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Bouzina A, Bouone YO, Sekiou O, Aissaoui M, Ouk TS, Djemel A, Mansouri R, Ibrahim-Ouali M, Bouslama Z, Aouf NE. In vitro antitumor activity, molecular dynamics simulation, DFT study, ADME prediction, and Eg5 binding of enastron analogues. RSC Adv 2023; 13:19567-19584. [PMID: 37388149 PMCID: PMC10301704 DOI: 10.1039/d3ra02904b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 06/16/2023] [Indexed: 07/01/2023] Open
Abstract
The objective of this study is to evaluate a series of molecules based on cyclosulfamide as potential anticancer agents. Additionally, the study aims to analyze the obtained results through in silico studies; by conducting experiments and utilizing theoretical methods. In this context, we investigated the cytotoxic activity of enastron analogues on three human cell lines PRI (lymphoblastic cell line) derived from B-cell lymphoma. JURKAT (ATCC TIB-152) acute T cell leukaemia and K562 (ATCC CLL-243) is a chronic myelogenous leukaemia. Most of the tested compounds showed good inhibitory activity compared with the reference ligand (chlorambucil). The 5a derivative demonstrated the strongest effect against all cancer cells used. Furthermore, molecular docking simulations of the Eg5-enastron analogue complex revealed that studied molecules have the ability to inhibit the Eg5 enzyme, as evidenced by their calculated docking score. Following the promising results from the molecular docking study, the complex Eg5-4a underwent a 100 ns molecular dynamics simulation using Desmond. During the simulation, the receptor-ligand pairing demonstrated substantial stability after the initial 70 ns. In addition, we used DFT calculations to analyze the electronic and geometric characteristics of the studied compounds. The HOMO and LUMO band gap energies, and the molecular electrostatic potential surface were also deducted for the stable structure of each compound. Also, we studied the prediction of absorption, distribution, metabolism and excretion (ADME) of the compounds.
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Affiliation(s)
- Abdeslem Bouzina
- Laboratory of Applied Organic Chemistry, Bioorganic Chemistry Group, Department of Chemistry, Sciences Faculty, Badji Mokhtar Annaba University Box 12 23000 Annaba Algeria
| | - Yousra Ouafa Bouone
- Laboratory of Applied Organic Chemistry, Bioorganic Chemistry Group, Department of Chemistry, Sciences Faculty, Badji Mokhtar Annaba University Box 12 23000 Annaba Algeria
| | - Omar Sekiou
- Environmental Research Center (CRE) 23000 Annaba Algeria
| | - Mohamed Aissaoui
- Laboratory of Applied Organic Chemistry, Bioorganic Chemistry Group, Department of Chemistry, Sciences Faculty, Badji Mokhtar Annaba University Box 12 23000 Annaba Algeria
| | - Tan-Sothea Ouk
- Laboratoire Peirene, EA7500 Université de Limoges 123 Avenue Albert Thomas 87000 Limoges Cedex France
| | - Abdelhak Djemel
- Research Unit in Medicinal Plants, URPM 3000 Laghouat Algeria
- Research Center of Biotechnology, CRBt 25000 Constantine Algeria
| | | | | | - Zihad Bouslama
- Environmental Research Center (CRE) 23000 Annaba Algeria
| | - Nour-Eddine Aouf
- Laboratory of Applied Organic Chemistry, Bioorganic Chemistry Group, Department of Chemistry, Sciences Faculty, Badji Mokhtar Annaba University Box 12 23000 Annaba Algeria
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Harish BS, Raja MRC, Mahapatra SK, Uppuluri KB. Production Enhancement of an Anticoagulant Trypsin Inhibitor from Oceanimonas sp. BPMS22 and Its Anti-cancer Activity. Int J Pept Res Ther 2021. [DOI: 10.1007/s10989-020-10078-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Jun JJ, Duscharla D, Ummanni R, Hanson PR, Malhotra SV. Investigation on the Anticancer Activity of Symmetric and Unsymmetric Cyclic Sulfamides. ACS Med Chem Lett 2021; 12:202-210. [PMID: 33603966 DOI: 10.1021/acsmedchemlett.0c00460] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 01/08/2021] [Indexed: 12/20/2022] Open
Abstract
The sulfamide functional group has been extensively employed in organic synthesis to discover probes and drugs in various applications such as cancer, human immunodeficiency virus (HIV), virus, and diabetes. Herein, we describe the synthesis of 7-membered symmetric and unsymmetric sulfamide compounds and their biological evaluation through the National Cancer Institute (NCI) panel of 60 human tumor cell lines (NCI-60) and the mechanism of action study. The results of a study from the NCI-60 cell line exhibited that many synthesized cyclic sulfamide compounds inhibited breast cancer (MDA-MB-468). The mechanism of action study of a representative compound 18 showed the inhibition of proliferation and apoptosis in A549 lung cancer cells.
