Protocols for bridging the peptide to nonpeptide gap in topological similarity searches.

Similarity searches based on chemical descriptors have proven extremely useful in aiding large-scale drug screening. Typically an investigator starts with a "probe", a drug-like molecule with an interesting biological activity, and searches a database to find similar compounds. In some projects, however, the only known actives are peptides, and the investigator needs to identify drug-like actives. 3D similarity methods are able to help in this endeavor but suffer from the necessity of having to specify the active conformation of the probe, something that is not always possible at the beginning of a project. Also, 3D methods are slow and are complicated by the need to generate low-energy conformations. In contrast, topological methods are relatively rapid and do not depend on conformation. However, unmodified topological similarity methods, given a peptide probe, will preferentially select other peptides from a database. In this paper we show some simple protocols that, if used with a standard topological similarity search method, are sufficient to select nonpeptide actives given a peptide probe. We demonstrate these protocols by using 10 peptide-like probes to select appropriate nonpeptide actives from the MDDR database.

Mining the chemical quarry with joint chemical probes: an application of latent semantic structure indexing (LaSSI) and TOPOSIM (Dice) to chemical database mining.

In this study we use a novel similarity search technique called latent semantic structure indexing (LaSSI) with joint chemical probes as queries to mine the MDL drug data report database. LaSSI is based on latent semantic indexing developed for searching textual databases. We use atom pair and topological torsion descriptors in our calculations. The results obtained with LaSSI are compared with another in-house similarity search technique TOPOSIM. The results from the similarity searches using joint chemical probes are significantly better than searches using single chemical probes for both LaSSI and TOPOSIM. The selected molecules are closely related in activity to their queries and are ranked among the top 300 scoring molecules of the 82 860 entries in the database. Our implementation of LaSSI is very fast and efficient in finding active compounds. The results also show that LaSSI consistently retrieves more diverse chemical structures representative of the joint chemical probes in comparison to TOPOSIM. The use of multimolecule topological probes to identify compounds complements the use of searching databases with 3D pharmacophore hypotheses.

Latent semantic structure indexing (LaSSI) for defining chemical similarity.

A novel method for computing chemical similarity from chemical substructure descriptors is described. This new method, called LaSSI, uses the singular value decomposition (SVD) of a chemical descriptor-molecule matrix to create a low-dimensional representation of the original descriptor space. Ranking molecules by similarity to a probe molecule in the reduced-dimensional space has several advantages over analogous ranking in the original descriptor space: matching latent structures is more robust than matching discrete descriptors, choosing the number of singular values provides a rational way to vary the "fuzziness" of the search, and the reduction in the dimensionality of the chemical space increases searching speed. LaSSI also allows the calculation of the similarity between two descriptors and between a descriptor and a molecule.

Chemical similarity searches using latent semantic structural indexing (LaSSI) and comparison to TOPOSIM.

Similarity searches based on chemical descriptors have proven extremely useful in aiding large-scale drug screening. Here we present results of similarity searching using Latent Semantic Structure Indexing (LaSSI). LaSSI uses a singular value decomposition on chemical descriptors to project molecules into a k-dimensional descriptor space, where k is the number of retained singular values. The effect of the projection is that certain descriptors are emphasized over others and some descriptors may count as partially equivalent to others. We compare LaSSI searches to searches done with TOPOSIM, our standard in-house method, which uses the Dice similarity definition. Standard descriptor-based methods such as TOPOSIM count all descriptors equally and treat all descriptors as independent. For this work we use atom pairs and topological torsions as examples of chemical descriptors. Using objective criteria to determine how effective one similarity method is versus another in selecting active compounds from a large database, we find for a series of 16 drug-like probes that LaSSI is as good as or better than TOPOSIM in selecting active compounds from the MDDR database, if the user is allowed to treat k as an adjustable parameter. Typically, LaSSI selects very different sets of actives than does TOPOSIM, so it can find classes of actives that TOPOSIM would miss.

Port-access minimally invasive cardiac surgery increases surgical complexity, increases operating room time, and facilitates early postoperative hospital discharge.

BACKGROUND: Proposed advantages of port-access cardiac surgery have yet to be substantiated. The authors retrospectively compared patients undergoing port-access cardiac surgery with a matched group undergoing conventional cardiac surgery. METHODS: Forty-six patients who underwent port-access cardiac surgery were matched with 46 who underwent conventional cardiac surgery. Absolute criteria for matching included morning-of-surgery admission, procedure undergone, and care being delivered by one of two surgeons. If possible, matching included care delivered by one of two anesthesiologists. Patients were matched as closely as possible for preoperative demographic and clinical characteristics. RESULTS: All 46 pairs of patients were matched for procedure and admitted the morning of surgery. All 92 operations were performed by one of two surgeons, and 89% were performed by one of two anesthesiologists. Preoperative demographic and clinical characteristics were equivalent between groups. Compared with conventional cardiac surgery, port-access cardiac surgery increased surgical complexity (it almost tripled cardiopulmonary bypass time during coronary artery bypass grafting and increased it almost 40% during mitral valve procedures) and increased total operating room time (P < 0.0001). Port-access cardiac surgery had no beneficial effect on earlier postoperative extubation, decreased incidence of atrial fibrillation, or intensive care unit time, yet it decreased postoperative duration of stay (P = 0.029, all patients), a benefit observed primarily in patients undergoing coronary artery bypass grafting (P = 0.002). CONCLUSIONS: This retrospective analysis revealed that port-access cardiac surgery increases surgical complexity, increases operating room time, has no effect on earlier postoperative extubation or decreased incidence of atrial fibrillation or intensive care unit time, and may facilitate postoperative hospital discharge (primarily in patients undergoing coronary artery bypass grafting). Properly designed prospective investigation is necessary to ascertain whether port-access cardiac surgery truly offers any benefits over conventional cardiac surgery.

