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Biomedical subjects

J R Rubin

Publications and source records attributed to J R Rubin.

At least 37 records · Page 2Linked to original sources
PubMed1998

Development of a binding model to protein tyrosine kinases for substituted pyrido[2,3-d]pyrimidine inhibitors.

Previously, our laboratories have reported on a new class of highly potent tyrosine kinase inhibitors based on the pyrido[2, 3-d]pyrimidine core template. To understand the structural basis for the potency and specificity, a model for the binding mode of this class of inhibitors to the tyrosine kinase domains of c-Src, PDGFr, FGFr, and EGFr tyrosine kinases was developed from structural information (principally utilizing the catalytic domain of c-AMP-dependent protein kinase as template) and structure-activity relationship (SAR) information. In the resulting docking mode, the pyrido[2,3-d]pyrimidine template shows a hydrogen-bonding pattern identical to that of olomoucine. The 6-aryl substituent of the heterocycle is located deep in the binding cleft in a pocket not used by ATP, which helps to confer high-affinity binding as well as specificity. The 2-anilino and 2-(dialkylamino)alkylamino substituents as well as the 7-urea substituent of inhibitors within this class are located at the entrance of the binding cleft and make contact with residues in the hinge region between the two kinase lobes. This allows considerable variability and bulk tolerance for C-2 and N-7 substituents. The models presented here are consistent with the SAR seen for the inhibition of a number of isolated enzymes and provide a structural basis to explain their specificity. They have been used successfully to design new highly potent protein kinase inhibitors.

Amino Acid Sequence↗
PubMed1997

Tyrosine kinase inhibitors. 12. Synthesis and structure-activity relationships for 6-substituted 4-(phenylamino)pyrimido[5,4-d]pyrimidines designed as inhibitors of the epidermal growth factor receptor.

A series of 6-substituted 4-anilinopyrimido[5,4-d]pyrimidines has been prepared and shown to be potent inhibitors of the tyrosine kinase activity of the epidermal growth factor receptor (EGFR). These compounds are structurally related to the pyrido[3,2-d]- and pyrido[3,4-d]-pyrimidines previously shown to be EGFR inhibitors. Their structure-activity relationships (SAR) for inhibition of the isolated enzyme more closely resemble those of the [3,2-d] than the [3,4-d] pyridopyrimidine isomers. This suggests the requirement of an aza atom in the 7- but not the 5-position (i.e., a carbon atom in the 5-position) for the enhanced potency shown by 6-N-methylated derivatives in each series. X-ray crystal structures were determined for the three NHMe derivatives 2, 3, and 5c in the pyrido[9,2-d]-, pyrido[3,4-d]-, and pyrimido[5,4-d]-pyrimidine series, respectively. These show that a carbon rather than a nitrogen atom at the 5-position leads to significant conformational changes in the molecule (a longer C5a-C4 bond and a 30 degrees out-of-plane rotation of the phenyl group), due to the requirement to relieve nonbonding interactions between the C5 and N9 protons. Pyrimido[5,4-d]pyrimidine analogues bearing bulky, weakly basic solubilizing side chains linked to the 6-position through a secondary amine generally retained potency both against the isolated enzyme and for inhibition of autophosphorylation of EGFR in intact A431 cells. This agrees with a recent binding model that suggests this general class of compounds binds to EGFR with the 6-position located in an area of comparative bulk tolerance at the entrance to the ATP-binding pocket. While these solubilized pyrimido[5,4-d]pyrimidine analogues were less potent than the NHMe derivative 5c in the isolated enzyme assay, some were considerably superior to 5c (and among the most potent ever reported) as inhibitors of EGFR autophosphorylation in cellular assays.

Adenosine Triphosphate↗
PubMed1997

Traumatic first rib fracture: is angiography necessary? A review of 730 cases.

The two most common sites of first rib fracture were at the subclavian sulcus and in the neck of the first rib, posteriorly. Five distinct mechanisms for rib fracture were identified and included: (i) posteriorly directed trauma to the upper thorax or shoulder girdle; (ii) a direct blow to the sternum and anterior chest wall; (iii) a blow fracturing the clavicle; (iv) a strong sudden contraction of the scalenus anticus muscle; and (v) radiographic findings of a first rib fracture without history of trauma. Isolated first rib fracture regardless of mechanism of injury, results in a low incidence of major vascular injury (mean 3%), although with fracture displacement, the incidence is higher. First rib fracture associated with concomitant head, thoracic, abdominal, or long bone trauma was associated with vascular injury in 24% of cases. According to this review, specific indications for subclavian artery and aortic arch arteriography in patients with traumatic first rib fracture include widened mediastinum on chest radiography, upper-extremity pulse deficit, posteriorly displaced first rib fracture, subclavian groove fracture anteriorly, brachial plexus injury and expanding hematoma.

