Discovery of potent inhibitor for matrix metalloproteinase-9 by pharmacophore based modeling and dynamics simulation studies.
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Lilly M Saleena | V. Subramanian | L. Saleena | E. R. Azhagiya Singam | V Subramanian | Sukesh Kalva | E R Azhagiya Singam | V Rajapandian | Sukesh Kalva | V. Rajapandian | E. R. A. Singam | V. Subramanian
[1] O. H. Lowry,et al. Protein measurement with the Folin phenol reagent. , 1951, The Journal of biological chemistry.
[2] L. Liotta,et al. Metastatic potential correlates with enzymatic degradation of basement membrane collagen , 1980, Nature.
[3] M. Baba,et al. An application of tetrazolium (MTT) colorimetric assay for the screening of anti-herpes simplex virus compounds. , 1991, Journal of virological methods.
[4] D. Scudiero,et al. Tetrazolium-based assays for cellular viability: a critical examination of selected parameters affecting formazan production. , 1991, Cancer research.
[5] L. Belov,et al. The MTT cell viability assay for cytotoxicity testing in multidrug-resistant human leukemic cells. , 1992, Leukemia research.
[6] S. Gruber,et al. Direct evidence linking expression of matrix metalloproteinase 9 (92-kDa gelatinase/collagenase) to the metastatic phenotype in transformed rat embryo cells. , 1994, Proceedings of the National Academy of Sciences of the United States of America.
[7] Y. Okada,et al. Expression of membrane-type matrix metalloproteinase 1 (MT1-MMP) in tumor cells enhances pulmonary metastasis in an experimental metastasis assay. , 1996, Cancer research.
[8] Berk Hess,et al. LINCS: A linear constraint solver for molecular simulations , 1997 .
[9] J. Skotnicki,et al. The synthesis and biological activity of a novel series of diazepine MMP inhibitors. , 1998, Bioorganic & medicinal chemistry letters.
[10] D. Azar,et al. Expression of gelatinases A and B, and TIMPs 1 and 2 during corneal wound healing. , 1998, Investigative ophthalmology & visual science.
[11] M. Dardenne. Role of thymic peptides as transmitters between the neuroendocrine and immune systems. , 1999, Annals of medicine.
[12] R. Goldberg,et al. Design and synthesis of thiol containing inhibitors of matrix metalloproteinases. , 1999, Bioorganic & medicinal chemistry letters.
[13] U. Ryde,et al. Protein strain in blue copper proteins studied by free energy perturbations , 1999, Proteins.
[14] S. Hanessian,et al. Picking the S1, S1' and S2' pockets of matrix metalloproteinases. A niche for potent acyclic sulfonamide inhibitors. , 1999, Bioorganic & medicinal chemistry letters.
[15] V. Kähäri,et al. Matrix metalloproteinases in tumor invasion , 2000, Cellular and Molecular Life Sciences CMLS.
[16] Z. Werb,et al. The many faces of metalloproteases: cell growth, invasion, angiogenesis and metastasis. , 2001, Trends in cell biology.
[17] Xiaojie Xu,et al. Binding Affinities for a Series of Selective Inhibitors of Gelatinase-A Using Molecular Dynamics with a Linear Interaction Energy Approach , 2001 .
[18] Björn O. Roos,et al. A theoretical study of the copper–cysteine bond in blue copper proteins , 2001 .
[19] J. S. Johnson,et al. Discovery of heterocyclic ureas as a new class of raf kinase inhibitors: identification of a second generation lead by a combinatorial chemistry approach. , 2001, Bioorganic & medicinal chemistry letters.
[20] Manuel Hidalgo,et al. Development of matrix metalloproteinase inhibitors in cancer therapy. , 2002, Hematology/oncology clinics of North America.
[21] A. Henney,et al. Crystal structure of human MMP9 in complex with a reverse hydroxamate inhibitor. , 2002, Journal of molecular biology.
[22] V. Kähäri,et al. Matrix metalloproteinases in cancer: Prognostic markers and therapeutic targets , 2002, International journal of cancer.
[23] B. Riedl,et al. Design and discovery of small molecules targeting raf-1 kinase. , 2002, Current pharmaceutical design.
[24] Z. Werb,et al. New functions for the matrix metalloproteinases in cancer progression , 2002, Nature Reviews Cancer.
[25] John Ellingboe,et al. Synthesis and structure-activity relationship of N-substituted 4-arylsulfonylpiperidine-4-hydroxamic acids as novel, orally active matrix metalloproteinase inhibitors for the treatment of osteoarthritis. , 2003, Journal of medicinal chemistry.
[26] X. Cheng,et al. Green tea catechins inhibit the cultured smooth muscle cell invasion through the basement barrier. , 2003, Atherosclerosis.
