Structure-based design of nitrogen-linked macrocyclic kinase inhibitors leading to the clinical candidate SB1317/TG02, a potent inhibitor of cyclin dependant kinases (CDKs), Janus kinase 2 (JAK2), and Fms-like tyrosine kinase-3 (FLT3).

Abstract:

:A high-throughput screen against Aurora A kinase revealed several promising submicromolar pyrimidine-aniline leads. The bioactive conformation found by docking these leads into the Aurora A ATP-binding site had a semicircular shape. Macrocycle formation was proposed to achieve novelty and selectivity via ring-closing metathesis of a diene precursor. The nature of the optimal linker and its size was directed by docking. In a kinase panel screen, selected macrocycles were active on other kinase targets, mainly FLT3, JAK2, and CDKs. These compounds then became leads in a CDK/FLT3/JAK2 inhibitor project. Macrocycles with a basic nitrogen in the linker form a salt bridge with Asp86 in CDK2 and Asp698 in FLT3. Interaction with this residue explains the observed selectivity. The Asp86 residue is conserved in most CDKs, resulting in potent pan-CDK inhibition by these compounds. Optimized macrocycles generally have good DMPK properties, and are efficacious in mouse models of cancer. Compound 5 (SB1317/TG02), a pan-CDK/FLT3/JAK2 inhibitor, was selected for preclinical development, and is now in phase 1 clinical trials.

journal_name

J Mol Model

authors

Poulsen A,William A,Blanchard S,Nagaraj H,Williams M,Wang H,Lee A,Sun E,Teo EL,Tan E,Goh KC,Dymock B

doi

10.1007/s00894-012-1528-7

subject

Has Abstract

pub_date

2013-01-01 00:00:00

pages

119-30

issue

1

eissn

1610-2940

issn

0948-5023

journal_volume

19

pub_type

杂志文章
  • Pressure effects on electronic, elastic, and vibration properties of metallic antiperovskite PbNCa3 by ab initio calculations.

    abstract::Ab initio computations are performed to study the structural, elastic, electronic, and vibrational characteristics of the cubic antiperovskite compound PbNCa3 under pressure up to 50 GPa. By using the generalized gradient approximation (GGA), the equilibrium structural parameters, energy band structure, density of sta...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-020-04656-2

    authors: Ciftci YO,Evecen M,Alp İO

    更新日期:2021-01-03 00:00:00

  • Importance of oligomerisation on Pseudomonas aeruginosaLectin-II binding affinity. In silico and in vitro mutagenesis.

    abstract::The effect of terminal GLY114* deletion on the binding affinity of the PA-IIL lectin toward L: -fucose was investigated. Both experimental (isothermal titration calorimetry) and computational (molecular dynamics simulations) methods have shown that the deletion mutation decreases the L-fucose affinity. It implies that...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-009-0464-7

    authors: Wimmerová M,Mishra NK,Pokorná M,Koca J

    更新日期:2009-06-01 00:00:00

  • Involvement of electron and hydrogen transfers through redox metabolism on activity and toxicity of the nimesulide.

    abstract::An electronic study of nimesulide was performed by using density functional theory calculations. The activities of the six different derivatives were related with electron donating or accepting capacities. All compounds which had nitro moiety had low electron donating and high electron accepting capacities. However, t...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-015-2712-3

    authors: Borges RS,Oliveira JP,Matos RF,Chaves Neto AM,Carneiro AS,Monteiro MC

    更新日期:2015-07-01 00:00:00

  • Rational design of organoboron derivatives as chemosensors for fluoride and cyanide anions and charge transport and luminescent materials for organic light-emitting diodes.

    abstract::The interactions between chemosensors, donor-π-acceptor (D-π-A) dipolar organoboron derivatives, and different (CN⁻, F⁻, Cl⁻, and Br⁻) anions have been theoretically investigated using DFT approaches. Theoretical investigations have been performed to explore the optical, electronic, charge transport, and stability pro...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-014-2169-9

    authors: Jin R,Tang S,Luo D

    更新日期:2014-03-01 00:00:00

  • Structural and electronic properties of 4H-cyclopenta[2,1-b,3;4-b']dithiophene S-oxide (BTO) derivatives with an S, S=O, O, SiH2, or BH2 bridge: semi-empirical and DFT study.

    abstract::In this paper, we theoretically studied the geometries, stabilities, and the electronic and thermodynamic properties of 4H-cyclopenta[2,1-b,3;4-b']dithiopene S-oxide derivatives (BTO-X, with X = BH(2), SiH(2), S, S=O, or O) using semi-empirical methods, ab initio methods, and density functional theory. The geometries ...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-011-1291-1

    authors: Banjo S,Ayobami OO,Ajibade AI

    更新日期:2012-06-01 00:00:00

  • Structures and stability of N13+ and N13- clusters.

