Biophysical Probes Reveal a “Compromise” Nature of the Methyl-lysine Binding Pocket in L3MBTL1

Histone lysine methylation (Kme) encodes essential information modulating many biological processes including gene expression and transcriptional regulation. However, the atomic-level recognition mechanisms of methylated histones by their respective adaptor proteins are still elusive. For instance, it is unclear how L3MBTL1, a methyl-lysine histone code reader, recognizes equally well both mono- and di-methyl marks, but ignores unmodified and trimethylated lysine residues. We made use of Molecular Dynamics (MD) and Free Energy Perturbation (FEP) techniques in order to investigate the energetics and dynamics of the methyllysine recognition. Isothermal Titration Calorimetry (ITC) was employed to experimentally validate the computational findings. Both computational and experimental methods were applied to a set of designed “biophysical” probes that mimic the shape of a single lysine residue and reproduce the binding affinities of cognate histone peptides. Our results suggest that, besides forming favorable interactions, the L3MBTL1 binding pocket energetically penalizes both methylation states and has most probably evolved as a “compromise” that non-optimally fit to both mono- and di-methyl-lysine marks

Identification of Non-Peptide Malignant Brain Tumor (MBT) Repeat Antagonists by Virtual Screening of Commercially Available Compounds

The Malignant Brain Tumor (MBT) repeat is an important epigenetic-code “reader” and is functionally associated with differentiation, gene silencing and tumor suppression1–3. Small molecule probes of MBT domains should enable a systematic study of MBT-containing proteins, and potentially reveal novel druggable targets. We designed and applied a virtual screening strategy, which identified potential MBT antagonists in a large database of commercially available compounds. A small set of virtual hits was purchased and submitted to experimental testing. Nineteen of the purchased compounds showed a specific dose-dependent protein binding and will provide critical structure-activity information for subsequent lead generation and optimization

Small-Molecule Ligands of Methyl-Lysine Binding Proteins: Optimization of Selectivity for L3MBTL3

Lysine methylation is a key epigenetic mark, the dysregulation of which is linked to many diseases. Small molecule antagonism of methyl-lysine (Kme) binding proteins that recognize such epigenetic marks can improve our understanding of these regulatory mechanisms and potentially validate Kme binding proteins as drug discovery targets. We previously reported the discovery of 1 (UNC1215), the first potent and selective small molecule chemical probe of a methyl-lysine reader protein, L3MBTL3, which antagonizes the mono- and dimethyl-lysine reading function of L3MBTL3. The design, synthesis, and structure activity relationship studies that led to the discovery of 1 are described herein. These efforts established the requirements for potent L3MBTL3 binding and enabled the design of novel antagonists, such as compound 2 (UNC1679), that maintain in vitro and cellular potency with improved selectivity against other MBT-containing proteins. The antagonists described were also found to effectively interact with unlabeled endogenous L3MBTL3 in cells

Radio Astronomy

Contains table of contents for Section 4 and reports on eight research projects.National Science Foundation Grant AST 88-19848National Aeronautics and Space Administration Goddard Space Flight Center Grant NAGW-2310SM Systems and Research, IncNational Aeronautics and Space Administration Goddard Space Flight Center Grant NAG 5-537National Aeronautics and Space Administration Goddard Space Flight Center Grant NAG 5-10Leaders for Manufacturing ProgramNational Aeronautics and Space Administration Goddard Space Flight Center Grant NAS 5-3079

Radio Astronomy

Contains table of contents for Section 4 and reports on ten research projects.National Science Foundation Grant AST 90-22501Alfred P. Sloan FellowshipDavid and Lucile Packard Fellowship Award for Science and EngineeringNational Aeronautics and Space AdministrationNational Science Foundation Presidential Young Investigator AwardNational Aeronautics and Space Administration Grant NAGW-2310MIT Lincoln Laboratory Agreement BX-4975National Aeronautics and Space Administration/Goddard Space Flight Center Contract NAS 5-31276MIT Leaders for Manufacturing Progra

Radio Astronomy

Contains table of contents for Section 4 and reports on nine research projects.National Science Foundation Grant AST 88-19848National Science Foundation Grant AST 90-22501Alfred P. Sloan FellowshipNational Science Foundation Presidential Young Investigator AwardNational Aeronautics and Space Administration Grant NAGW-2310David and Lucile Packard FellowshipSM Systems and Research CorporationNational Aeronautics and Space Administration/Goddard Space Flight Center Contract NAS 5-30791National Aeronautics and Space Administration/Goddard Space Flight Center Grant NAG5-10Leaders for Manufacturing Progra

Radio Astronomy

Contains table of contents for Section 4 and reports on ten research projects.National Science Foundation Grant AST 90-22501National Aeronautics and Space Administration Grant NAGW 1386National Science Foundation Presidential Young Investigator AwardDavid and Lucile Packard Fellowship for Science and EngineeringNational Aeronautics and Space Administration Grant NAGW-2310MIT Lincoln LaboratorySM Systems and Research CorporationNational Aeronautics and Space Administration/Goddard Space Flight Center Contract NAS 5-30791National Aeronautics and Space Administration/Goddard Space Flight Center Grant NAG 5-10MIT Leaders for Manufacturing Progra

Radio Astronomy

Contains table of contents for Section 4 and reports on seven research projects.National Science Foundation Grant AST 92-24191MIT Class of 1948/Career Development ChairNational Science Foundation Presidential Young Investigator AwardDavid and Lucile Packard FellowshipMIT Lincoln Laboratory Agreement BX-4975National Aeronautics and Space Administration/Goddard Space Flight Center Grant NAS5-31276National Aeronautics and Space Administration/Goddard Space Flight Center Grant NAG5-10MIT Leaders for Manufacturing Progra