Abstract: The invention describes an explicit solvent all-atom molecular dynamics methodology (SILCS: Site Identification by Ligand Competitive Saturation) that uses no small aliphatic and aromatic molecules plus water molecules to map the affinity pattern of a large molecule for hydrophobic groups, aromatic groups, hydrogen bond donors, and hydrogen bond acceptors. By simultaneously incorporating ligands representative of all these functionalities, the method is an in silico free energy-based competition assay that generates three-dimensional probability maps of fragment binding (FragMaps) indicating favorable fragment:large molecule interactions. The FragMaps may be used to qualitatively inform the design of small-molecule ligands or as scoring grids for high-throughput in silico docking that incorporates both an atomic-level description of solvation and the large molecule's flexibility.

Abstract: Compounds, and methods of using the same, are provided as therapies for the treatment leucine-rich repeat kinase-2 (LRRK2)-related disorders including, but not limited to, neurodegenerative and neuroinflammatory disorders, such as Parkinson's Disease.

Abstract: A compound, having the formula A-1: Wherein R1 and R2 are defined herein. Methods of using the compound and compositions containing the compound are provided.

Abstract: A compound, having the formula A-1: Wherein R1 and R2 are defined herein. Methods of using the compound and compositions containing the compound are provided.

Abstract: A method of treating SHP-2 phosphatase associated diseases in a subject includes administering a SHP-2 inhibitor to the subject.

Abstract: Disclosed are compositions and methods for treating and/or preventing infections in mammals, by administering to a mammal a therapeutically effective amount of at least one defensin-like molecule, e.g., in a composition that includes such molecule. Also disclosed are kits that include such molecules, or compositions that include such molecules, as well as instructions for using such molecules to treat a mammal.

Abstract: Disclosed are methods of treating and/or preventing infections in mammals caused by microorganisms, by administering to a mammal a therapeutically effective amount of at least one defensin-like molecule, e.g., in a composition that includes such molecule. Also disclosed are the use of such defensin-like molecules for treating and/or preventing infections in mammals; and kits that may include such molecules, or compositions that include such molecules, as well as instructions for using such molecules to treat a mammal.

Abstract: Provided are methods of inhibiting BCL6 repression in a mammalian cell. Also provided are methods of treating cancer in a mammal.

Abstract: The invention describes an explicit solvent all-atom molecular dynamics methodology (SILCS: Site Identification by Ligand Competitive Saturation) that uses small aliphatic and aromatic molecules plus water molecules to map the affinity pattern of a large molecule for hydrophobic groups, aromatic groups, hydrogen bond donors, and hydrogen bond acceptors. By simultaneously incorporating ligands representative of all these functionalities, the method is an in silico free energy-based competition assay that generates three-dimensional probability maps of fragment binding (FragMaps) indicating favorable fragment:large molecule interactions. The FragMaps may be used to qualitatively inform the design of small-molecule ligands or as scoring grids for high-throughput in silico docking that incorporates both an atomic-level description of solvation and the large molecule's flexibility.

Abstract: A method of treating SHP-2 phosphatase associated diseases in a subject includes administering a SHP-2 inhibitor to the subject.

Abstract: This invention describes a series of methods and compositions for prevention and treatment of diseases such as cancer. One aspect of the invention describes small molecule-based drugs that can be used to bind to death receptors TRAIL-R1/DR4 and/or TRAIL-R2/DR5 and induce apoptosis in cancer cells, while sparing normal cells. The invention also describes TRAIL Death Receptor Agonists/Activators (DRAs) and their uses, such as the induction of apoptosis through caspase-8 and caspase-3 activation. The present invention also describes the methods of treating cancers, such as breast, prostate, colon, pancreatic, ovarian, lung, and brain cancers, leukemia, lymphoma, multiple myeloma, and mesothelioma, using DRAs either as single-agent treatments, or in combination with other therapies.

Abstract: This invention describes a series of methods and compositions for prevention and treatment of diseases such as cancer. One aspect of the invention describes small molecule-based drugs that can be used to bind to death receptors TRAIL-R1/DR4 and/or TRAIL-R2/DR5 and induce apoptosis in cancer cells, while sparing normal cells. The invention also describes TRAIL Death Receptor Agonists/Activators (DRAs) and their uses, such as the induction of apoptosis through caspase-8 and caspase-3 activation. The present invention also describes the methods of treating cancers, such as breast, prostate, colon, pancreatic, ovarian, lung, and brain cancers, leukemia, lymphoma, multiple myeloma, and mesothelioma, using DRAs either as single-agent treatments, or in combination with other therapies.

Abstract: Provided are methods of inhibiting BCL6 repression in a mammalian cell. Also provided are methods of treating cancer in a mammal.

Abstract: Provided herein are compounds and methods of using compounds that selectively inhibit binding to one or more docking domain regions of an extracellular signal-recognition kinase to inhibit in a cell having an extracellular signal-regulated kinase activity. Such methods may be used to inhibit cell proliferation of a neoplastic cell, to treat a cancer and further may be used in conjunction with administration of an anticancer drug at a reduced dosage to treat a cancer with a concomitant reduction in toxicity to an individual receiving the treatment. Also provided is a method to design and screen for compounds to inhibit binding within the extracellular signal-regulated kinase docking domain region, using at least in part computer-aided drug design modeling.