Effect of topical local anesthetic application to skin harvest sites for pain management in burn patients undergoing skin-grafting procedures.

OBJECTIVE: To determine if topical administration of local anesthesia, applied to fresh skin-harvest sites, reduces pain and analgesic requirements after surgery. SUMMARY BACKGROUND DATA: Nonopioid treatments for pain after therapeutic procedures on patients with burns have become popular because of the side effects associated with narcotics. The topical administration of local anesthesia originally offered little advantage because of poor epidermal penetration. METHODS: This study compares 2% lidocaine with 0.5% bupivacaine or saline, topically applied after skin harvest, to determine what effect this may have on pain and narcotic use. Sixty patients with partial- or full-thickness burns to approximately 10% to 15% of their body were randomly divided into three groups: group 1 received normal saline, group 2 had 0.5% bupivacaine, and group 3 had 2% lidocaine sprayed onto areas immediately after skin harvest. Blood samples were subsequently obtained to measure concentrations of the local anesthetic. Hemodynamic variables after surgery, wake-up times, emetic symptoms, pain, and narcotic use were compared. RESULTS: Higher heart rates were noted in the placebo group than in those receiving lidocaine or bupivacaine. No differences were noted in recovery from anesthesia or emetic symptoms. Pain scores were lower and 24-hour narcotic use was less in patients who received lidocaine. Plasma lidocaine levels were greater than bupivacaine at all time points measured. CONCLUSIONS: Topical lidocaine applied to skin-harvest sites produced an analgesic effect that reduced narcotic requirements compared with patients who received bupivacaine or placebo. Local anesthetic solutions aerosolized onto skin-harvest sites did not affect healing or produce toxic blood concentrations.

Intrathecal morphine for coronary artery bypass grafting and early extubation.

Aggressive control of pain during the immediate postoperative period after cardiac surgery with early tracheal extubation may decrease morbidity and mortality. This prospective, randomized, double-blinded, placebo-controlled clinical study examined the use of intrathecal morphine in patients undergoing cardiac surgery and its influence on early tracheal extubation and postoperative analgesic requirements. Patients were randomized to receive either 10 micrograms/kg of intrathecal morphine (n = 19) or intrathecal placebo (n = 21). Perioperative anesthetic management was standardized (intravenous (IV) fentanyl, 20 micrograms/kg, and IV midazolam, 10 mg) and included postoperative patient-controlled morphine analgesia. Of the patients who were tracheally extubated during the immediate postoperative period, the mean time from intensive care unit arrival to extubation was significantly prolonged in patients who received intrathecal morphine (10.9 h) when compared to patients who received intrathecal placebo (7.6 h). Three patients who received intrathecal morphine had extubation substantially delayed because of prolonged ventilatory depression. Although mean postoperative IV morphine use for 48 h was less in patients who received intrathecal morphine (42.8 mg) when compared to patients who received intrathecal placebo (55.0 mg), the difference between groups was not statistically significant. In conclusion, intrathecal morphine offers promise as a useful adjunct in controlling postoperative pain in patients after cardiac surgery. However, the optimal dose of intrathecal morphine in this setting, along with the optimal intraoperative baseline anesthetic that will provide significant analgesia, yet not delay extubation in the immediate postoperative period, remains to be elucidated.

rRNA operon restriction derived taxa for Streptomyces (RiDiTS).

A method for grouping Streptomyces strains by fingerprints of their rRNA operons is described. In polyacrylamide gels, multicopy rRNA operon fragments in Streptomyces genomic MseI fingerprints produced intense bands which are well resolved from the less conspicuous low copy fragments interspersed between them. The high intensity multicopy rRNA bands are easily distinguished from the low intensity bands, eliminating the need for Southern blot hybridization to visualize the rRNA fragments. Direct evidence that the high-intensity bands in these polyacrylamide gels originated from rRNA operons was provided by a 'differential' Southern blot technique. We have used this method to assign 98 strains to 11 rRNA fingerprint type groups. This clustering method may be applicable to any prokaryote with a high G+C content genome.

Structure of human neutrophil elastase in complex with a peptide chloromethyl ketone inhibitor at 1.84-A resolution.

Human neutrophil elastase (HNE) has been implicated as a major contributor to tissue destruction in various disease states, including emphysema. The structure of HNE, at neutral pH, in complex with methoxysuccinyl-Ala-Ala-Pro-Ala chloromethyl ketone (MSACK), has been solved and refined to an R factor of 16.4% at 1.84-A resolution. Results are consistent with the currently accepted mechanism of peptide chloromethyl ketone inhibition of serine proteases, in that MSACK cross-links the catalytic residues His-57 and Ser-195. The structure of the HNE-MSACK complex is compared with that of porcine pancreatic elastase in complex with L-647,957, a beta-lactam inhibitor of both elastases. The distribution of positively charged residues on HNE is highly asymmetric and may play a role in its specific association with the underlying negatively charged proteoglycan matrix of the neutrophil granules in which the enzyme is stored.