Targeting HIV reverse transcriptase for anti-AIDS drug design: structural and biological considerations for chemotherapeutic strategies

The reverse transcriptase of HIV is a key target for the antiviral treatment of AIDS. Numerous potent inhibitors of RT have been described including all of the drugs that have been currently licensed for the treatment of AIDS, but their efficacy has been limited by the emergence of drug-resistant HIV variants. Extensive biochemical, genetic, and clinical data about HIV RT enzymatic mechanisms, inhibition, and drug resistance have been reported. This information, taken together with structural data from crystallographic studies of HIV-1 RT, has set the stage for structure-based design of improved inhibitors of this essential viral enzyme. Comparisons of the different crystal structures of HIV-1 RT shows that the enzyme has great conformational flexibility, providing additional possibilities for drug targeting. Recent clinical and virological data suggest that HIV-1 RT enzymes that carry drug-resistance mutations can be substantially impaired and that combinations of RT inhibitors can produce significant clinical benefit in the treatment of AIDS. An immediate goal is to use the available information to design specific inhibitors or combination therapies that will select for relatively less fit HIV variants.

Development of a genus specific primer set for detection of Leishmania parasites by polymerase chain reaction

We have compared the sequences of a major class of kinetoplast DNA (kDNA) minicircle (pLURkE3) of Leishmania strain UR6 with other minicircle sequences from different Leishmania species. Alignment of these sequences allowed the selection of a pair of oligonucleotides suitable as primers in polymerase chain reaction (PCR) which is specific for Leishmania parasites. PCR with this genus-specific primer set is capable of detecting 1 femtogram of kDNA. These primers have been tested with kDNAs from both old world and new world Leishmania species. The results indicate that the primers may be suitable for detection of any kind of leishmaniasis.

Helicobacter pylori eradication--evaluation of triple therapy containing omeprazole

BACKGROUND

There is a need to develop alternative regimen(s) for treating Helicobacter pylori infection because of problems of drug compliance, side-effects and resistance with the conventional regimen consisting of bismuth, metronidazole and an antibiotic.

AIMS

To compare prospectively the efficacy of conventional triple therapy (bismuth subcitrate 120 mg QID, amoxycillin 500 mg QID and metronidazole 400 mg TID for 2 weeks with one containing omeprazole (20 mg OD), bismuth subcitrate and amoxycillin (regimen B).

METHODS

Sixty two consecutive patients with H pylori infection associated with antral gastritis and/or duodenal ulcer were randomized to two treatment groups and re- evaluated after completion of 2 weeks of therapy and then after a further 4 weeks for eradication of H pylori, ulcer healing and drug side-effects.

RESULTS

Regimen B resulted in higher H pylori eradication rate as compared to regimen A (76.7% vs 63.3%, better ulcer healing rate (90.9%, vs 70.6%), lesser side-effects (10.0% vs 36.7%) and better drug compliance (100% vs 93.3%). The difference between the two regimens was significant (p < 0.05) only in respect to side-effects.

CONCLUSION

For H pylori eradication, omeprazole, bismuth and amoxycillin combination for 2 weeks is as effective as the conventional therapy and is better tolerated.

Immunoglobulin levels in populations with low hemoglobin levels: study of five tribes of central India

Average hemoglobin levels for 424 individuals belonging to 5 tribes of central India vary between 10.64 g/dl and 11.30 g/dl among males and between 9.62 g/dl and 9.97 g/dl among females. These ranges indicate the poor state of health and nutrition in these tribes. Three immunoglobulin levels (IgG, IgA, and IgM) measured in a subset of the 424 individuals reveal that immunoglobulin and hemoglobin levels are inversely related to some extent. Levels of all three classes of immunoglobulins were found to be significantly correlated. This suggests that humoral immunity is not impaired even under acute nutritional stress.

Selective killing of cholinergic neurons by microglial activation in basal forebrain mixed neuronal/glial cultures

Microglia activation by lipopolysaccharides (LPS) significantly decreased choline acetyltransferase-immunopositive (ChAT+) neuron number and ChAT activity in rat primary basal forebrain mixed neuronal/glial cultures. The number of non-cholinergic (ChAT(-)) neurons was unaffected. LPS induced nitric oxide synthase (NOS) in microglia, increased the media level of the NO metabolite nitrite, and the NOS inhibitor Ng-nitro-L-arginine methylester (NAME) protected the ChAT+ neurons from LPS. The combination of beta-amyloid peptide (1-42) and interferon-gamma (INF-gamma) also increased the media nitrite level and decreased ChAT+ neuron number. Cholinergic neurons are lost early in the course of Alzheimer's disease, and the enhanced sensitivity of these neurons to microglial activation in mixed neuronal/glial culture may be useful for modeling Alzheimer's disease and developing therapeutic strategies to combat this disease.

