Defining the landscape of ATP-competitive inhibitor resistance residues in protein kinases.

Kinases are involved in disease development and modulation of their activity can be therapeutically beneficial. Drug-resistant mutant kinases are valuable tools in drug discovery efforts, but the prediction of mutants across the kinome is challenging. Here, we generate deep mutational scanning data to identify mutant mammalian kinases that drive resistance to clinically relevant inhibitors. We aggregate these data with subsaturation mutagenesis data and use it to develop, test and validate a framework to prospectively identify residues that mediate kinase activity and drug resistance across the kinome. We validate predicted resistance mutations in CDK4, CDK6, ERK2, EGFR and HER2. Capitalizing on a highly predictable residue, we generate resistance mutations in TBK1, CSNK2A1 and BRAF. Unexpectedly, we uncover a potentially generalizable activation site that mediates drug resistance and confirm its impact in BRAF, EGFR, HER2 and MEK1. We anticipate that the identification of these residues will enable the broad interrogation of the kinome and its inhibitors.

Dose-dependent effects of CRF-like diuretic peptide on transcellular and paracellular transport pathways.

The mechanism of action of synthetic Culex corticotropin-releasing factor (CRF)-like diuretic peptide (CCRF-DP) was investigated in isolated, perfused Malpighian tubules of the yellow fever mosquito, Aedes aegypti. Low concentrations of CCRF-DP (10(-10) and 10(-9) M) caused depolarizing oscillations of the lumen-positive transepithelial voltage (Vt) in Malpighian tubules, whereas high concentrations (10(-8) and 10(-7) M) first depolarized and then transiently hyperpolarized Vt; CCRF-DP always lowered transepithelial resistance (Rt), regardless of voltage depolarization or hyperpolarization. The short-circuit current (Isc), an electrical estimate of active transepithelial transport of Na and K, remained unchanged at low concentrations of CCRF-DP, but Isc more than doubled at high concentrations. These effects of CCRF-DP suggest dose-dependent sites of action: low concentrations of CCRF-DP affect the paracellular pathway, and high concentrations affect both paracellular and transcellular pathways.

The concentration-dependence of CRF-like diuretic peptide: mechanisms of action.

The mechanism of action of synthetic CCRF-DP, the corticotropin-releasing factor (CRF)-related diuretic peptide of the salt marsh mosquito Culex salinarius, was investigated in isolated Malpighian tubules of the yellow fever mosquito Aedes aegypti. A low concentration of CCRF-DP (10(-9)mol l-1) caused a small but insignificant increase in transepithelial secretion of NaCl and fluid, but significantly reduced transepithelial voltage and resistance without a change in short-circuit current, pointing to the stimulation of passive Cl- transport through the paracellular pathway as the principal mechanism of a mild diuresis. Significant changes in voltage and resistance but not in short-circuit current were duplicated by the ionophore A23187 (0.4 micromol l-1), suggesting Ca2+ as a second messenger at 10(-9)mol l-1 CCRF-DP. A high concentration of CCRF-DP (10(-7)mol l-1) significantly increased transepithelial secretion of NaCl and fluid and significantly increased short-circuit current, pointing to the stimulation of active Na+ transport through the transcellular pathway as the mechanism of a strong diuresis. This effect was mimicked by dibutyryl-cAMP, suggesting cAMP as a second messenger at 10(-7)mol l-1 CCRF-DP. Dibutyryl-cGMP had no effects. These results suggest dose-dependent, receptor-mediated effects of CCRF-DP that target discrete transport pathways via discrete second messengers: low concentrations of CCRF-DP cause a mild diuresis, apparently via Ca2+-mediated effects on paracellular Cl- transport, and high concentrations cause a strong diuresis via cAMP-mediated effects on active transcellular Na+ transport in addition to the effects on the paracellular pathway.

Inactivation of Dip-allatostatin 5 by membrane preparations from the cockroach Diploptera punctata.

Incubation of Dip-AST 5 (Asp-Arg-Leu-Tyr-Ser-Phe-Gly-Leu-NH2) with membrane preparations of midgut, hindgut, brain, or corpora allata (CA) results in its inactivation in terms of the inhibition of juvenile hormone biosynthesis. Dip-AST 5 is initially cleaved at Gly7-Leu8 to yield the N-terminal heptapeptide (Asp-Arg-Leu-Tyr-Ser-Phe-Gly). At supraphysiological concentration, the half-life of Dip-AST 5 varied from 24 min by membrane preparations of brain to approximately 53 min following incubation with midgut membrane preparations. At more physiological concentrations (nanomolar), Dip-AST 5 was still initially cleaved to yield the inactive N-terminal heptapeptide with a half-life ranging from 23 min with brain membrane preparations to 85 min with membrane preparations of midgut. The fact that Dip-AST 5 is rapidly degraded to an inactive product by membrane preparations or whole tissues (CA) indicates that Dip-AST 5 has a different metabolic fate in tissue preparations than in diluted hemolymph (Garside et al., 1997). These findings demonstrate that the degradation of allatostatins by tissue preparations of D. punctata may play an important role in the termination of their ability to inhibit juvenile hormone biosynthesis by the CA and/or to modulate muscle activity in the hindgut.

