List of publications and patents
Scientific publications by MMDD B.V. staff
- de Jonge MR,
Vinkers HM, van Lenthe JH, Daeyaert F, Bush IJ, van Dam HJJ, Sherwood P,
Guest MF
Ab Initio potential grid based docking: From High Performance Computing to In Silico Screening.
AIP Conf. Proc. COMPLIFE 2007. 2007 Sep 18;940:168-178.
[DOI:10.1063/1.2793399] - de Jonge MR, Koymans LH, Guillemont JE, Koul A, Andries K.
A computational model of the inhibition of Mycobacterium tuberculosis ATPase by a new drug candidate R207910.
Proteins. 2007 Mar 23.
[PMID: 17387738] - Daeyaert F, De Jonge MR, Koymans LMH, Vinkers HM
An ant algorithm for the conformational analysis of flexible molecules.
Journal of Computational Chemistry. 2007 Jan 19;28(5):890-8.
[PMID: 17238172] - de Jonge MR, Koymans LM, Vinkers HM, Daeyaert FF, Heeres J, Lewi PJ, Janssen PA.
Structure based activity prediction of HIV-1 reverse transcriptase inhibitors.
Journal of medicinal chemistry. 2005 Mar 24;48(6):2176-83.
PMID: 15771460 [PubMed - indexed for MEDLINE] - Boutton CW, De Bondt HL, De Jonge MR.
Genotype dependent QSAR for HIV-1 protease inhibition.
Journal of medicinal chemistry. 2005 Mar 24;48(6):2115-20.
PMID: 15771454 [PubMed - indexed for MEDLINE] - Guillemont J, Pasquier E, Palandjian P, Vernier D, Gaurrand S, Lewi PJ, Heeres J, de Jonge MR, Koymans LM, Daeyaert FF, Vinkers MH, Arnold E, Das K, Pauwels R, Andries K, de Bethune MP, Bettens E, Hertogs K, Wigerinck P, Timmerman P, Janssen PA.
Synthesis of novel diarylpyrimidine analogues and their antiviral activity against human immunodeficiency virus type 1.
Journal of medicinal chemistry. 2005 Mar 24;48(6):2072-9.
PMID: 15771449 [PubMed - indexed for MEDLINE] - Heeres J, de Jonge MR, Koymans LM, Daeyaert FF, Vinkers M, Van Aken KJ, Arnold E, Das K, Kilonda A, Hoornaert GJ, Compernolle F, Cegla M, Azzam RA, Andries K, de Bethune MP, Azijn H, Pauwels R, Lewi PJ, Janssen PA.
Design, synthesis, and SAR of a novel pyrazinone series with non-nucleoside HIV-1 reverse transcriptase inhibitory activity.
Journal of medicinal chemistry. 2005 Mar 24;48(6):1910-8.
PMID: 15771435 [PubMed - indexed for MEDLINE] - Janssen PA, Lewi PJ, Arnold E, Daeyaert F, de Jonge M, Heeres J, Koymans L, Vinkers M, Guillemont J, Pasquier E, Kukla M, Ludovici D, Andries K, de Bethune MP, Pauwels R, Das K, Clark AD Jr, Frenkel YV, Hughes SH, Medaer B, De Knaep F, Bohets H, De Clerck F, Lampo A, Williams P, Stoffels P.
In search of a novel anti-HIV drug: multidisciplinary coordination in the discovery of 4-[[4-[[4-[(1E)-2-cyanoethenyl]-2,6-dimethylphenyl]amino]-2- pyrimidinyl]amino]benzonitrile (R278474, rilpivirine).
Journal of medicinal chemistry 2005 Mar 24;48(6):1901-9. Review.
PMID: 15771434 [PubMed - indexed for MEDLINE] - Lewi P, Arnold E, Andries K, Bohets H, Borghys H, Clark A, Daeyaert F, Das K, de Bethune MP, de Jonge M, Heeres J, Koymans L, Leempoels J, Peeters J, Timmerman P, Van den Broeck W, Vanhoutte F, Van't Klooster G, Vinkers M, Volovik Y, Janssen PA.
Correlations between factors determining the pharmacokinetics and antiviral activity of HIV-1 non-nucleoside reverse transcriptase inhibitors of the diaryltriazine and diarylpyrimidine classes of compounds.
Drugs in R&D. 2004;5(5):245-57.
PMID: 15357624 [PubMed - in process] - Das K, Clark AD Jr, Lewi PJ, Heeres J, De Jonge MR, Koymans LM, Vinkers HM, Daeyaert F, Ludovici DW, Kukla MJ, De Corte B, Kavash RW, Ho CY, Ye H, Lichtenstein MA, Andries K, Pauwels R, De Bethune MP, Boyer PL, Clark P, Hughes SH, Janssen PA, Arnold E.
Roles of conformational and positional adaptability in structure-based design of TMC125-R165335 (etravirine) and related non-nucleoside reverse transcriptase inhibitors that are highly potent and effective against wild-type and drug-resistant HIV-1 variants.
Journal of medicinal chemistry. 2004 May 6;47(10):2550-60.
PMID: 15115397 [PubMed - indexed for MEDLINE] - Daszykowski M, Walczak B, Xu QS, Daeyaert F, de Jonge MR, Heeres J, Koymans LM, Lewi PJ, Vinkers HM, Janssen PA, Massart DL.
Classification and regression trees--studies of HIV reverse transcriptase inhibitors.
Journal of chemical information and computer sciences. 2004 Mar-Apr;44(2):716-26.