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Affiliation(s)
- Jaden Jungho Jun
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, National Institutes of Health (NIH) National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Department of Chemistry, University of Kansas, 1567 Irving Hill Road, Lawrence, Kansas 66045-7582, United States
| | - Divya Duscharla
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, India
| | - Ramesh Ummanni
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, India
| | - Paul R. Hanson
- Department of Chemistry, University of Kansas, 1567 Irving Hill Road, Lawrence, Kansas 66045-7582, United States
| | - Sanjay V. Malhotra
- Department of Cell, Development and Cancer Biology, Oregon Health & Science University, Portland, Oregon 97201, United States
- Center for Experimental Therapeutics, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97201, United States
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Demay J, Bernard C, Reinhardt A, Marie B. Natural Products from Cyanobacteria: Focus on Beneficial Activities. Mar Drugs 2019; 17:E320. [PMID: 31151260 PMCID: PMC6627551 DOI: 10.3390/md17060320] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 05/21/2019] [Accepted: 05/21/2019] [Indexed: 12/28/2022] Open
Abstract
Cyanobacteria are photosynthetic microorganisms that colonize diverse environments worldwide, ranging from ocean to freshwaters, soils, and extreme environments. Their adaptation capacities and the diversity of natural products that they synthesize, support cyanobacterial success in colonization of their respective ecological niches. Although cyanobacteria are well-known for their toxin production and their relative deleterious consequences, they also produce a large variety of molecules that exhibit beneficial properties with high potential in various fields (e.g., a synthetic analog of dolastatin 10 is used against Hodgkin's lymphoma). The present review focuses on the beneficial activities of cyanobacterial molecules described so far. Based on an analysis of 670 papers, it appears that more than 90 genera of cyanobacteria have been observed to produce compounds with potentially beneficial activities in which most of them belong to the orders Oscillatoriales, Nostocales, Chroococcales, and Synechococcales. The rest of the cyanobacterial orders (i.e., Pleurocapsales, Chroococcidiopsales, and Gloeobacterales) remain poorly explored in terms of their molecular diversity and relative bioactivity. The diverse cyanobacterial metabolites possessing beneficial bioactivities belong to 10 different chemical classes (alkaloids, depsipeptides, lipopeptides, macrolides/lactones, peptides, terpenes, polysaccharides, lipids, polyketides, and others) that exhibit 14 major kinds of bioactivity. However, no direct relationship between the chemical class and the respective bioactivity of these molecules has been demonstrated. We further selected and specifically described 47 molecule families according to their respective bioactivities and their potential uses in pharmacology, cosmetology, agriculture, or other specific fields of interest. With this up-to-date review, we attempt to present new perspectives for the rational discovery of novel cyanobacterial metabolites with beneficial bioactivity.
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Affiliation(s)
- Justine Demay
- UMR 7245 MCAM, Muséum National d'Histoire Naturelle-CNRS, Paris, 12 rue Buffon, CP 39, 75231 Paris CEDEX 05, France.
