
- Department of Chemistry, Stanford University, Stanford, California 94305-5580, USA
| | - Michael C Ryan
- Department of Chemistry, Stanford University, Stanford, California 94305-5580, USA
| | - Meera Rao
- Department of Chemistry, Stanford University, Stanford, California 94305-5580, USA
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97
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Shibaeva KS, Nazarova AA, Kuznetsova DI, Stoikov II. Synthesis of aminobismethylenephosphonic acids on a platform of p-tert-Butylthiacalix[4]arene in 1,3-alternate configuration. RUSS J GEN CHEM+ 2016. [DOI: 10.1134/s1070363216030130] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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98
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Abstract
On the basis of many literature measurements, a critical overview is given on essential noncovalent interactions in synthetic supramolecular complexes, accompanied by analyses with selected proteins. The methods, which can be applied to derive binding increments for single noncovalent interactions, start with the evaluation of consistency and additivity with a sufficiently large number of different host-guest complexes by applying linear free energy relations. Other strategies involve the use of double mutant cycles, of molecular balances, of dynamic combinatorial libraries, and of crystal structures. Promises and limitations of these strategies are discussed. Most of the analyses stem from solution studies, but a few also from gas phase. The empirically derived interactions are then presented on the basis of selected complexes with respect to ion pairing, hydrogen bonding, electrostatic contributions, halogen bonding, π-π-stacking, dispersive forces, cation-π and anion-π interactions, and contributions from the hydrophobic effect. Cooperativity in host-guest complexes as well as in self-assembly, and entropy factors are briefly highlighted. Tables with typical values for single noncovalent free energies and polarity parameters are in the Supporting Information.
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Affiliation(s)
- Frank Biedermann
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT) , Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Hans-Jörg Schneider
- FR Organische Chemie der Universität des Saarlandes , D-66041 Saarbrücken, Germany
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99
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Li M, Hoeck C, Schoffelen S, Gotfredsen CH, Meldal M. Specific Electrostatic Molecular Recognition in Water. Chemistry 2016; 22:7206-14. [PMID: 27073143 DOI: 10.1002/chem.201600231] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Indexed: 11/11/2022]
Abstract
The identification of pairs of small peptides that recognize each other in water exclusively through electrostatic interactions is reported. The target peptide and a structure-biased combinatorial ligand library consisting of ≈78 125 compounds were synthesized on different sized beads. Peptide-peptide interactions could conveniently be observed by clustering of the small, fluorescently labeled target beads on the surface of larger ligand-containing beads. Sequences of isolated hits were determined by MS/MS. The interactions of the complex showing the highest affinity were investigated by a novel single-bead binding assay and by 2D NMR spectroscopy. Molecular dynamics (MD) studies revealed a putative mode of interaction for this unusual electrostatic binding event. High binding specificity occurred through a combination of topological matching and electrostatic and hydrogen-bond complementarities. From MD simulations binding also seemed to involve three tightly bound water molecules in the interface between the binding partners. Binding constants in the submicromolar range, useful for biomolecular adhesion and in nanostructure design, were measured.
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Affiliation(s)
- Ming Li
- Department of Chemistry, Center for Evolutionary Chemical Biology, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark
| | - Casper Hoeck
- Department of Chemistry, Technical University of Denmark, Building 207, 2800, Kongens Lyngby, Denmark
| | - Sanne Schoffelen
- Department of Chemistry, Center for Evolutionary Chemical Biology, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark
| | - Charlotte H Gotfredsen
- Department of Chemistry, Technical University of Denmark, Building 207, 2800, Kongens Lyngby, Denmark
| | - Morten Meldal
- Department of Chemistry, Center for Evolutionary Chemical Biology, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark.
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100
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Bourguet E, Brazhnik K, Sukhanova A, Moroy G, Brassart-Pasco S, Martin AP, Villena I, Bellon G, Sapi J, Nabiev I. Design, Synthesis, and Use of MMP-2 Inhibitor-Conjugated Quantum Dots in Functional Biochemical Assays. Bioconjug Chem 2016; 27:1067-81. [DOI: 10.1021/acs.bioconjchem.6b00065] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Erika Bourguet
- Institut de Chimie Moléculaire de Reims, UMR 7312-CNRS, SFR Cap-Santé, UFR de Pharmacie, Université de Reims Champagne-Ardenne, 51 rue Cognacq Jay, 51100 Reims, France
| | - Kristina Brazhnik
- Laboratoire de Recherche en Nanosciences, LRN - EA4682, UFR de Pharmacie, Université de Reims Champagne-Ardenne, 51 rue Cognacq Jay, 51100 Reims, France
- Laboratory of Nano-Bioengineering, National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 31 Kashirskoe shosse, 115409 Moscow, Russian Federation
| | - Alyona Sukhanova
- Laboratoire de Recherche en Nanosciences, LRN - EA4682, UFR de Pharmacie, Université de Reims Champagne-Ardenne, 51 rue Cognacq Jay, 51100 Reims, France
- Laboratory of Nano-Bioengineering, National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 31 Kashirskoe shosse, 115409 Moscow, Russian Federation
| | - Gautier Moroy
- Molécules Thérapeutiques In Silico, INSERM UMR-S 973, Université Paris Diderot, Sorbonne Paris Cité, 35 rue Hélène Brion, 75013 Paris, France
| | - Sylvie Brassart-Pasco
- Laboratoire de Biochimie et de Biologie moléculaire, MEDyC, UMR CNRS/URCA 7369, SFR Cap-Santé, UFR de Médecine, Université de Reims Champagne-Ardenne, 51 rue Cognacq Jay, 51100 Reims, France
| | - Anne-Pascaline Martin
- Laboratoire de Biochimie et de Biologie moléculaire, MEDyC, UMR CNRS/URCA 7369, SFR Cap-Santé, UFR de Médecine, Université de Reims Champagne-Ardenne, 51 rue Cognacq Jay, 51100 Reims, France
- Laboratoire de Parasitologie-Mycologie, EA3800, SFR Cap-Santé, UFR de Médecine, Université de Reims Champagne-Ardenne, 51 rue Cognacq-Jay, 51100 Reims, France
| | - Isabelle Villena
- Laboratoire de Parasitologie-Mycologie, EA3800, SFR Cap-Santé, UFR de Médecine, Université de Reims Champagne-Ardenne, 51 rue Cognacq-Jay, 51100 Reims, France
| | - Georges Bellon
- Laboratoire de Biochimie et de Biologie moléculaire, MEDyC, UMR CNRS/URCA 7369, SFR Cap-Santé, UFR de Médecine, Université de Reims Champagne-Ardenne, 51 rue Cognacq Jay, 51100 Reims, France
| | - Janos Sapi
- Institut de Chimie Moléculaire de Reims, UMR 7312-CNRS, SFR Cap-Santé, UFR de Pharmacie, Université de Reims Champagne-Ardenne, 51 rue Cognacq Jay, 51100 Reims, France
| | - Igor Nabiev
- Laboratoire de Recherche en Nanosciences, LRN - EA4682, UFR de Pharmacie, Université de Reims Champagne-Ardenne, 51 rue Cognacq Jay, 51100 Reims, France
- Laboratory of Nano-Bioengineering, National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 31 Kashirskoe shosse, 115409 Moscow, Russian Federation
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