MALDI-MS as a monitor of the purification and folding of synthetic eclosion hormone.

Analogues of the small protein Manduca sexta eclosion hormone (62 amino acids) were synthesized by Fmoc solid-phase methodology. Matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) was used to analyze the products of the syntheses and this information was used to design an efficient purification scheme. MALDI-MS was used to monitor the target products through purification and it was also used to monitor folding of the purified materials. The folded EH analogues were shown to be biologically active proteins with an in vivo bioassay using pharate adult moths, Heliothis virescens.

Degradation of Dip-allatostatins by hemolymph from the cockroach, Diploptera punctata.

Incubation of Dip-AST 7 (APSGAQRLYGFGLa) or Dip-AST 9 (GDGRLYAFGLa) (5 microM) with hemolymph for 30 min results in cleavage by a putative endopeptidase, yielding the C-terminal hexapeptide. This metabolic product is subsequently cleaved by an amastatin-sensitive aminopeptidase to yield the the C-terminal pentapeptide, as treatment with the competitive aminoexopeptidase inhibitor, amastatin, results in a significant accumulation of the C-terminal hexapeptide. Interestingly, Dip-AST 5 (DRLYSFGLa) (6 microM), which in common with Dip-AST 7 and 9 possesses Arg-Leu-Tyr, is not rapidly cleaved. However, [3H-Tyr]Dip-AST 5 at physiological concentrations (4 nM), appears to be cleaved by the same enzymes that cleave Dip-AST 7 and 9, albeit at a reduced rate. Incubation of other members of the Dip-allatostatin family with hemolymph also results in cleavage of the peptides, suggesting that there are a variety of endo- and/or exopeptidases present in the hemolymph of D. punctata.

Identification and partial characterization of receptors for allatostatins in brain and corpora allata of the cockroach Diploptera punctata using a binding assay and photoaffinity labeling.

We have developed both an in vitro binding assay and a photoaffinity labeling assay to demonstrate and partially characterize putative receptors for allatostatins in brain and in corpora allata of Diploptera punctata. Isolated brain membranes were photoaffinity labeled with 125I-RYBPA (photoaffinity analogue of dip-allatostatin 5). Following labeling with 125I-RYBPA, SDS-PAGE and autoradiography revealed the presence of a putative receptor (37 kDa) for dip-allatostatin 5 and dip-allatostatin 7. Specific labeling was demonstrated by dose-dependent competition with either dip-allatostatin 5 or dip-allatostatin 7. The in vitro binding assay indicated that the receptor for dip-allatostatin 5 had a Kd of (9.0 +/- 0.9).10(-10) M and Bmax of 2.2 +/- 0.3 pmol/mg membrane protein. For dip-allatostatin 7, two Kd values of (1.5 +/- 0.1).10(-9) M and (3.8 +/- 0.3).10(-9) M were obtained, with Bmax values of 7.2 +/- 0.7 pmol/mg membrane protein and 11.4 +/- 1.0 pmol/mg membrane protein respectively. This indicates that there were probably two putative receptor sites for dip-allatostatin 7 although only one band was observable following photoaffinity labeling. Binding was saturable, specific and reversible. Using the in vitro binding assay, the Kd of the putative receptor in CA for dip-allatostatin 7 was shown to be (7.2 +/- 0.9).10(-10) M.

Cross reactivity studies of CRF-related peptides on insect Malpighian tubules.

Manduca sexta diuretic peptide II (Mas-DPII) stimulates fluid secretion by adult Malpighian tubules and cyclic AMP production by larval proximal and adult tubules of M. sexta in a dose-dependent manner. Mas-DPII has no effect on fluid transport across the larval cryptonephric complex. M. sexta diuretic hormone (Mas-DH) and CRF-related insect diuretic peptides from Acheta domesticus, Locusta migratoria, and Periplaneta americana also cause similar increases in the production of cyclic AMP by the Malpighian tubules of both larval and adult M. sexta. Insect CRF-related diuretic peptides exhibit varying degrees of potency when assayed on Malpighian tubules from L. migratoria and A. domesticus. Sauvagine, bovine-CRF, and human-CRF have only a small, but significant, effect on cyclic AMP production by M. sexta Malpighian tubules. However, sauvagine, bovine-CRF, and sucker fish urotensin-I have no effect on L. migratoria tubules. Stimulation of cyclic AMP production by M. sexta Malpighian tubules could potentially be used as a screening assay to identify other insect CRF-related diuretic peptides.