    abstract::The structures and stabilities of eleven N13+ and N13- isomers have been investigated with second-order Moller-Plesset (MP2) and density functional theory (DFT) methods. Five N13+ isomers and six N13- isomers are all reasonable local minima on their potential energy hypersurfaces. The most stable N13+ cation is struct...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-003-0160-y

    authors: Yin PG,Li QS

    更新日期:2004-02-01 00:00:00

  • Ligand binding to anti-cancer target CD44 investigated by molecular simulations.

    abstract::CD44 is a cell-surface glycoprotein and receptor for hyaluronan, one of the major components of the tumor extracellular matrix. There is evidence that the interaction between CD44 and hyaluronan promotes breast cancer metastasis. Recently, the molecule F-19848A was shown to inhibit hyaluronan binding to receptor CD44 ...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-016-3029-6

    authors: Nguyen TT,Tran DP,Pham Dinh Quoc Huy,Hoang Z,Carloni P,Van Pham P,Nguyen C,Li MS

    更新日期:2016-07-01 00:00:00

  • Photoluminescence spectrum using DFT for double-walled carbon nanotubes with metallic constituents.

    abstract::A theoretical study of the photoluminescence (PL) of double-walled carbon nanotubes (DWCNTs) using density functional theory (DFT) theory is reported in this work. The DWCNTs are of the armchair/armchair type and the structures studied have the arrangements (3,3)/(2,2), (8,8)/(4,4), (12,12)/(6,6), (16,16)/(8,8), (6,6)...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-019-4148-7

    authors: Victoria APR,de la Luz ADH,Juárez JM,Espinosa-Torres ND,Robles-Águila MJ,López JAL,Juárez-Díaz G

    更新日期:2019-08-26 00:00:00

  • Computational models for the shuttling motion of the macrocycle in rotaxane-based molecular switches.

    abstract::The shuttling motion of a macrocycle in rotaxane-based molecular switching devices has been studied by computational density functional methods. In the test case, energy profiles corresponding to the dethreading process of different types of guest molecules in a cyclobis(paraquat-p-phenylene) host verified the experim...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-008-0331-y

    authors: Hirva P,Haukka M,Pakkanen TA

    更新日期:2008-10-01 00:00:00

  • Stereodynamic study of the reaction H(²S) + ClO(²Π) → HO(²Π) + Cl(²P) via quasi-classical trajectory calculations.

    abstract::Quasi-classical trajectory calculations were performed to investigate the stereodynamics of the reaction H(²S) + ClO(²Π) → HO(²Π) + Cl(²P) using the ground-state potential energy surface 1¹A'. The alignment and orientation of the product molecules as well as the four polarization-dependent differential cross-sections ...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-014-2151-6

    authors: Huang Y

    更新日期:2014-03-01 00:00:00

  • WaterScore: a novel method for distinguishing between bound and displaceable water molecules in the crystal structure of the binding site of protein-ligand complexes.

    abstract::We have performed a multivariate logistic regression analysis to establish a statistical correlation between the structural properties of water molecules in the binding site of a free protein crystal structure, with the probability of observing the water molecules in the same location in the crystal structure of the l...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-003-0129-x

    authors: García-Sosa AT,Mancera RL,Dean PM

    更新日期:2003-06-01 00:00:00

  • Theoretical investigations on the mechanistic pathway of the thermal rearrangement of substituted N-acyl-2,2-dimethylaziridines.

    abstract::The mechanism of the thermal rearrangement of substituted N-acyl-2,2-dimethylaziridines 1 has been studied using quantum chemistry methods. Geometries of reactants, transition states and products have been optimized at the B3LYP/6-311++G(2d,2p) level. Relative energies for various stationary points have been determine...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-013-1959-9

    authors: Arfaoui Y,Efrit ML,Besbes N

    更新日期:2013-10-01 00:00:00

  • Rotational model for nematic phase stability of fluorinated phenylbicyclohexane liquid crystals.

    abstract::A mechanical molecular rotation model for liquid crystal (LC) systems is employed to evaluate phase transition temperature of fluorinated phenylbicyclohexane isomeric LC compounds. Results show that when a fluorine atom is substituted along the molecular long axis, an LC molecule acquires high rotational speed and its...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-008-0341-9

    authors: Ma H,Li ZX,Shi DH,Liu YF

    更新日期:2008-11-01 00:00:00

  • Synthesis, spectroscopy, and theoretical calculations of some 2-thiohydantoin derivatives as possible new fungicides.