[27] Qiang Xu,et al. Quercetin inhibits the invasion of murine melanoma B16-BL6 cells by decreasing pro-MMP-9 via the PKC pathway , 2003, Cancer Chemotherapy and Pharmacology.
[28] R. Black,et al. Acetylenic TACE inhibitors. Part 1. SAR of the acyclic sulfonamide hydroxamates. , 2003, Bioorganic & medicinal chemistry letters.
[29] A. Chollet,et al. Stereospecific synthesis of 5-substituted 2-bisarylthiocyclopentane carboxylic acids as specific matrix metalloproteinase inhibitors. , 2003, Journal of medicinal chemistry.
[30] John Ellingboe,et al. Synthesis and structure-activity relationship of alpha-sulfonylhydroxamic acids as novel, orally active matrix metalloproteinase inhibitors for the treatment of osteoarthritis. , 2003, Journal of medicinal chemistry.
[31] Irwin D Kuntz,et al. A molecular basis for the selectivity of thiadiazole urea inhibitors with stromelysin-1 and gelatinase-A from generalized born molecular dynamics simulations. , 2004, Journal of medicinal chemistry.
[32] J. Skotnicki,et al. Synthesis and structure-activity relationships of 4-alkynyloxy phenyl sulfanyl, sulfinyl, and sulfonyl alkyl hydroxamates as tumor necrosis factor-α converting enzyme and matrix metalloproteinase inhibitors , 2004 .
[33] I. Pucci‐Minafra,et al. Zymographic detection and clinical correlations of MMP-2 and MMP-9 in breast cancer sera , 2004, British Journal of Cancer.
[34] G. Sutherland,et al. High levels of gelatinase-B and active gelatinase-A in metastatic glioblastoma , 2004, Journal of Neuro-Oncology.
[35] Robert K Szilagyi,et al. Electronic structures of metal sites in proteins and models: contributions to function in blue copper proteins. , 2004, Chemical reviews.
[36] Weihua Li,et al. POSSIBLE PATHWAY(S) OF TESTOSTERONE EGRESS FROM THE ACTIVE SITE OF CYTOCHROME P450 2B1: A STEERED MOLECULAR DYNAMICS SIMULATION , 2005, Drug Metabolism and Disposition.
[37] F. Mannello,et al. Matrix metalloproteinase inhibitors as anticancer therapeutics. , 2005, Current cancer drug targets.
[38] A. Clowes,et al. MMP-9 regulates both positively and negatively collagen gel contraction: a nonproteolytic function of MMP-9. , 2005, Cardiovascular research.
[39] R. Ala-aho,et al. Matrix metalloproteinases as therapeutic targets in cancer. , 2005, Current cancer drug targets.
[40] O. Schober,et al. C-5-disubstituted barbiturates as potential molecular probes for noninvasive matrix metalloproteinase imaging. , 2005, Journal of medicinal chemistry.
[41] Holger Gohlke,et al. The Amber biomolecular simulation programs , 2005, J. Comput. Chem..
[42] B. G. Rao,et al. Recent developments in the design of specific Matrix Metalloproteinase inhibitors aided by structural and computational studies. , 2005, Current pharmaceutical design.
[43] C. Dennison. Investigating the structure and function of cupredoxins , 2005 .
[44] J. Pandit,et al. Potent, selective pyrimidinetrione-based inhibitors of MMP-13. , 2006, Bioorganic & medicinal chemistry letters.
[45] E. Hazai,et al. Molecular modeling of non-covalent binding of homochiral (3S,3'S)-astaxanthin to matrix metalloproteinase-13 (MMP-13). , 2006, Bioorganic & medicinal chemistry.
[46] Ferdinando Mannello,et al. Natural bio-drugs as matrix metalloproteinase inhibitors: new perspectives on the horizon? , 2006, Recent patents on anti-cancer drug discovery.
[47] David E. Shaw,et al. PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results , 2006, J. Comput. Aided Mol. Des..
[48] Matthew P. Repasky,et al. Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. , 2006, Journal of medicinal chemistry.
[49] B. Turk. Targeting proteases: successes, failures and future prospects , 2006, Nature Reviews Drug Discovery.
[50] Philippe Cuniasse,et al. Development of Selective Inhibitors and Substrate of Matrix Metalloproteinase-12* , 2006, Journal of Biological Chemistry.
[51] C. Hansch,et al. Matrix metalloproteinases (MMPs): chemical-biological functions and (Q)SARs. , 2007, Bioorganic & medicinal chemistry.
[52] Angelo Carotti,et al. Screening of Matrix Metalloproteinases Available from the Protein Data Bank: Insights into Biological Functions, Domain Organization, and Zinc Binding Groups , 2007, J. Chem. Inf. Model..