Angiography↗
PubMed1996

X-ray structure of a hydroxamate inhibitor complex of stromelysin catalytic domain and its comparison with members of the zinc metalloproteinase superfamily.

BACKGROUND: Stromelysin belongs to a family of zinc-dependent endopeptidases referred to as matrix metalloproteinases (MMPs, matrixins) because of their capacity for selective degradation of various components of the extracellular matrix. Matrixins play key roles in diseases as diverse as arthritis and cancer and hence are important targets for therapeutic intervention. RESULTS: The crystal structure of the stromelysin catalytic domain (SCD) with bound hydroxamate inhibitor, solved by multiple isomorphous replacement, shows deep S1' specificity pocket which explains differences in inhibitors binding between the collagenases and stromelysin. The binding of calcium ions by loops at the two ends of a beta-strand which marks the boundary of the active site provides a structural rationale for the importance of these cations for stability and catalytic activity. Major differences between the matrixins are clustered in two regions forming the entrance to the active site and hence may be determinants of substrate selectivity. CONCLUSIONS: Structural comparisons of SCD with representative members of the metalloproteinase superfamily clearly highlight the conservation of key secondary structural elements, in spite of major variations in the sequences including insertions and deletions of functional domains. However, the three-dimensional structure of SCD, which is generally closely related to the collagenases, shows significant differences not only in the peripheral regions but also in the specificity pockets; these latter differences should facilitate the rational design of specific inhibitors.

Amino Acid Sequence↗
PubMed1996

Designing inhibitors of the metalloproteinase superfamily: comparative analysis of representative structures.

Structural comparisons of representative members of the zinc metalloproteinase superfamily show that the key secondary structural elements are conserved, in spite of major variations in the sequences including insertions and deletions of functional domains. Major differences between the matrix metalloproteinases (matrixins) are clustered in two regions forming the entrance to the active site and hence may be determinants of substrate selectivity. A comparison of the structures of matrixin-inhibitor complexes shows that there are significant differences even among the closely related matrixins, not only in the peripheral regions but also in the specificity pockets; these differences offer an excellent opportunity for the design of specific inhibitors targetted to individual members.

Binding Sites↗
PubMed1993

Structure of recombinant bovine interferon-gamma at 3.0 A resolution.

The three-dimensional crystal structure of recombinant bovine interferon-gamma was determined using the multiple isomorphous replacement method at 3.0 A and refined to an R factor of 19.2%. This protein crystallizes in space group P2(1)2(1)2(1) with unit-cell parameters of a = 42.8, b = 79.9 and c = 85.4 A. There is one functional dimer in the asymmetric unit. The two polypeptide chains are related by a non-crystallographic twofold symmetry axis. The secondary structure is predominantly alpha-helical with extensive interdigitation of the alpha-helical segments of the polypeptide chains that make up the dimer. The secondary structure, tertiary structure and topology of this molecule are identical to the previously reported structures of recombinant rabbit interferon-gamma and recombinant human interferon-gamma. The molecular topology is also similar to that of murine interferon-beta. These structural similarities strongly indicate the presence of a unique topological feature (fold) among gamma-interferons from different species, and also among the different classes of interferons.

Journal Article↗
PubMed1993

Crystallization and preliminary X-ray diffraction studies of dogfish C-reactive protein.

Crystals of dogfish (Mustelus canis) C-reactive protein were obtained through vapor phase equilibration using the sitting drop rod technique with ammonium sulfate as the precipitating agent. The space group was determined to be P1 (triclinic lattice) with unit cell dimensions of a = 82.91, b = 92.25 and c = 103.40 A; alpha = 83.36 degrees, beta = 89.76 degrees, and gamma = 81.30 degrees. These crystals diffract to about 2.6 A resolution and contain two hexamers in the asymmetric unit.

Animals↗
PubMed1993

The effect of inguinal lymphatic manipulation on regional lymph flow patterns.

PURPOSE: Because of the proximity of the inguinal lymphatics and the femoral vessels, lymph vessel manipulation during inguinal dissection is unavoidable, and this project was undertaken to evaluate the consequences. METHODS: Thirty-five greyhound dogs underwent popliteal lymph node dissection, cannulation with microvascular silastic tubing, and infusion of 2.5% Patent blue violet (Sigma Chemical Co., St. Louis, Mo.) (visual enhancement) and technetium 99m-labeled human serum albumin (HSA). Animals underwent inguinal exploration with no manipulation (group 1; n = 9), local lymphatic ligation (group 2; n = 11), or radical excision and ligation (group 3; n = 15) of the inguinal lymph vessels. Lymphatic flow was calculated by 99mTc-HSA clearance (counts per minute) at the popliteal, inguinal, and iliac regions, before and after lymph vessel manipulation and was converted into percent change between the regions. RESULTS: There was statistically reduced intralymphatic radioactivity in groups 2 and 3 compared with group 1 (p < 0.001; Student t test), whereas there was no significant difference between groups 2 and 3. CONCLUSIONS: This demonstrates that lymphatic flow in this experimental model is significantly reduced when major channels are identified and ligated, although radical obliteration does not reduce flow more significantly than local ligation, implying that there is an alternate pathway for lymph flow.