- Thermes de Balaruc-les-Bains, 1 rue du Mont Saint-Clair BP 45, 34540 Balaruc-Les-Bains, France.
| | - Cécile Bernard
- UMR 7245 MCAM, Muséum National d'Histoire Naturelle-CNRS, Paris, 12 rue Buffon, CP 39, 75231 Paris CEDEX 05, France.
| | - Anita Reinhardt
- Thermes de Balaruc-les-Bains, 1 rue du Mont Saint-Clair BP 45, 34540 Balaruc-Les-Bains, France.
| | - Benjamin Marie
- UMR 7245 MCAM, Muséum National d'Histoire Naturelle-CNRS, Paris, 12 rue Buffon, CP 39, 75231 Paris CEDEX 05, France.
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Microbial serine protease inhibitors and their therapeutic applications. Int J Biol Macromol 2017; 107:1373-1387. [PMID: 28970170 DOI: 10.1016/j.ijbiomac.2017.09.115] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 09/28/2017] [Indexed: 12/22/2022]
Abstract
Serine protease inhibitors, inhibit serine proteases either partially or completely after forming complexes with their respective proteases. Protease actions are significant for many physiological pathways found in living forms and any anomalies may lead to numerous physiological complications. Each cell or organism has its own mechanism for controlling these protease actions. It is often regulated by the action of inhibitors or activators. Among the proteases, serine proteases are the most common that are involved in many life and death processes. Selective inhibitors of physiologically relevant proteases can be used as a lead compound for the drug development. Therefore, it is imperative to identify small peptides and proteins that selectively inhibit serine proteases from various sources. Microbes can be considered as a major source of diverse serine protease inhibitors since they have the prominent and diverse domain in nature. Most of the microbial serine protease inhibitors are intracellular and few are extracellular. Microbes produce protease inhibitors for protection against its own proteases or against other environmental factors. The status and future prospects of microbial serine protease inhibitors and their therapeutic benefits in treating cancer, blood coagulation disorders and viral infections, are reviewed here.
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Abstract
The pursuit of serine protease inhibitors as anticoagulants and anti-hepatitis C virus drugs continues to be an active area of research. Compounds such as P1-P3 macrocyclic peptides and linear peptides have been registered as potent hepatitis C virus protease inhibitors and compounds such as phenylglycinamide derivatives, substituted biaryls, tetrahydroquinoline derivatives, arylpropionamides, arylacrylamides, arylpropynamides, arylmethylurea analogs and peptides as factor XIa inhibitors. Given the recent US FDA approval of telaprevir and boceprevir for the treatment of hepatitis C virus, the development of new serine protease inhibitors is likely to be one of the hottest areas in the pharmaceutical industry. This review covers the patent literature on serine protease inhibitors during the period between 2009 and 2010.
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Venkatraj M, Messagie J, Joossens J, Lambeir AM, Haemers A, Van der Veken P, Augustyns K. Synthesis and evaluation of non-basic inhibitors of urokinase-type plasminogen activator (uPA). Bioorg Med Chem 2012; 20:1557-68. [DOI: 10.1016/j.bmc.2011.12.040] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Revised: 12/15/2011] [Accepted: 12/17/2011] [Indexed: 11/16/2022]
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Mulchande J, Simões SI, Gaspar MM, Eleutério CV, Oliveira R, Cruz MEM, Moreira R, Iley J. Synthesis, stability, biochemical and pharmacokinetic properties of a new potent and selective 4-oxo-β-lactam inhibitor of human leukocyte elastase. J Enzyme Inhib Med Chem 2010; 26:169-75. [PMID: 20545486 DOI: 10.3109/14756366.2010.486794] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The 4-oxo-β-lactams (azetidine-2,4-diones) are potent acylating agents of the human leukocyte elastase (HLE), a neutrophil serine protease that plays a key role in several inflammatory diseases. A novel 4-oxo-β-lactam containing a N-(4-(phenylsulphonylmethyl)phenyl) group, 3, was designed as a potential mechanism-based inhibitor capable of undergoing elimination of phenylsulphinate upon Ser-195 acylation. Compound 3 was found to be a potent slow-tight binding inhibitor of HLE, presenting a remarkable second-order rate constant of 1.46 x 10⁶ M⁻¹s⁻¹ and displaying selectivity over the proteinase 3 and cathepsin G. However, liberation of phenylsulphinate was not observed in the hydrolysis of 3 in both pH 7.4 phosphate buffer and human plasma. The C(max) values of 1207 μg/total blood, 179 μg/g spleen and 106 μg/g lung were determined by HPLC, following a single 30 mg/kg dose of 3 given intraperitoneally to NMRI mice, suggesting that the inhibitor distributes well into tissues. Although being a powerful selective inhibitor of HLE, 4-oxo-β-lactam 3 has a limited stability, being susceptible to off-target reactions (plasma and liver enzymes).