PMID: 15032554 [PubMed - indexed for MEDLINE] - Daeyaert FFD, de Jonge MR, Heeres J, Koymans LMH, Lewi PJ, van den Broeck W, Vinkers HM.
Pareto optimal flexible alignment of molecules using a non-dominated sorting genetic algorithm.
Chemometrics and Intelligent Laboratory Systems. 2005 77:232-37. - Daeyaert F, de Jonge M, Heeres J, Koymans L, Lewi P, Vinkers MH, Janssen PA.
A pharmacophore docking algorithm and its application to the cross-docking of 18 HIV-NNRTI's in their binding pockets.
Proteins. 2004 Feb 15;54(3):526-33.
PMID: 14748000 [PubMed - indexed for MEDLINE] - Daeyaert FFD, Vinkers HM, de Jonge MR, Heeres J, Koymans LMH, Lewi PJ, Janssen PAJ.
Ligand-based Computation of HIV-1 Integrase Inhibition Strength within a Series of beta-ketoamide Derivatives.
Internet Electronic Journal of Molecular Design. 2004 3:528-43. - Xu QS, Daszykowski M, Walczak B, Daeyaert FFD, de Jonge MR, Heeres J, Koymans LMH, Lewi PJ, Vinkers HM, Janssen PAJ, Massart DL.
Multivariate adaptive regression splines - studies of HIV reverse transcriptase inhibitors.
Chemometrics and Intelligent Laboratory Systems. 2004 72:27-34. - Vinkers HM, de Jonge MR, Daeyaert ED, Heeres J, Koymans LM, van Lenthe JH, Lewi PJ, Timmerman H, Janssen PA.
Inhibition and substrate recognition--a computational approach applied to HIV protease.
Journal of computer-aided molecular design. 2003 Sep;17(9):567-81.
PMID: 14713189 [PubMed - indexed for MEDLINE] - Lewi PJ, de Jonge M, Daeyaert F, Koymans L, Vinkers M, Heeres J, Janssen PA, Arnold E, Das K, Clark AD Jr, Hughes SH, Boyer PL, de Bethune MP, Pauwels R, Andries K, Kukla M, Ludovici D, De Corte B, Kavash R, Ho C.
On the detection of multiple-binding modes of ligands to proteins, from biological, structural, and modeling data.
Journal of computer-aided molecular design. 2003 Feb-Apr;17(2-4):129-34. Erratum in: J Comput Aided Mol Des. 2003 May-Jun;17(5-6):398. Lewis PJ [corrected to Lewi PJ].
PMID: 13677481 [PubMed - indexed for MEDLINE] - Vinkers HM, de Jonge MR, Daeyaert FF, Heeres J, Koymans LM, van Lenthe JH, Lewi PJ, Timmerman H, Van Aken K, Janssen PA.
SYNOPSIS: SYNthesize and OPtimize System in Silico.
Journal of medicinal chemistry. 2003 Jun 19;46(13):2765-73.
PMID: 12801239 [PubMed - indexed for MEDLINE] - Ludovici DW, De Corte BL, Kukla MJ, Ye H, Ho CY, Lichtenstein MA, Kavash RW, Andries K, de Bethune MP, Azijn H, Pauwels R, Lewi PJ, Heeres J, Koymans LM, de Jonge MR, Van Aken KJ, Daeyaert FF, Das K, Arnold E, Janssen PA.
Evolution of anti-HIV drug candidates. Part 3: Diarylpyrimidine (DAPY) analogues.
Bioorganic & medicinal chemistry letters. 2001 Sep 3;11(17):2235-9.
PMID: 11527705 [PubMed - indexed for MEDLINE] - Ludovici DW, Kavash RW, Kukla MJ, Ho CY, Ye H, De Corte BL, Andries K, de Bethune MP, Azijn H, Pauwels R, Moereels HE, Heeres J, Koymans LM, de Jonge MR, Van Aken KJ, Daeyaert FF, Lewi PJ, Das K, Arnold E, Janssen PA.
Evolution of anti-HIV drug candidates. Part 2: Diaryltriazine (DATA) analogues.
Bioorganic & medicinal chemistry letters. 2001 Sep 3;11(17):2229-34.
PMID: 11527704 [PubMed - indexed for MEDLINE]
- WO2006035051
A bacterial ATP synthase binding domain - WO2006015985
HIV Inhibiting 1,2,4-triazinone derivatives - WO2005028479
HIV replication inhibiting purine derivatives - WO2004074266
HIV inhibiting 1,2,4-triazines - WO2004074261
HIV replication inhibiting pyrimidines and triazines - WO2004074262
HIV replication inhibiting pyrimidines and triazines - WO2004069812
Pyrimidine derivatives for the prevention of HIV infection - WO03037891
Heteroaryl amines as glycogen synthase kinase 3-beta inhibitors (GSK3 inhibitors) - WO03037877
Aminobenzamide derivatives as glycogen synthase kinase 3-beta inhibitors - WO03037869
Amide derivatives as glycogen synthase kinase 3-beta inhibitors - WO03016306
HIV inhibiting pyrimidines derivatives - WO02078708
HIV inhibiting pyrazinone derivatives - WO0185700
HIV Replication Inhibitors - WO0185699
Prodrugs of HIV Replication Inhibiting Pyrimidines - WO0027828
2,4-disubstituted Triazine Derivatives - WO0027825
HIV Replication Inhibiting Pyrimidines - WO9950256
Trisubstituted 1,3,5-Triazine Derivatives For Treatment Of HIV Infections - WO9950250
HIV Inhibiting Pyrimidine Derivatives