    abstract::We present the synthesis and structure determination for two thiohydantoin compounds (5-benzylidene-2-sulfanylideneimidazolidin-4-one and 5-cinnamylidene-2-sulfanylideneimidazolidin-4-one), proposed as potential novel fungicides. The exact chemical structure of these molecules has not yet been determined since they ca...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-019-4146-9

    authors: Kobyłka K,Żuchowski G,Tejchman W,Zborowski KK

    更新日期:2019-08-24 00:00:00

  • Fast learning optimized prediction methodology (FLOPRED) for protein secondary structure prediction.

    abstract::Computational methods are rapidly gaining importance in the field of structural biology, mostly due to the explosive progress in genome sequencing projects and the large disparity between the number of sequences and the number of structures. There has been an exponential growth in the number of available protein seque...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-012-1410-7

    authors: Saraswathi S,Fernández-Martínez JL,Kolinski A,Jernigan RL,Kloczkowski A

    更新日期:2012-09-01 00:00:00

  • Ab initio molecular dynamics of free radical-induced oxidation of ergothioneine.

    abstract::Ergothioneine (2-mercaptohistidine trimethylbetaine) is a very stable natural compound largely present in cells and tissues of plants and mammals. The biological role of ET is still incompletely understood but its antioxidant properties are well assessed experimentally. However, no theoretical study had been performed...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-019-4220-3

    authors: Lespade L

    更新日期:2019-10-26 00:00:00

  • A comparison of computational methodologies for the structural modelling of biologically relevant zinc complexes.

    abstract::The impact of a variety of modern computational methods on the structure of biologically relevant zinc complexes is studied. Different density functionals and a Hartree-Fock-based method, scalar-relativistic effects, and basis set integration grid choices, among others, are assessed for set of high-resolution crystall...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-019-4139-8

    authors: Savasci G,Borges-Martínez M,Berger RJF,Ochsenfeld C,Mera-Adasme R

    更新日期:2019-08-09 00:00:00

  • DFT modeling, UV-Vis and IR spectroscopic study of acetylacetone-modified zirconia sol-gel materials.

    abstract::Theoretical and spectroscopic studies of a series of monomeric and dimeric complexes formed through the modification of a zirconium butoxide precursor with acetylacetone and subsequent hydrolysis and/or condensation have been performed by applying DFT/B3LYP/6-31++G(d) and highly accurate RI-ADC(2) methods as well as I...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-011-1257-3

    authors: Georgieva I,Danchova N,Gutzov S,Trendafilova N

    更新日期:2012-06-01 00:00:00

  • Effects of local protein environment on the binding of diatomic molecules to heme in myoglobins. DFT and dispersion-corrected DFT studies.

    abstract::The heme-AB binding energies (AB = CO, O2) in a wild-type myoglobin (Mb) and two mutants (H64L, V68N) of Mb have been investigated in detail with both DFT and dispersion-corrected DFT methods, where H64L and V68N represent two different, opposite situations. Several dispersion correction approaches were tested in the ...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-013-1864-2

    authors: Liao MS,Huang MJ,Watts JD

    更新日期:2013-08-01 00:00:00

  • Spectroscopic and nonlinear optical properties of new chalcone fluorescent probes for bioimaging applications: a theoretical and experimental study.

    abstract::In this study, the newly synthesized non-centrosymmetric, 4-dimethylamino-3'-isothiocyanatochalcone (PKA) compound was presented. This compound belongs to the chalcone group, and its main purpose is to be used in biomedical imaging as a fluorescence dye. For this reason, the linear and nonlinear properties in solvents...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-016-2990-4

    authors: Krawczyk P,Pietrzak M,Janek T,Jędrzejewska B,Cysewski P

    更新日期:2016-06-01 00:00:00

  • Stereochemistry and spectroscopic analysis of bis-Betti base derivatives of 2,3-dihydroxynaphthalene.

    abstract::Density functional theory (DFT) was used to study the stereochemistry, thermodynamic stability, and spectra of recently synthesized bis-Betti base derivatives of 2,3-dihydroxynaphthalene obtained through multicomponent reactions of 2,3-dihydroxynaphthalene with aminoisoxazole and benzaldehyde derivatives. The stereoch...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-016-2936-x

    authors: Zamani M,Shafiee M,Keshavarz MH

    更新日期:2016-04-01 00:00:00

  • De novo design of anticancer peptides by ensemble artificial neural networks.

    abstract::Membranolytic anticancer peptides (ACPs) are drawing increasing attention as potential future therapeutics against cancer, due to their ability to hinder the development of cellular resistance and their potential to overcome common hurdles of chemotherapy, e.g., side effects and cytotoxicity. In this work, we present ...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-019-4007-6

    authors: Grisoni F,Neuhaus CS,Hishinuma M,Gabernet G,Hiss JA,Kotera M,Schneider G