Animals↗
PubMed1993

Risk assessment in patients undergoing carotid endarterectomy.

Factors that contribute to the outcome of carotid endarterectomy include appropriate patient selection, preoperative medical optimization, meticulous operative technique and postoperative management. This study was designed to evaluate associated medical and operative risk factors with surgical outcomes for 9795 consecutive carotid endarterectomies performed by members of a voluntary regional vascular society. All data were reviewed and subject to a variety of statistical analyses in a blinded retrospective fashion. Factors including sex, increased age (> 70 years), cigarette smoking, chronic pulmonary disease and diabetes did not contribute independently to either increased operative neurologic morbidity or mortality rates. Cardiac disease (P < 0.0001) and chronic renal failure (P < 0.001) correlated independently with increased operative mortality, while hypertension (P < 0.05), cardiac disease (P < 0.01), renal failure (P < 0.0001), emergency surgery (P < 0.0001) and advanced neurologic symptoms at the time of operation (P < 0.0001) were associated with an increased operative stroke rate. In a group of 9021 patients who underwent 9795 carotid endarterectomies with a combined 3.1% incidence of operative neurologic morbidity or mortality (neurologic morbidity, 2.0%; mortality, 1.5%), specific preoperative medical risk factors could be identified. Only cardiac disease and chronic renal failure were associated with both significantly increased operative neurologic morbidity and operative mortality rates.

Adult↗
PubMed1992

Crystallization and preliminary characterization of three crystal forms of human recombinant transforming growth factor-alpha.

Three crystal forms of human recombinant TGF-alpha have been grown from solutions containing 2-methyl-2,4-pentanediol. One of the forms belongs to the orthorhombic space group C222(1) and the other two belong to the monoclinic space group C2. Two of the crystal forms diffract to approximately 2.3 A Bragg spacings. X-ray diffraction data has been collected for all three forms. These data appear to be suitable for crystal structure determination, using either heavy atom isomorphous replacement methods or molecular replacement, for phase determination.

Crystallization↗
PubMed1992

Structure of the anti-malarial drug primaquine diphosphate.

8-(4-Amino-1-methylbutylamino)-6-methoxyquinoline bis(dihydrogenphosphate), C15H23N3O2+.2(H2PO4)-, Mr = 455.35, triclinic, P1, Z = 2, a = 7.389 (6), b = 8.862 (4), c = 16.055 (10) A, alpha = 97.57 (2), beta = 100.21 (3), gamma = 77.01 (2) degrees, V = 1003.6 (5) A3, Dm = 1.495 (by flotation), Dx = 1.507 g cm-3, lambda (Cu K alpha) = 1.5418 A, mu(Cu K alpha) = 24.48 cm-1, F(000) = 480, room temperature, R = 0.068 for 3448 observed reflections. The above working cell is related to the reduced cell with angles alpha = 82.43, beta = 79.79 and gamma = 77.01 degrees by the transformation (-100/0 -10/001). Primaquine diphosphate was crystallized in the dicationic form with protonation on the quinoline ring nitrogen atom and on the terminal amino group. One dihydrogenphosphate anion is chelated by the quinoline ring and the butylamino side chain. The other dihydrogenphosphate anion is hydrogen bonded to the terminal amino group. The C(14) atom is nearly in the plane of the quinoline ring with a C(9)-C(8)-N(13)-C(14) torsion angle of 169 degrees. The butyl-diamino side chain is kinked by rotation about the C(14)-C(16) bond with a N(13)-C(14)-C(16)-C(17) torsion angle of -59 degrees. The C(15) methyl substituent is in line with the rest of the butyl chain. The terminal amino group N(19) is hydrogen bonded to three symmetry-related phosphate groups while N(1) and N(13) are 'chelated' to a fourth phosphate group.

Antimalarials↗
PubMed1992

Lower-extremity amputation with immediate postoperative prosthetic placement.

To study the efficacy of an immediate postoperative prosthesis (IPOP) program, a retrospective review of 167 major lower-extremity amputations was performed. Patient enrollment in the IPOP program was based on the individual's potential for rehabilitation and participation in an aggressive postoperative physical therapy regimen, as determined by the surgeon, prosthetist, physical therapist, and social worker. Indications for amputation were intractable infection and/or severe unreconstructable arterial insufficiency. Sixty-five patients underwent 69 amputations with IPOP (59 below knee; 10 above knee). Successful program completion was defined as independent ambulation and occurred in 86% of those patients enrolled. The average interval from amputation to ambulation was 15.2 days for the below-knee amputees and 9.3 days for the above-knee amputees. Failure to complete the program occurred in 14% of patients and was due to noncompliance, stump infection, stump trauma, and death. The results of this review support the use of IPOP after major lower-extremity amputation.