Place of transvaginal sonography in the evaluation of reproductive endocrinology

A high frequency vaginal probe with improved resolution offers a remarkable sharp clear image of pelvic organs. This is possible because of its closed proximity with target organ and non-intervention by gut or omentum. Study of ovarian follicular dynamics (folliculometry), identification of proliferative, secretory and decidual changes of endometrium (endometrial dating) in different phases of menstrual cycle and imaging of mucus secretion in the cervical canal (cervical mucus study) in the pre-ovulatory phase is possible by transvaginal probe. It is non-invasive, acceptable to patients, and thus can be repeated any number of times. A close serial monitoring offers immense wealth of information about the anatomical as well as reproductive endocrinal status of the patient. Ovulation can be predicted in advance. The case of dysovulation can be identified in first cycle of study; corrective therapy can be started in another two or three cycles, aiming at achieving perfect folliculogenesis. Once well tuned synchronised cycle is restored, the pregnancy outcome is remarkable. Thus transvaginal sonography offers one of the best reproductive endocrinology evaluation in the hand of a modern gynaecological sonologist and infertility specialist.

Role of transvaginal sonography in pelvic scan for female reproductive system

Three hundred twenty-nine cases of early pregnancy and 116 pelvic pathology studied by transabdominal sonography were compared with 81 cases of early pregnancy and 88 cases of pelvic pathology subjected to transvaginal sonography. A high frequency vaginal probe, because of its close proximity with the target organ, produces remarkably sharp image. An accurate diagnosis is possible in great majority of cases within a short time. Vaginal sonography is done with an empty bladder. A close serial monitoring of ovarian follicles, endometrium and cervical mucus with transvaginal sonography offers an immense wealth of information about the structural and reproductive endocrinal status of the patient. Ovulation can be predicted in advance. Imaging of female reproductive system by transvaginal sonography is indispensable for any modern gynaecological care and for infertility assessment in particular.

Structure of HIV-1 RT/TIBO R 86183 complex reveals similarity in the binding of diverse nonnucleoside inhibitors

We report the structure of HIV-1 reverse transcriptase (RT) complexed with the nonnucleoside inhibitor TIBO R 86183 at 3.0 A resolution. Comparing this structure with those of complexes of HIV-1 RT/alpha-APA R 95845 and HIV-1 RT/nevirapine provides a basis for understanding the nature of nonnucleoside inhibitor binding, the structure of the binding site and the interactions between the bound inhibitors and surrounding amino acid residues as well as for understanding mechanisms of inhibition by and resistance to nonnucleoside inhibitors. All three inhibitors considered assume a similar butterfly-like shape and bind to HIV-1 RT in a very similar way. Important differences occur in the conformation of amino acid residues that form the binding pocket.

Hysteroscopic cannulation for proximal tubal obstruction: a change for the better?

OBJECTIVE

To compare overall the results of hysteroscopic tubal cannulations and resection anastomosis for proximal tubal occlusion.

DESIGN

Nonrandomized retrospective analysis of patients operated on by two surgeons.

SETTING

University and large tertiary referral private practice.

PATIENTS

Seventy-four patients over a 10-year period, with bilateral or unilateral proximal occlusion of a single tube.

INTERVENTIONS

Hysteroscopic cannulation, resection anastomosis, or both.

MAIN OUTCOME MEASURES

Intrauterine and ectopic pregnancy rates, long-term tubal patency, and pathology of tubal segments.

RESULTS

In patients with normal distal tubes, intrauterine pregnancy rates were similar (12/21, 57% versus 12/24, 50%) and ectopic pregnancy rates were lower (0/21, 0% versus 7/24, 29.1%) in the cannulation group. One-year patency rates in nonpregnant patients was higher in the anastomosis group (12/15, 80% versus 3/8, 33%).

CONCLUSIONS

Hysteroscopic cannulation should be first choice in the management of proximal tubal obstructions in selected patients. It may be a treatment option for delayed occlusion after successful cannulation or resection anastomosis.