    更新日期:2019-04-05 00:00:00

  • Distinct interactions between the human adrenergic beta(2) receptor and Galpha(s)--an in silico study.

    abstract::The aim of this study was to perform an in silico analysis of the interaction of the human beta(2) adrenergic receptor with Galpha(s). In a first step, a systematic surface-interaction-scan between the inactive or active human beta(2) adrenergic receptor and Galpha(s) was performed in order to gain knowledge about ene...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-010-0646-3

    authors: Strasser A,Wittmann HJ

    更新日期:2010-08-01 00:00:00

  • Binding free energy calculations of N-sulphonyl-glutamic acid inhibitors of MurD ligase.

    abstract::The increasing incidence of bacterial resistance to most available antibiotics has underlined the urgent need for the discovery of novel efficacious antibacterial agents. The biosynthesis of bacterial peptidoglycan, where the MurD enzyme is involved in the intracellular phase of UDP-MurNAc-pentapeptide formation, repr...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-009-0455-8

    authors: Perdih A,Bren U,Solmajer T

    更新日期:2009-08-01 00:00:00

  • In silico identification of inhibitors against Plasmodium falciparum histone deacetylase 1 (PfHDAC-1).

    abstract::In erythrocytes, actively multiplying Plasmodium falciparum parasites exhibit a unique signature of virulence associated histone modifications, thereby epigenetically regulating the expression of the majority of genes. Histone acetylation is one such modification, effectuated and maintained by the dynamic interplay of...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-018-3761-1

    authors: Kumar A,Dhar SK,Subbarao N

    更新日期:2018-08-14 00:00:00

  • DFT-based molecular modeling and vibrational study of the La(III) complex of 3,3'-(benzylidene)bis(4-hydroxycoumarin).

    abstract::Molecular modeling of the La(III) complex of 3,3'-(benzylidene)bis(4-hydroxycoumarin) (PhDC) was performed using density functional theory (DFT) methods at B3LYP/6-31G(d) and BP86/TZP levels. Both Stuttgart-Dresden effective core potential and ZORA approximation were applied to the La(III) center. The electron density...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-008-0277-0

    authors: Mihaylov T,Trendafilova N,Georgieva I

    更新日期:2008-05-01 00:00:00

  • DFT, QTAIM, and NBO investigations of the ability of the Fe or Ni doped CNT to absorb and sense CO and NO.

    abstract::The structures and intramolecular interactions of complexes (FeCNT-CO, FeCNT-NO, NiCNT-CO, and NiCNT-NO) formed by the Fe or Ni doped single-wall carbon nanotube (FeCNT or NiCNT) and gas CO or NO were studied using density functional theory, quantum theory of atom in molecule (QTAIM), and natural bond orbital methods....

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-015-2778-y

    authors: Zhang X,Gong X

    更新日期:2015-09-01 00:00:00

  • Hydrogen sequential dissociative chemisorption on Ni n(n = 2~9,13) clusters: comparison with Pt and Pd.

    abstract::Hydrogen dissociative chemisorption and desorption on small lowest energy Ni(n) clusters up to n=13 as a function of H coverage was studied using density functional theory. H adsorption on the clusters was found to be preferentially at edge sites followed by 3-fold hollow sites and on-top sites. The minimum energy pat...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-011-1059-7

    authors: Zhou C,Yao S,Zhang Q,Wu J,Yang M,Forrey RC,Cheng H

    更新日期:2011-09-01 00:00:00

  • Detection of symmetrical decomposition of molecules--isotopomeric analysis of the M/2 clusters.

    abstract::The interpretation of mass spectra (ms) of molecules containing poly-isotopic elements (e.g. Ge, Se, W, Os, Sn, Te, Zn, Yb) can be difficult due to the occurrence of fragments resulting from isotopomeric composition. MS-clusters located in the range lower than or equal to M/2 are very difficult to interpret. In this a...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-009-0486-1

    authors: Goraczko AJ,Szewczykowska K

    更新日期:2009-06-01 00:00:00

  • Erratum to: First hyperpolarizability of cyclooctatetraene modulated by alkali and alkaline earth metals.

    abstract::The original version of this article unfortunately contained a mistake. Schemes I and II were missing. These important components are given below. ...

    journal_title:Journal of molecular modeling

    pub_type: 已发布勘误

    doi:10.1007/s00894-017-3466-x

    authors: Roy RS,Mondal A,Nandi PK

    更新日期:2017-11-01 00:00:00