Adult↗
PubMed1992

A new approach for three-dimensional reconstruction of arterial ultrasonography.

This report describes a computerized approach that allows the creation of realistic three-dimensional arterial images from two-dimensional contiguous slices derived from a conventional ultrasound scan. Furthermore, the study assesses the method's feasibility and accuracy by performing in vitro cadaver artery three-dimensional reconstructions. Images are digitized into a computer, with a resolution of 512 x 480 pixels, and a dynamic range of 8 bits/pixel (256 gray scale). After edge enhancement with convolution filters through the original binary data, the intraluminal and outer edges are traced and converted to a polygon vector within a defined three-dimensional space. Serial cuts, 2 mm apart, are then "stacked" into a three-dimensional model, with interpolation of polyhedra between slices. Sixteen normal and arteriosclerotic distal aortic and common iliac arteries were obtained from fresh cadavers. Three-dimensional reconstruction models were compared with gross examination of the original artery. Anatomically accurate reconstructions were obtained, all with detailed surface information. Data analyzed included diameter, area, residual lumen, and percent stenosis. Pearson's coefficients determined for the pairs of data indicated excellent correlation (greater than or equal to 0.90) between separate measurements. With use of the described technology it is feasible to perform arterial three-dimensional reconstructions on a personal computer, with detailed and accurate surface information. The three-dimensional reconstruction method used can reliably and consistently reproduce the anatomic specimens.

Arteries↗
PubMed1992

Peripheral vascular surgery.

Patients may present with a wide range of manifestations of arterial occlusive disease. The clinician must be able to assess the magnitude of the arterial flow diminution and thereby determine the appropriate treatment regimen. A careful history, physical examination, and pertinent noninvasive vascular laboratory tests should provide adequate information for the clinician to establish the severity of disease and the need to pursue a medical or surgical treatment plan. Patient evaluation must be carried out expeditiously, especially when limb-threatening conditions such as infection or gangrene exist, because these problems may progress rapidly and result in major lower extremity amputation.

Arterial Occlusive Diseases↗
PubMed1991

Crystal structure of recombinant rabbit interferon-gamma at 2.7-A resolution.

The crystal structure of recombinant rabbit interferon-gamma was solved by the multiple isomorphous replacement technique at 2.7-A resolution and refined to a crystallographic R-factor of 26.2%. The interferon crystallizes with one-half of the functional dimer in the asymmetric unit, with the two polypeptide chains of the dimer related by a crystallographic 2-fold symmetry axis. The structure is predominantly alpha-helical with extensive interdigitation of the alpha-helical segments of the two polypeptide chains.

Amino Acid Sequence↗
PubMed1991

Structure of the anti-cancer drug complex tetrakis (mu-acetato)-bis(1-methyladenosine)dirhodium(II) monohydrate.

[Rh2(C2H3O2)4(C11H16N5O4)2].H2O, Mr = 1024.6, triclinic, P1, a = 7.808 (3), b = 11.469 (4), c = 12.091 (2) A, alpha = 69.55 (2), beta = 79.46 (2), gamma = 76.61 (3) degrees, V = 980.7 (6) A3, Z = 1, Dx = 1.735 g cm-3, lambda (Cu K alpha) = 1.5418 A, mu = 77.6 cm-1, F(000) = 522, room temperature, R = 0.053 for 3638 unique reflections. Structure consists of two rhodium(II) ions in a metal--metal bond bridged by four acetate groups. The remaining axial coordination sites on the rhodium ions are coordinated to the N(7) positions of two 1-methyladenosine molecules.

Adenosine↗
PubMed1991

Crystallization and preliminary x-ray diffraction studies of recombinant rabbit interferon-gamma.

Two different crystal forms of recombinant rabbit IFN-gamma were obtained under different crystallization conditions. The first, a tetragonal form with space group P43212 or P41212, was obtained through vapor phase equilibration using the sitting drop rods technique with ammonium citrate as the major precipitating agent. The unit cell dimensions of this crystal form are a = b = 82.1 A and C = 116.3 A. These crystals diffract to 2.8 A resolution and contain a dimer in the asymmetric unit. A second crystal form was obtained by the batch method at pH 8.0 using sodium chloride as the precipitating agent. The crystals are hexagonal, space group P6122 or P6522, and with unit cell dimensions of a = b = 58.0 A and c = 169 A. This form contains monomer in the asymmetric unit and diffracts to greater than 2.7 A resolution. Both forms appear to be eminently suitable for further analyses and crystal structure solution.

Animals↗