Structure of HIV-1 reverse transcriptase in a complex with the non-nucleoside inhibitor alpha-APA R 95845 at 2.8 A resolution

BACKGROUND

HIV-1 reverse transcriptase (RT) is a multifunctional enzyme that copies the RNA genome of HIV-1 into DNA. It is a heterodimer composed of a 66 kDa (p66) and a 51 kDa (p51) subunit. HIV-1 RT is a crucial target for structure-based drug design, and potent inhibitors have been identified, whose efficacy, however, is limited by drug resistance.

RESULTS

The crystal structure of HIV-1 RT in complex with the non-nucleoside inhibitor alpha-anilinophenyl-acetamide (alpha-APA) R95845 has been determined at 2.8 A resolution. The inhibitor binds in a hydrophobic pocket near the polymerase active site. The pocket contains five aromatic amino acid residues and the interactions of the side chains of these residues with the aromatic rings of non-nucleoside inhibitors appear to be important for inhibitor binding. Most of the amino acid residues where mutations have been correlated with high levels of resistance to non-nucleoside inhibitors of HIV-1 RT are located close to alpha-APA. The overall fold of HIV-1 RT in complex with alpha-APA is similar to that found when in complex with nevirapine, another non-nucleoside inhibitor, but there are significant conformational changes relative to an HIV-1 RT/DNA/Fab complex.

CONCLUSIONS

The non-nucleoside inhibitor-binding pocket has a flexible structure whose mobility may be required for effective polymerization, and may be part of a hinge that permits relative movements of two subdomains of the p66 subunit denoted the 'palm' and 'thumb'. An understanding of the structure of the inhibitor-binding pocket, of the interactions between HIV-1 RT and alpha-APA, and of the locations of mutations that confer resistance to inhibitors provides a basis for structure-based design of chemotherapeutic agents for the treatment of AIDS.

Linkage disequilibrium and haplotype analysis among Polish families with spinal muscular atrophy

Spinal Muscular Atrophy (SMA) is an inherited degenerative disorder of anterior horn cells that results in progressive muscle weakness and atrophy. The autosomal recessive forms of childhood-onset SMA have been mapped to chromosome 5q11.2-13.3, in a number of studies examining different populations. A total of 9 simple sequence repeat markers were genotyped against 32 Polish families with SMA. The markers span an approximately 0.7 cM region defined by the SMA flanking markers D5S435 and MAP1B. Significant linkage disequilibrium (corrected P < .05) was detected at four of these markers, with D/Dmax values of < or = .89. Extended haplotype analysis revealed a predominant haplotype associated with SMA. The apparently high mutation rate of some of the markers has resulted in a number of haplotypes that vary slightly from this predominant haplotype. The predominant haplotype and these closely related patterns represent 25% of the disease chromosomes and none of the nontransmitted parental chromosomes. This predominant haplotype is present both in patients with acute (type I) and in chronic (types II and III) forms of SMA and occurs twice in a homozygous state, both times in children with chronic SMA.

Ultrastructure of cellular components of human trophoblasts during early pregnancy

Two cell types, the cyto- and syncytio-trophoblasts, were identified in human chorionic villi of 6-10 weeks' gestation. The intracellular organization of these cells was examined. Ultrathin sections of small pieces of chorionic villi revealed the presence of a multinucleate syncytiotrophoblastic layer, whose surface was covered with microvilli. The cytotrophoblasts, however, had a single large nucleus with a prominent nucleolus. An interesting feature of the basement membrane of these cells was the presence of aggregates of dark granules in samples of the earlier gestational age (6-8 weeks) and granular bodies having a dense outer ring and a translucent inner ring with a lucid central area in samples of 8-10 weeks' gestation. Both types of granules are mineralized and are assumed to perform a buffering role for maintaining the neutrality of the layer.

A possible vulnerability locus for bipolar affective disorder on chromosome 21q22.3

In a preliminary genome scan of 47 bipolar disorder families, we detected in one family a lod score of 3.41 at the PFKL locus on chromosome 21q22.3. The lod score is robust to marker allele frequencies, phenocopy rates and age-dependent penetrance, and remains strongly positive with changes in affection status. Fourteen other markers in 21q22.3 were tested on this family, with largely positive lod scores. Five of the other 46 families also show positive, but modest lod scores with PFKL. When all 47 families are analysed together, there is little support for linkage to PFKL under homogeneity or heterogeneity using lod score analysis, but the model-free affected-pedigree-member method yields statistically significant results (p < 0.0003). Our results are consistent with the presence of a gene in 21q22.3 predisposing at least one family to bipolar disorder.

