Characterization of molecular recognition of STAT3 SH2 domain inhibitors through molecular simulation

Abstract

Signal transducer and activator of transcription 3 (STAT3) is an anti-cancer target protein due to its over-activation in tumor cells. The Tyr705-phosphorylated (pTyr) STAT3 binds to the pTyr-recognition site of its Src Homology 2 (SH2) domain of another STAT3 monomer to form a homo-dimer, which then causes cellular anti-apoptosis, proliferation, and tumor invasion. Recently, many STAT3 SH2 dimerization inhibitors have been discovered via both computational and experimental methods. To systematically assess their binding affinities and specificities, for eight representative inhibitors, we utilized molecular docking, molecular dynamics simulation, and ensuing energetic analysis to compare their binding characteristics. The inhibitors' binding free energies were calculated via MMPB(GB)SA, and the STAT3 SH2 binding "hot spots" were evaluated through binding energy decomposition and hydrogen bond (H-bond) distribution analysis. Several conclusions can be drawn: (1) the overall enthalpy-entropy compensation paradigm is preserved for the STAT3 SH2/ligand binding thermodynamics; (2) at one end of the binding spectrum, two compounds bind to SH2 due to their minimum entropic penalties that result from their relative rigidities and increased dynamics of SH2 upon their binding; at the other end of the binding spectrum, one compound shows a typical weak binder behavior due to its loose binding in the SH2's strongest enthalpy-contributing binding subsite; (3) hydrogen bonding seems a strong indicator to evaluate the SH2/ligand binding potency, which echoes a finding that CH/π non-classical H-bond is responsible for some pTyr peptides binding to their corresponding SH2 domains; (4) STAT3 SH2 domain possesses three binding "hot spots": pTyr705-binding pocket with polar residues and contributing the largest binding enthalpy (two-thirds); Leu706 subsite which is the most dynamic and hardest to target; a hydrophobic side pocket which is unique to STAT3 and very targetable, which may offer unique opportunity to design STAT3-specific inhibitors, particularly with fragment-based approach.

The Essential Roles of Chemistry in High-Throughput Screening Triage

“…For example, the number, document type, and abstract of the available references can often allow us to bin series with respect to their priority for follow-up. The essential roles of chemistry in high-throughput screening triage Perspective ≥90%: Compounds that are greater than 90% similar; Biol: Compounds that were reported in a 'biological study' from a journal article [155,[159][160][161][162][163][164][165][166][167][168][169][170][171][172]; Exact: Exact substructure found; Sources: Commercial sources of exact compound. 6 [160][161][162][163][164] [165] [156,166,167,168,169] [ 168,169,170,171,172,173] future science group Perspective Dahlin & Walters otherwise following up on HTS results.…”

“…This apparent disregard or lack of knowledge of the preceding literature is not an isolated phenomenon. The two other most recent publications, references [165] and [169], make no mention of PAINS and no mention of the work on similar compounds reported in references [155,[165][166][167][168] and [167][168][169][170][171][172], respectively (admittedly, reference [169] does reference an earlier paper by that describes the protocol for detecting compounds capable of redox interference [81]).…”

Nanomolar-Potency Small Molecule Inhibitor of STAT5 Protein

“… 20 , 21 Superimposition of structures revealed that STAT3′s SH2 domain structure is not significantly altered upon phosphopeptide binding. 22 Thus, we reasoned that the unphosphorylated STAT5 structure (PDB: 1Y1U) is suitable for in silico -based drug design. Analogous to the canonical pY-SH2 domain binding, the STAT5 pY likely docks proximal to the conserved R618 (βB strand), making H-bonding/electrostatic interactions with nearby polar residues, K600 (αA), T628 (βC), and S622 (βB and βC) Figure 2 A.…”

Development of new N-arylbenzamides as STAT3 dimerization inhibitors

“…The p -cyclohexylbenzyl group places the cyclohexyl group deep within the hydrophobic pY-X pocket. 34 …”