Structure-Based Virtual Screening
(finding a needle in haystacks)

​

- Pavlic A. et al., Inhibition of Neutral Sphingomyelinase 2 by Novel Small Molecule Inhibitors Results in Decreased Release of Extracellular Vesicles by Vascular Smooth Muscle Cells and Attenuated Calcification, Int. J. Mol. Sci. 2023; 24(3): 2027

- Braza M.S. et al. Inhibiting Inflammation with Myeloid Cell-Specific Nanobiologics Promotes Organ Transplant Acceptance. Immunity. 2018 Nov 20;49(5):819-828.e6.

- Seijkens TTP et al., Targeting CD40-Induced TRAF6 Signaling in Macrophages Reduces Atherosclerosis, J. Am. Coll. Cardiol., 2018; 71(5): 527-542

- Aarts S.A.B.M. et al. Inhibition of CD40-TRAF6 interactions by the small molecule inhibitor 6877002 reduces neuroinflammation. Neuroinflammation. 2017 May 12;14(1):105.

- Zarzycka B. et al., Discovery of small molecule CD40-TRAF6 inhibitors, J. Chem. Inf. Model, 2015; 55(2): 294-307

- Chatzigeorgiou A. et al., Blocking CD40-TRAF6 signaling is a therapeutic target in obesity-associated insulin resistance, Proc. Natl. Acad. Sci. U. S. A., 2014; 111(7): 2686-2691

- Du J et al., Optimization of compound ranking for structure-based virtual ligand screening using an established FRED-Surflex consensus approach, Chem. Biol. Drug Des., 2014; 83(1): 37-51.

- Sperandio O et al., Identification of novel small molecule inhibitors of activated protein C, Thromb. Res., 2014; 133(6): 1105-1114

- Nicolaes GA et al., Rational design of small molecules targeting the C2 domain of coagulation factor VIII, Blood, 2014; 123(1): 113-120.

- Wichapong K et al., Application of docking and QM/MM-GBSA rescoring to screen for novel Myt1 kinase inhibitors, J. Chem. Inf. Model, 2014; 54(3): 881-893

- Wichapong K et al., Identification of potential hit compounds for Dengue virus NS2B/NS3 protease inhibitors by combining virtual screening and binding free energy calculations, Trop Biomed., 2013; 30(3): 388-408.

- Segers K et al., Design of protein membrane interaction inhibitors by virtual ligand screening, proof of concept with the C2 domain of factor V, Proc. Natl. Acad. Sci. U. S. A., 2007;104(31): 12697-12702

 

Structure-based peptide design

 

- Hrdinova J et al., Structure-Based Cyclic Glycoprotein Ibα-Derived Peptides Interfering with von Willebrand Factor-Binding, Affecting Platelet Aggregation under Shear, Int. J. Mol. Sci., 2022; 23(4): 2046

- Wichapong K et al., Structure-based peptide design targeting intrinsically disordered proteins: Novel histone H4 and H2A peptidic inhibitors, Comput. Struct. Biotechnol. J., 2021; 19: 934-948.

- Schumski A et al., Endotoxinemia Accelerates Atherosclerosis Through Electrostatic Charge-Mediated Monocyte Adhesion, Circulation, 2021; 143(3): 254-266.

- Silvestre-Roig C et al., Externalized histone H4 orchestrates chronic inflammation by inducing lytic cell death, Nature, 2019; 569(7755): 236-240

- Wichapong K et al., Structure-Based Design of Peptidic Inhibitors of the Interaction between CC Chemokine Ligand 5 (CCL5) and Human Neutrophil Peptides 1 (HNP1), J. Med. Chem., 2016; 59(9): 4289-301.

- Alard JE et al., Recruitment of classical monocytes can be inhibited by disturbing heteromers of neutrophil HNP1 and platelet CCL5, Sci. Transl. Med., 2015; 7(317): 317ra196.

 

Engineered Proteins

 

- Ercig B et al., N-glycan-mediated shielding of ADAMTS13 prevents binding of pathogenic autoantibodies in immune-mediated TTP, Blood, 2021; 137(19): 2694-2698.

- Ungethüm L., Engineered annexin A5 variants have impaired cell entry for molecular imaging of apoptosis using pretargeting strategies. J Biol Chem. 2011 Jan 21;286(3):1903-10.