Incidence of neural tube defects of Lucknow over a 10 year period from 1982-1991

Open neural tube defects (NTD) in babies, occurring over a 10 yr period (1982-91), in four major maternity hospitals of Lucknow, were identified to analyse the incidence of this disorder. The overall incidence of NTD was found to be 3.9/1000. It was significantly higher in the teaching hospital compared to non-teaching hospitals. But there was no significant difference in the incidence of NTD between the Government and Private hospitals. During the decade (1982-91) under study there was no decline in NTD births. These data could serve as base-line for the incidence of NTD in north India, as NTD is expected to decline with the introduction of folic acid for the prevention of NTD.

Purification and characterization of bacterially expressed mammalian translation initiation factor 5 (eIF-5): demonstration that eIF-5 forms a specific complex with eIF-2

Eukaryotic translation initiation factor 5, eIF-5, has been purified to apparent electrophoretic homogeneity from overproducing Escherichia coli cells expressing the cDNA of the initiation factor under the control of the T7 promoter-T7 RNA polymerase system. Purified recombinant eIF-5 mimics natural eIF-5 isolated from mammalian cells in size, in specific activity, in its ability to catalyze the hydrolysis of GTP bound to the 40S initiation complex, and in the subsequent joining with 60S ribosomal subunits to form the 80S initiation complex. Further characterization of eIF-5 demonstrates that eIF-5 specifically associates with eIF-2, forming an eIF-2.eIF-5 complex. The protein complex sediments in glycerol gradients with an apparent M(r) of 160,000, suggesting that the two proteins associate in a 1:1 stoichiometry. The association between the two initiation factors is highly specific. Addition of 32P-labeled eIF-5 to a partially purified rabbit reticulocyte initiation factor preparation that contained, in addition to eIF-2 and eIF-5, other initiation factors and many other proteins resulted in the specific binding of labeled eIF-5 only to eIF-2, forming a 160-kDa protein complex. In agreement with these observations, we found that in crude initiation factor preparations derived from rabbit reticulocyte lysates, eIF-5 was present as an eIF-2.eIF-5 complex. The significance of eIF-2.eIF-5 complex formation in the overall mechanism of GTP hydrolysis in protein synthesis initiation is discussed.

Crystal structure of peanut lectin, a protein with an unusual quaternary structure

The x-ray crystal structure of the tetrameric T-antigen-binding lectin from peanut, M(r) 110,000, has been determined by using the multiple isomorphous replacement method and refined to an R value of 0.218 for 22,155 reflections within the 10- to 2.95-A resolution range. Each subunit has essentially the same characteristic tertiary fold that is found in other legume lectins. The structure, however, exhibits an unusual quaternary arrangement of subunits. Unlike other well-characterized tetrameric proteins with identical subunits, peanut lectin has neither 222 (D2) nor fourfold (C4) symmetry. A noncrystallographic twofold axis relates two halves of the molecule. The two monomers in each half are related by a local twofold axis. The mutual disposition of the axes is such that they do not lead to a closed point group. Furthermore, the structure of peanut lectin demonstrates that differences in subunit arrangement in legume lectins could be due to factors intrinsic to the protein molecule and, contrary to earlier suggestions, are not necessarily caused by interactions involving covalently linked sugar. The structure provides a useful framework for exploring the structural basis and the functional implications of the variability in the subunit arrangement in legume lectins despite all of them having nearly the same subunit structure, and also for investigating the general problem of "open" quaternary assembly in oligomeric proteins.

HP, GC and PI polymorphisms in sixteen central Indian tribal populations

HP, GC and PI polymorphisms have been typed on 16 Central Indian tribal populations with a total of 1658 individuals. The distribution of allele frequencies shows a statistically highly significant heterogeneity, which may be caused by several microevolutionary factors, such as genetic drift, social and geographic isolation. Some new variants were observed in both the GC system (GC 2Cmah) and in the PI system (PI Yori). The PI variants are more frequent and are found in most of the 16 populations under study whereas the GC variants are rather infrequent and restricted to only three populations.