Structure-activity relationships for Periplaneta americana hypertrehalosemic hormone. I: The importance of side chains and termini.

Single amino acid replacement analogues for the native hypertrehalosemic hormone I of the American cockroach, Periplaneta americana (Pea-CAH-I: pGlu-Val-Asn-Phe-Ser-Pro-Asn-Trp-NH2), have been prepared by solid-phase peptide synthesis, and complete dose-response curves have been measured in P. americana monitoring the carbohydrate-mobilizing activity in vivo. All analogues that elicited hypertrehalosemia showed similar time-response courses, indicating that transport and degradation rates were comparable. Comparison of the potency and efficacy parameters of the analogues under study in the dose-response curves revealed four activity groups: 1) analogues that had the aromatic amino acids at positions 4 (phenylalanine) or 8 (tryptophan) replaced by alanine and glycine, respectively, had trace activity; 2) analogues with alanine at positions 1 or 2 had low potencies and an apparent biphasic dose-response relationship without much observable loss of efficacy; 3) analogues with glycine at positions 6 and 7 had potencies and efficacies most similar to Pea-CAH-I; and 4) analogues that had either an alanine instead of asparagine residue at position 3, or had a substitution of the carboxylamide function at the C-terminus by a carboxyl function reached apparent saturation, but only achieved 50-57% of the maximum activity of the native peptide. The potency profile for the analogue set is consistent with the importance of the N-terminal pentapeptide and the C-terminal tryptophan interacting with receptor(s) more closely than the side chains at positions 6 and 7, which are predicted to be the corner residues of a beta-turn. Finally, the biphasic dose-response curves observed for more than one analogue suggest the potential that receptors for Pea-CAH-I exist in more than one form.

Culekinin depolarizing peptide: a mosquito leucokinin-like peptide that influences insect Malpighian tubule ion transport.

A peptide termed culekinin depolarizing peptide (CDP) was isolated from approximately 1.2 million mosquitos (94% Culex salinarius). The peptide was isolated on the basis of a rapid myotropic assay that utilized a hindgut preparation from Leucophaea maderae and a transepithelial voltage assay that used mosquito Malpighian tubules from Aedes aegypti. A 15% trifluoroacetic acid extraction from the mosquitos, two solid phase extraction steps, and six HPLC steps resulted in the isolation of 9.7 nmol of CDP. This value corresponds to approximately 8 fmol/mosquito. Edman degradation indicated the following sequence for CDP: Asn-Pro-Phe-His-Ser-Trp-Gly-NH2. The sequence was confirmed as the suspected C-terminal amide form of the peptide, since native and synthetic CDP had identical chemical and biological properties. CDP is a member of the leucokinin family of neuropeptides. The leucokinins have been found in three other insect species (Leucophaea maderae, Acheta domesticus and Locusta migratoria) where these peptides were isolated by their myotropic properties alone. CDP shares a C-terminal sequence homology (i.e., Phe-X-Ser-Trp-Gly-NH2) with the rest of the leucokinins. CDP corresponds to the strongest tubule depolarizing activity in the C. salinarius extract. These findings agree with previous structure-activity studies that suggest that mosquitos would contain a leucokinin-like factor that had Phe-His-Ser-Trp-Gly-NH2 as the C-terminal pentapeptide. This is the first leucokinin isolated from blood feeding or holometabolous insects.

Isolation and characterization of a diuretic peptide common to the house fly and stable fly.

An identical CRF-related diuretic peptide (Musca-DP) was isolated and characterized from whole-body extracts of the house fly, Musca domestica, and stable fly, Stomoxys calcitrans. The peptide stimulates cyclic AMP production in Manduca sexta Malpighian tubules and increases the rate of fluid secretion by isolated Musca domestica tubules. The 44-residue peptide, with a mol.wt. of 5180, is amidated, and has the primary structure: NKPSLSIVNPLDVLRQRLLLEIARRQMKENTRQVELNRAILKNV-NH2. Musca-DP has a high percentage of sequence identity with other characterized CRF-related insect diuretic peptides.

Structure-activity studies of allatostatin 4 on the inhibition of juvenile hormone biosynthesis by corpora allata: the importance of individual side chains and stereochemistry.