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Affiliation(s)
- Jalmira Mulchande
- Medicinal Chemistry, iMed.UL, Faculty of Pharmacy, University of Lisbon, Av. Prof. Gama Pinto, Lisbon, Portugal.
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Matthew S, Paul VJ, Luesch H. Tiglicamides A-C, cyclodepsipeptides from the marine cyanobacterium Lyngbya confervoides. PHYTOCHEMISTRY 2009; 70:2058-63. [PMID: 19815244 PMCID: PMC2787822 DOI: 10.1016/j.phytochem.2009.09.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2009] [Revised: 08/13/2009] [Accepted: 09/08/2009] [Indexed: 05/19/2023]
Abstract
The Floridian marine cyanobacterium Lyngbya confervoides afforded cyclodepsipeptides, termed tiglicamides A-C (1-3), along with their previously reported analogues largamides A-C (4-6), all of which possess an unusual tiglic acid moiety. Their structures were deduced by one- and two-dimensional NMR combined with mass spectrometry and the absolute configurations established by chiral HPLC and Marfey's analysis of the degradation products. Compounds 1-3 moderately inhibited porcine pancreatic elastase in vitro with IC(50) values from 2.14 to 7.28 microM. Compounds 1-6 differ from each other by one amino acid residue within the cyclic core structure, suggesting an unusually relaxed substrate specificity of the nonribosomal peptide synthetase that is the putative biosynthetic enzyme responsible for the corresponding amino acid incorporation.
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Affiliation(s)
- Susan Matthew
- Department of Medicinal Chemistry, University of Florida, Gainesville, Florida 32610, USA
| | - Valerie J. Paul
- Smithsonian Marine Station, 701 Seaway Drive, Fort Pierce, Florida 34949, USA
| | - Hendrik Luesch
- Department of Medicinal Chemistry, University of Florida, Gainesville, Florida 32610, USA
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Kawai SH, Aubry N, Duceppe JS, Llinàs-Brunet M, LaPlante SR. Dimethylthiazolidine Carboxylic Acid as a Rigid P3 Unit in Inhibitors of Serine Proteases: Application to Two Targets. Chem Biol Drug Des 2009; 74:517-22. [DOI: 10.1111/j.1747-0285.2009.00870.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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11
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Nilsson M, Hämäläinen M, Ivarsson M, Gottfries J, Xue Y, Hansson S, Isaksson R, Fex T. Compounds binding to the S2-S3 pockets of thrombin. J Med Chem 2009; 52:2708-15. [PMID: 19371038 DOI: 10.1021/jm8011849] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A set of compounds designed to bind to the S2-S3 pockets of thrombin was prepared. These compounds included examples with no interactions in the S1 pocket. Proline, a common P2 in many thrombin inhibitors, was combined with known P3 residues and P1 substituents of varying size and lipophilicity. Binding constants were determined using surface plasmon resonance (SPR) biosensor technology and were found to be in good agreement with results from an enzyme assay. A dramatic increase in affinity (100-1000 times) was seen for compounds incorporating an amino group capable of forming a hydrogen bond with gly216 in the protein backbone. The ligand efficiency was increased by including substituents that form stronger hydrophobic interactions with the P1 pocket. The binding mode was confirmed by X-ray analysis, which revealed the anticipated binding motif that included hydrogen bonds as well as a tightly bound water molecule. A QSAR model indicated that hydrogen bonding and lipophilicity were important for the prediction of binding constants. The results described here may have implications for how directed compound libraries for shallow protein pockets, like S2 and S3 in serine proteases, can be designed.
