In-silico based screening system to develop allosteric modulators of Bruton’s tyrosine kinase

Ibrutinib is a covalent inhibitor that binds to the Bruton’s tyrosine kinase (BTK) ATP-dependent active site and it is currently used for treating a variety of B cell tumors. A high rate of drug resistance develops in Ibrutinib-treated patients through mutations at the BTK kinase domain, resulting in more aggressive diseases. Thus, there is significant interest in identifying modulators that inhibit BTK in an active site-independent manner, specifically via allosteric modulation. We used an in-silico system to identify small molecules that bind outside of the BTK active site. Candidate compounds were then tested for direct binding to full length BTK protein using Saturated Transfer Difference Nuclear Magnetic Resonance (STD-NMR) and were subsequently used in primary mouse B cell-based assays to determine their functional relevance. Ex vivo B cells were triggered via the BCR in the presence of compounds and signaling events downstream of the BCR, including Nur77 upregulation and calcium flux, were measured by flow cytometry. A series of candidate allosteric BTK inhibitors were then confirmed to retain suppressive activity in an ABC-DLBC lymphoma line that carries the Ibrutinib resistant mutation. Additionally, primary human CLL, but not healthy B cells, were susceptible to candidate inhibitor-mediated death. These results indicate that a screening approach integrating in silico docking, NMR measurements, and cellular assays with primary B cells can be used to identify BTK inhibitors that act outside of the kinase domain. Allosteric BTK inhibitors will broaden the range of treatment options for B cell cancers, possibly overcoming or preventing the Ibrutinib-induced resistance when used as a combination therapy.

Targeting of ITK-SYK fusion oncogene through in-silico generated and biologically validated ITK-PH domain modulators

A subset of human Peripheral T cell Lymphomas, Not Otherwise Specified (PTCL-NOS), harbors a chromosomal translocation of interleukin-2 (IL-2) inducible T cell kinase (ITK) and spleen tyrosine kinase (SYK), giving rise to the composite ITK-SYK protein. ITK, a TEC family member kinase, plays an essential role in TCR and CD28 signaling. SYK signaling pathway is more broadly linked to activation of diverse lymphoid and myeloid cell types. ITK-SYK fusion protein consists of the PH domain of ITK and the SYK kinase domain allowing localization to the signalosome complex at the membrane via the PH domain and constitutive activity in T cells. Given the ubiquitous activity of SYK, it is predicted that targeting the ITK-PH domain of the fusion protein with small molecules can be a precise and less toxic approach to suppress ITK-SYK+PTCL-NOS in vivo. To this end, we performed a computational screen of small molecule libraries to identify candidate ITK-PH domain interacting compounds. A thermal shift assay was used to verify the specificity of binding of candidates to the target protein domain. Cellular assays tested small molecule activity in human and mouse T cells constitutively expressing the ITK-SYK fusion protein. We showed that the first-pass small molecule candidates specific to ITK-PH domain inhibit cytokine production driven by ITK-SYK fusion protein in human and mouse T cells. Our results demonstrate the efficiency of the virtual screening to identify drug candidates with biological activity in lymphocytes. Development of drugs that target ITK-PH domain is a rationale strategy towards first-in-class therapeutics for this subset of PTCL-NOS with very poor prognoses.

Proteolytic activation of human cathepsin A

Galactosialidosis is a human lysosomal storage disease caused by deficiency in the multifunctional lysosomal protease cathepsin A (also known as protective protein/cathepsin A, PPCA, catA, HPP, and CTSA; EC 3.4.16.5). Previous structural work on the inactive precursor human cathepsin A (zymogen) led to a two-stage model for activation, where proteolysis of a 1.6-kDa excision peptide is followed by a conformational change in a blocking peptide occluding the active site. Here we present evidence for an alternate model of activation of human cathepsin A, needing only cleavage of a 3.3-kDa excision peptide to yield full enzymatic activity, with no conformational change required. We present x-ray crystallographic, mass spectrometric, amino acid sequencing, enzymatic, and cellular data to support the cleavage-only activation model. The results clarify a longstanding question about the mechanism of cathepsin A activation and point to new avenues for the design of mechanism-based inhibitors of the enzyme.

Purification and characterization of an alkaline keratinase from Streptomyces sp

A protease producing bacterial culture ('S7') was isolated from slaughterhouse waste samples, Hyderabad, India. It was related to Streptomyces sp. on the basis of biochemical properties and 16S rRNA gene sequencing. Purification of the protease present in the culture medium supernatant on sephacryl S-100 indicated that it contains a keratinase with 67% recovery, 2.5-fold purification and an estimated molecular mass of approximately 44,000 Da. Keratinase showed an optimal activity at 45 degrees C and pH 11. Keratinase activity increased substantially in presence of Ca(2+) and was inhibited in presence of PMSF and EDTA identifying it as a serine metalloprotease. Stability in the presence of detergents, surfactants and solvents make this keratinase extremely useful for biotechnological process involving keratin hydrolysis or in the leather industry.