[53] T. Tuccinardi,et al. Development of a receptor-based 3D-QSAR study for the analysis of MMP2, MMP3, and MMP9 inhibitors. , 2008, Bioorganic & medicinal chemistry.
[54] Seth M Cohen,et al. Zinc‐Binding Groups Modulate Selective Inhibition of MMPs , 2008, ChemMedChem.
[55] T. A. Gureeva,et al. Expression of gelatinases A and B and their endogenous regulators in immortal and transformed fibroblasts , 2009, Biomeditsinskaia khimiia.
[56] Calculation of binding free energies for non-zinc chelating pyrimidine dicarboxamide inhibitors with MMP-13. , 2009, Bioorganic & medicinal chemistry letters.
[57] Peter Comba,et al. Computation of structures and properties of transition metal compounds , 2009 .
[58] Jin-Ao Duan,et al. Selective matrix metalloproteinase inhibitors for cancer. , 2009, Current medicinal chemistry.
[59] Vishal Prakash Zambre,et al. Development of predictive pharmacophore model for in silico screening, and 3D QSAR CoMFA and CoMSIA studies for lead optimization, for designing of potent tumor necrosis factor alpha converting enzyme inhibitors , 2010, J. Comput. Aided Mol. Des..
[60] M. Martí,et al. Inhibitory effect of quercetin on matrix metalloproteinase 9 activity molecular mechanism and structure-activity relationship of the flavonoid-enzyme interaction. , 2010, European journal of pharmacology.
[61] Dimitris Georgiadis,et al. Third generation of matrix metalloprotease inhibitors: Gain in selectivity by targeting the depth of the S1' cavity. , 2010, Biochimie.
[62] Renxiao Wang,et al. Systematic Derivation of AMBER Force Field Parameters Applicable to Zinc-Containing Systems. , 2010, Journal of chemical theory and computation.
[63] P. Ferdinandy,et al. Matrix metalloproteinase activity assays: Importance of zymography. , 2010, Journal of pharmacological and toxicological methods.
[64] M. Blomberg,et al. Quantum chemical studies of proton-coupled electron transfer in metalloenzymes. , 2010, Chemical reviews.
[65] S. Sakkiah,et al. Ligand and structure based pharmacophore modeling to facilitate novel histone deacetylase 8 inhibitor design. , 2010, European journal of medicinal chemistry.
[66] Kenneth M Merz,et al. Structural Survey of Zinc Containing Proteins and the Development of the Zinc AMBER Force Field (ZAFF). , 2010, Journal of chemical theory and computation.
[67] V. Hakkim,et al. Molecular dynamics studies on native, loop-contracted, and metal ion-substituted azurins. , 2010, The journal of physical chemistry. B.
[68] Yong Wang,et al. P450 enzymes: their structure, reactivity, and selectivity-modeled by QM/MM calculations. , 2010, Chemical reviews.
[69] Arpit Tandon,et al. Structural insights into the binding of MMP9 inhibitors , 2011, Bioinformation.
[70] Haichun Liu,et al. Pharmacophore modeling and virtual screening studies to identify new c-Met inhibitors , 2012, Journal of Molecular Modeling.
[71] Roman A. Laskowski,et al. LigPlot+: Multiple Ligand-Protein Interaction Diagrams for Drug Discovery , 2011, J. Chem. Inf. Model..
[72] Thomas E. Cheatham,et al. Quantum mechanically derived AMBER‐compatible heme parameters for various states of the cytochrome P450 catalytic cycle , 2012, J. Comput. Chem..
[73] Sukesh Kalva,et al. Lead identification and optimization of novel collagenase inhibitors; pharmacophore and structure based studies , 2012, Bioinformation.
[74] Woody Sherman,et al. Generation of Receptor Structural Ensembles for Virtual Screening Using Binding Site Shape Analysis and Clustering , 2012, Chemical biology & drug design.
[75] M. Lindsey,et al. Matrix metalloproteinase (MMP)-9: a proximal biomarker for cardiac remodeling and a distal biomarker for inflammation. , 2013, Pharmacology & therapeutics.
[76] Tomasz Makarewicz,et al. Molecular Dynamics Simulation by GROMACS Using GUI Plugin for PyMOL , 2013, J. Chem. Inf. Model..
[77] B. Vincenzi,et al. Plasma levels of matrix metalloproteinases 2 and 9 correlate with histological grade in breast cancer patients. , 2013, Oncology letters.
[78] S. Chomdej,et al. A modified colorimetric method of gelatinolytic assay using bacterial collagenase type II as a model. , 2013, Analytical biochemistry.
[79] P. E. Van den Steen,et al. Biochemistry and molecular biology of gelatinase B or matrix metalloproteinase-9 (MMP-9): The next decade , 2013, Critical reviews in biochemistry and molecular biology.