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Affiliation(s)
- Mikael Nilsson
- School of Pure and Applied Natural Sciences, University of Kalmar, S-391 82 Kalmar, Sweden.
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Frederickson M, Callaghan O, Chessari G, Congreve M, Cowan SR, Matthews JE, McMenamin R, Smith DM, Vinković M, Wallis NG. Fragment-Based Discovery of Mexiletine Derivatives as Orally Bioavailable Inhibitors of Urokinase-Type Plasminogen Activator. J Med Chem 2007; 51:183-6. [DOI: 10.1021/jm701359z] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Martyn Frederickson
- Astex Therapeutics Ltd, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom
| | - Owen Callaghan
- Astex Therapeutics Ltd, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom
| | - Gianni Chessari
- Astex Therapeutics Ltd, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom
| | - Miles Congreve
- Astex Therapeutics Ltd, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom
| | - Suzanna R. Cowan
- Astex Therapeutics Ltd, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom
| | - Julia E. Matthews
- Astex Therapeutics Ltd, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom
| | - Rachel McMenamin
- Astex Therapeutics Ltd, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom
| | - Donna-Michelle Smith
- Astex Therapeutics Ltd, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom
| | - Mladen Vinković
- Astex Therapeutics Ltd, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom
| | - Nicola G. Wallis
- Astex Therapeutics Ltd, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom
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Perekhodtsev G. Neighborhood Behavior: Validation of Two-Dimensional Molecular Similarity as a Predictor of Similar Biological Activities and Docking Scores. ACTA ACUST UNITED AC 2007. [DOI: 10.1002/qsar.200610052] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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14
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Winum JY, Scozzafava A, Montero JL, Supuran CT. Therapeutic potential of sulfamides as enzyme inhibitors. Med Res Rev 2006; 26:767-92. [PMID: 16710859 DOI: 10.1002/med.20068] [Citation(s) in RCA: 155] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Sulfamide, a quite simple molecule incorporating the sulfonamide functionality, widely used by medicinal chemists for the design of a host of biologically active derivatives with pharmacological applications, may give rise to at least five types of derivatives, by substituting one to four hydrogen atoms present in it, which show specific biological activities. Recently, some of these compounds started to be exploited for the design of many types of therapeutic agents. Among the enzymes for which sulfamide-based inhibitors were designed, are the carbonic anhydrases (CAs), a large number of proteases belonging to the aspartic protease (HIV-1 protease, gamma-secretase), serine protease (elastase, chymase, tryptase, and thrombin among others), and metalloprotease (carboxypeptidase A (CPA) and matrix metalloproteinases (MMP)) families. Some steroid sulfatase (STS) and protein tyrosine phosphatase inhibitors belonging to the sulfamide class of derivatives have also been reported. In all these compounds, many of which show low nanomolar affinity for the target enzymes for which they have been designed, the free or substituted sulfamide moiety plays important roles for the binding of the inhibitor to the active site cavity, either by directly coordinating to a metal ion found in some metalloenzymes (CAs, CPA, STS), usually by means of one of the nitrogen atoms present in the sulfamide motif, or as in the case of the cyclic sulfamides acting as HIV protease inhibitors, interacting with the catalytically critical aspartic acid residues of the active site by means of an oxygen atom belonging to the HN-SO2-NH motif, which substitutes a catalytically essential water molecule. In other cases, the sulfamide moiety is important for inducing desired physico-chemical properties to the drug-like compounds incorporating it, such as enhanced water solubility, better bioavailability, etc., because of the intrinsic properties of this highly polarized moiety when attached to an organic scaffold. This interesting motif is thus of great value for the design of pharmacological agents with a lot of applications.
