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Ragno R, Simeoni S, Rotili D, Caroli A, Botta G, Brosch G, Massa S, Mai A. Class II-selective histone deacetylase inhibitors. Part 2: Alignment-independent GRIND 3-D QSAR, homology and docking studies. Eur J Med Chem 2008; 43:621-32. [PMID: 17698257 DOI: 10.1016/j.ejmech.2007.05.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2007] [Revised: 05/10/2007] [Accepted: 05/14/2007] [Indexed: 10/23/2022]
Abstract
(Aryloxopropenyl)pyrrolyl hydroxamates were recently reported by us as first examples of class II-selective HDAC inhibitors and can be useful tools to probe the biology of such enzymes. Molecular modelling and 3-D QSAR studies have been performed on a series of 25 (aryloxopropenyl)pyrrolyl hydroxamates to gain insights about their activity and selectivity against both maize HD1-B and HD1-A, two enzymes homologous of mammalian class I and class II HDACs, respectively. The studies have been accomplished by calculating alignment-independent descriptors (GRIND descriptors) using the ALMOND software. Highly descriptive and predictive 3-D QSAR models were obtained using either class I or class II inhibitory activity displaying r(2)/q(2) values of 0.96/0.81 and 0.98/0.85 for HD1-B and HD1-A, respectively. A deeper inspection revealed that in general a bent molecular shape structure is a prerequisite for HD1-A-selective inhibitory activity, while straight shape molecular skeleton leads to selective HD1-B compounds. The same conclusions could be achieved by molecular docking studies of the most selective inhibitors.
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Affiliation(s)
- Rino Ragno
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Studi Farmaceutici, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185 Roma, Italy.
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Abe F, Amidei D, Apollinari G, Ascoli G, Atac M, Auchincloss P, Baden AR, Barbaro-Galtieri A, Barnes VE, Bedeschi F, Belforte S, Bellettini G, Bellinger J, Bensinger J, Beretvas A, Berge P, Bertolucci S, Bhadra S, Binkley M, Blair R, Blocker C, Bofill J, Booth AW, Brandenburg G, Brown D, Byon A, Byrum KL, Campbell M, Carey R, Carithers W, Carlsmith D, Carroll JT, Cashmore R, Cervelli F, Chadwick K, Chapin T, Chiarelli G, Chinowsky W, Cihangir S, Cline D, Connor D, Contreras M, Cooper J, Cordelli M, Curatolo M, Day C, DelFabbro R, Dell'Orso M, DeMortier L, Devlin T, DiBitonto D, Diebold R, Dittus F, DiVirgilio A, Elias JE, Ely R, Errede S, Esposito B, Flaugher B, Focardi E, Foster GW, Franklin M, Freeman J, Frisch H. Search for heavy stable particles in 1.8-TeV pp-bar collisions at the Fermilab collider. PHYSICAL REVIEW LETTERS 1989; 63:1447-1450. [PMID: 10040575 DOI: 10.1103/physrevlett.63.1447] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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Abe K, Amako K, Arai Y, Asano Y, Chiba M, Chiba Y, Daigo M, Emura T, Endo I, Fukawa M, Fukui T, Fukushima Y, Haba J, Haidt D, Hayashibara I, Hemmi Y, Higuchi M, Hirose T, Hojyo Y, Homma Y, Hoshi Y, Ikegami Y, Ishihara N, Kamitani T, Kanematsu N, Kanzaki J, Kikuchi R, Kondo T, Koseki T, Kurashige H, Matsui T, Minami M, Miyake K, Mori S, Nagashima Y, Nakamura T, Nakano I, Narita Y, Odaka S, Ogawa K, Ohama T, Ohsugi T, Okamoto A, Ono A, Osabe H, Oyama T, Saito H, Sakae H, Sakamoto H, Sakamoto S, Sakano M, Sakuda M, Sasao N, Sato M, Shioden M, Shirai J, Sugimoto S, Sumiyoshi T, Suzuki Y, Takada Y, Takasaki F, Taketani A, Tamura N, Tanaka R. Search for a fourth-generation quark with ||Q||=e/3 in e+e- collisions at sqrt s =56-57 GeV. PHYSICAL REVIEW. D, PARTICLES AND FIELDS 1989; 39:3524-3527. [PMID: 9959607 DOI: 10.1103/physrevd.39.3524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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