The production of juvenile hormone III (JH III) by the corpora allata of the cockroach Diploptera punctata is regulated in part by peptides originating from the brain. One group of these peptides, termed allatostatins, reversibly inhibits the biosynthesis of JH in vitro. Allatostatin 4 (AST4: Asp-Arg-Leu-Tyr-Ser-Phe-Gly-Leu-amide) is the smallest member of the AST family yet defined and was used as the benchmark peptide for these initial structure-activity studies. Two initial analog series of AST4 were examined for the ability of each analog to inhibit JH biosynthesis by corpora allata in vitro. Each analog series consisted of analogs that contained a single amino acid change from the native AST4 sequence. The first series contained Ala replacement analogs and the second contained analogs with D-amino acid replacements. The first analog series used Ala replacements to help indicate which amino acid side chains were most important for inhibition of JH biosynthesis. The most important side chain appeared to be Leu8 followed by Phe6 and Tyr4. Additionally, the D-amino acid series suggested that a secondary structural element(s) at the C-terminus of AST4 could be important to the biological activity.

Structure-activity relationships for inhibitory insect myosuppressins: contrast with the stimulatory sulfakinins.

Unusual among insect neuropeptides, the decapeptide myosuppressins are capable of inhibiting contractions of visceral muscle, including the isolated cockroach hindgut. The C-terminal pentapeptide Val-Phe-Leu-Arg-Phe-NH2 has been identified as the myosuppressin active core, the minimum number of residues required to elicit hindgut myoinhibitory activity. Activity of the same magnitude as the parent neuropeptide requires the C-terminal heptapeptide fragment Asp-His-Val-Phe-Leu-Arg-Phe-NH2. Evaluation of a series of substitution analogs delineates structural features critical for myoinhibitory activity within this important fragment. The branched, hydrophobic residues in myosuppressin position 6 (Val) and particularly position 8 (Leu), their absence in the myostimulatory sulfakinins, and the different roles played by the shared Asp residue (myosuppressin position 4; leucosulfakinin position 5) in peptide-receptor interaction, account in large degree for the contrasting biological activities elicited by these otherwise structurally similar peptide families. The results may have broad significance for other invertebrate myotropic systems, such as the locust heart and the pharyngeal retractor muscle of the mollusc Helix aspersa.

A comparison of the effects of two putative diuretic hormones from Locusta migratoria on isolated locust malpighian tubules.

Previous work has shown that a peptide related to arginine vasopressin is present in the suboesophageal ganglion of the locust, Locusta migratoria. This peptide was determined to be an anti-parallel dimer of the nonapeptide Cys-Leu-Ile-Thr-Asn-Cys-Pro-Arg-Gly-NH2 and was reported to stimulate cyclic AMP production and fluid secretion in a combined Malpighian tubules and midgut preparation from locusts. For these reasons the peptide has been called the arginine-vasopressin-like insect diuretic hormone (AVP-like IDH). Recently, a second diuretic peptide (Locusta-DP), which is related to corticotropin releasing factor, has been identified: this is a potent stimulant of fluid secretion and cyclic AMP production by isolated locust tubules. Because water balance in insects is likely to be controlled by a cocktail of hormones acting on both Malpighian tubules and hindgut, this study directly compares the activity of these two peptides in fluid secretion and cyclic AMP production bioassays on one target organ, the isolated Malpighian tubule of Locusta migratoria. Locusta-DP was synthesised directly, whereas the dimeric AVP-like IDH was obtained by oxidation of a synthetic nonapeptide monomer. Products were separated by RP-HPLC and their structures unequivocally confirmed by enzymatic digestion, sequence analysis and electrospray mass spectrometry. We show that Locusta-DP causes strong stimulation of fluid secretion and cyclic AMP production, whereas the AVP-like IDH has no effect in either assay. These findings are discussed in the light of recent work on the anatomy and physiology of the vasopressin-like immunoreactive (VPLI) neurones in the suboesophageal ganglion of Locusta migratoria, the proposed source of the AVP-like peptide.

Detection and partial characterization of an anti-steroidogenic peptide from the humoral immune system of the chicken.