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Affiliation(s)
- Jean-Yves Winum
- Université Montpellier II, Laboratoire de Chimie Biomoléculaire, UMR 5032, Ecole Nationale Supérieure de Chimie de Montpellier, 8 rue de l'Ecole Normale, 34296 Montpellier Cedex, France.
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15
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Lazarova TI, Jin L, Rynkiewicz M, Gorga JC, Bibbins F, Meyers HV, Babine R, Strickler J. Synthesis and in vitro biological evaluation of aryl boronic acids as potential inhibitors of factor XIa. Bioorg Med Chem Lett 2006; 16:5022-7. [PMID: 16876411 DOI: 10.1016/j.bmcl.2006.07.043] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2006] [Accepted: 07/14/2006] [Indexed: 10/24/2022]
Abstract
A series of functionalized aryl boronic acids were synthesized and evaluated as potential inhibitors of factor XIa. Crystal structures of the protein-inhibitor complexes led to the design and synthesis of second generation compounds showing single digit micromolar inhibition against FXIa and selectivity against thrombin, trypsin, and FXa.
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Affiliation(s)
- Tsvetelina I Lazarova
- Medicinal Chemistry, Daiichi Asubio Medical Research Laboratories, LLC, One Kendall Square, Building 700, Cambridge, MA 02139, USA.
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16
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Pearce BC, Sofia MJ, Good AC, Drexler DM, Stock DA. An Empirical Process for the Design of High-Throughput Screening Deck Filters. J Chem Inf Model 2006; 46:1060-8. [PMID: 16711725 DOI: 10.1021/ci050504m] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A process for objective identification and filtering of undesirable compounds that contribute to high-throughput screening (HTS) deck promiscuity is described. Two methods of mapping hit promiscuity have been developed linking SMARTS-based structural queries with historical primary HTS data. The first compares an expected assay hit rate to actual hit rates. The second examines the propensity of an individual compound to hit multiple assays. Statistical evaluation of the data indicates a correlation between the resultant functional group filters and compound promiscuity. These data corroborate a number of commonly applied filters as well as producing some unexpected results. Application of these models to HTS collection triage reduced the number of in-house compounds considered for screening by 12%. The implications of these findings are further discussed in the context of the HTS screening set and combinatorial library design as well as compound acquisition.
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Affiliation(s)
- Bradley C Pearce
- Bristol-Myers Squibb Pharmaceutical Research Institute, 5 Research Parkway, Wallingford, Connecticut 06492, USA.
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17
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Rossi C, Hess S, Eckl RW, di Lena A, Bruno A, Thomas O, Poggi A. Effect of MCM09, an active site-directed inhibitor of factor Xa, on B16-BL6 melanoma lung colonies in mice. J Thromb Haemost 2006; 4:608-13. [PMID: 16460443 DOI: 10.1111/j.1538-7836.2006.01793.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND Treatment with anticoagulant drugs has shown potential inhibitory effect on tumor invasion, although the relationship with clotting inhibition was not clear. AIM The aim of our study was to evaluate the potential antitumor activity of MCM09, a newly developed, active site-directed, small molecule inhibitor of factor Xa (FXa) [WO0216312], and to relate the findings to anticlotting potency. METHODS MCM09 (0.1-10 mg kg(-1)) or heparin (H; 10 mg kg(-1)) was injected intravenously (i.v.), with 5 x 10(4) B16-BL6 melanoma cells, in C57BL/6 mice. Mice were killed after 18 days, to count lung colonies. Ex vivo anticoagulant activity was measured by activated partial thromboplastin time (APTT) on mouse plasma. RESULTS AND CONCLUSIONS MCM09, a selective inhibitor of FXa (IC-50 = 2.4 nm against human FXa), inhibited in a dose-dependent manner B16-BL6 melanoma lung colonies in mice. Mean lung metastasis number was 20.9 +/- 4.8 in controls (n = 10), 1.2 +/- 0.4 in mice treated with H, 10 mg kg(-1) i.v. (P < 0.01), 0.9 +/- 0.3, 9.2 +/- 2.2 and 15.5 +/- 2.6 in mice treated with MCM09, at 10 (P < 0.01), 1 (P < 0.05) and 0.1 mg kg(-1) i.v. (ns), respectively. MCM09 (10 mg kg(-1) i.v.) significantly prolonged APTT (57.1 +/- 10.2 s) 30 min after i.v. injection when compared with controls (25.3 +/- 1.6 s; P < 0.05). Lung colonies were 74.2-72.6% reduced by MCM09 (10 mg kg(-1)) given 60 or 120 min before cells, but not by MCM09 given 60 min thereafter, suggesting a direct cell interaction as a mechanism underlying antitumor activity.
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Affiliation(s)
- C Rossi
- Consorzio Mario Negri Sud, Santa Maria Imbaro (CH), Italy
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18
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Perekhodtsev GD. Similarity study of serine proteases inhibitors. Mol Divers 2006; 10:81-3. [PMID: 16404529 DOI: 10.1007/s11030-006-2153-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2005] [Accepted: 08/02/2005] [Indexed: 11/26/2022]
Abstract
Two-dimensional structural similarity calculations have been applied to estimate binding affinities of serine proteases inhibitors. 1103 trypsin binders, 1268 thrombin binders and 714 fXa binders have been used to compare experimental and predicted data. The predictions generally provide reasonable estimates of the observed binding affinities. The accuracy of the predictions depends on the size of the dataset, but not dramatically. The accuracy also depends on the number of similar structures used to make the calculations, with a number from 3 to 6 usually being optimal. The binding affinity is noticeably more sensitive to the inhibitor structure in the case of fXa relative to thrombin.
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Affiliation(s)
- Gleb D Perekhodtsev
- Algodign LLC, entrance 4, Bolshaya Sadovaya street 8, Moscow 123001, Russia.
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19
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Winum JY, Scozzafava A, Montero JL, Supuran CT. The sulfamide motif in the design of enzyme inhibitors. Expert Opin Ther Pat 2005; 16:27-47. [DOI: 10.1517/13543776.16.1.27] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Dickopf S, Frank M, Junker HD, Maier S, Metz G, Ottleben H, Rau H, Schellhaas N, Schmidt K, Sekul R, Vanier C, Vetter D, Czech J, Lorenz M, Matter H, Schudok M, Schreuder H, Will DW, Nestler HP. Custom chemical microarray production and affinity fingerprinting for the S1 pocket of factor VIIa. Anal Biochem 2004; 335:50-7. [PMID: 15519570 DOI: 10.1016/j.ab.2004.08.033] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2004] [Indexed: 10/26/2022]
Abstract
The goal of this study was to explore the applicability of surface plasmon resonance (SPR)-based fragment screening to identify compounds that bind to factor VIIa (FVIIa). Based on pharmacophore models virtual screening approaches, we selected fragments anticipated to have a reasonable chance of binding to the S1-binding pocket of FVIIa and immobilized these compounds on microarrays. In affinity fingerprinting experiments, a number of compounds were identified to be specifically interacting with FVIIa and shown to fall into four structural classes. The results demonstrate that the chemical microarray technology platform using SPR detection generates unique chemobiological information that is useful for de novo discovery and lead development and allows the detection of weak interactions with ligands of low molecular weight.
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Affiliation(s)
- Stefan Dickopf
- Graffinity Pharmaceuticals AG, Im Neuenheimer Feld 518-519, D-69120 Heidelberg, Germany
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Novel tripeptide inhibitors of hepatitis C virus NS3 serine protease. Expert Opin Ther Pat 2003. [DOI: 10.1517/13543776.13.2.267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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