Phenomenological association of alterations of immune system function at the time of puberty (e.g. involution of the chicken bursa of Fabricius) has led to postulation that the humoral immune system may negatively affect the hypothalamo-adenohypophyseal-gonadal axis of the neonate. Presently, we examined the effect of an acidic aqueous bursa of Fabricius extract, derived from prepubescent chickens, on in vitro basal and LH-stimulated progesterone biosynthesis by isolated ovarian granulosa cells of the largest preovulatory chicken follicles (F1 and F2). Crude extracts of < 5kDa and > 3kDa inhibited LH-stimulated progesterone secretion (P < 0.05). The bioactive component was observed to be heat labile and is sensitive to the endopeptidases chymotrypsin, trypsin and papain. The peptide is not sensitive to the exopeptidase, aminopeptidase M. Partial purification by reversed phase HPLC resulted in a fraction capable of inhibiting in vitro steroidogenesis. This fraction suppressed LH-stimulated progesterone biosynthesis to approximately basal levels (79% suppression). Following removal of the peptide, granulosa cells were capable of LH-stimulated progesterone biosynthesis similar to control cells. Bursal extract significantly inhibited cAMP analog-stimulated progesterone biosynthesis. These data indicate that the anti-steroidogenic peptide derived from the chicken bursa of Fabricius is a single heat labile, amino terminally blocked peptide with bioactivity independent of the gonadotropin receptor of the granulosa cell.

Locustatachykinin I and II, two novel insect neuropeptides with homology to peptides of the vertebrate tachykinin family.

Two myotropic peptides termed locustatachykinin I (Gly-Pro-Ser-Gly-Phe-Tyr-Gly-Val-Arg-NH2) and locustatachykinin II (Ala-Pro-Leu-Ser-Gly-Phe-Tyr-Gly-Val-Arg-NH2) were isolated from brain-corpora cardiaca-corpora allata-suboesophageal ganglion extracts of the locust, Locusta migratoria. Both peptides exhibit sequence homologies with the vertebrate tachykinins. Sequence homology is greater with the fish and amphibian tachykinins (up to 45%) than with the mammalian tachykinins. In addition, the intestinal myotropic activity of the locustatachykinins is analogous to that of vertebrate tachykinins. The peptides discovered in this study may just be the first in a whole series of substances from arthropod species to be identified as tachykinin family peptides. Moreover, both chemical and biological similarities of vertebrate and insect tachykinins substantiate the evidence for a long evolutionary history of the tachykinin peptide family.

Structure-activity relationships on hyperglycemia by representatives of the adipokinetic/hyperglycemic hormone family in Blaberus discoidalis cockroaches.

Several members of the adipokinetic/hyperglycemic neurohormone family from several different invertebrate species have been prepared by solid-phase peptide synthesis and assayed by a modified in vivo hyperglycemic bioassay in Blaberus discoidalis cockroaches. The hypertrehalosemic hormone (HrTH) is the endogenous hypertrehalosemic factor for B. discoidalis and was the most potent peptide in the assay. The more divergent the sequence of a family member from Blaberus HrTH, the less potent was the bioanalog. Manduca adipokinetic hormone is the most divergent peptide of the family and was totally inactive in the bioassay. Locusta adipokinetic hormone I had reduced maximum activity in the assay, which suggests that Ser5 is an important residue for the transduction of the hyperglycemic response. The direct relation between bioanalog similarity to Blaberus HrTH sequence and potency suggests that the hormone and target cell receptor for HrTH have evolved to maintain an "optimal fit".

Structure-activity relationships for myotropic activity of the gastrin/cholecystokinin-like insect sulfakinins.

The sulfakinins constitute a family of real and putative peptide sequences characterized from the cockroach Leucophaea maderae (leucosulfakinin subfamily) and fruitfly Drosophila melanogaster (drosulfakinin subfamily) with homology to the sulfated mammalian hormones gastrin II and cholecystokinin (CCK). The leucosulfakinin (LSK) subfamily of neuropeptides stimulate contractions of the isolated cockroach hindgut. In this paper, we have ascertained some of the primary structural requirements of the sulfakinins for myotropic (muscle-contracting) activity. The myotropic "active core" of this family has been determined to be the C-terminal hexapeptide, though the C-terminal octapeptide (Glu-Asp-Tyr(SO3H)-Gly-His-Met-Arg-Phe-NH2) is required for full activity. The LSKs demonstrate considerable tolerance to Ala substitution in positions 7 and 9 within the active core without complete loss of activity. Conversely, Ala substitution in positions 8, 10 and 11 led to inactive compounds. Basicity is a critical feature of LSK position 10, while aromatic character is an important characteristic for positions 8 and 11 for myotropic activity. Only trace activity could be observed upon replacement of the Tyr(SO3H) residue in LSK-position 6 with a Ser(SO3H). One analog ([3MeHis8] LSK) proved more active as a contractile stimulant than the natural product, while another ([7-11,Tyr(SO3H)7] LSK), conversely, demonstrated inhibition of spontaneous contractions of the cockroach hindgut.