Resiniferatoxin-amide and analogues as ligands for protein kinase C and vanilloid receptors and determination of their biological activities as vanilloids

The naturally occurring diterpene resiniferatoxin (RTX) is an ultrapotent analogue of capsaicin. Acting on polymodal afferent neurons, RTX induces a generally similar pattern of responses as does capsaicin. However, the two compounds, as well as other vanilloid derivatives, display different relative potencies for different responses. In the present study, we examined the vanilloid-like activities of two new derivatives, the amide analogue of RTX and phorbol 12,13-dibenzoate 20-homovanillylamide. Structurally, RTX-amide resembles capsaicin more closely than does RTX, and after cleavage of the amide bond the resulting amine would be predicted to not bind to protein kinase C in contrast to resiniferonol 9,13,14-orthophenylacetate, the parent diterpene of RTX. In contrast to our expectations the binding potency of the RTX-amide for the vanilloid receptor present in rat spinal cord was 450-fold lower than that of RTX (Ki values for the RTX-amide and RTX were 10.4 +/- 0.7 nM and 23.1 +/- 3.2 pM, respectively). In the case of phorbol 12,13-dibenzoate 20-homovanillylamide, there was a further loss of affinity for the vanilloid receptor compared with RTX; nonetheless, the Ki (8.56 +/- 0.61 microM) was comparable with that of capsaicin (5.31 +/- 0.37 microM). Computer fitting of the binding data yielded Hill coefficient values of 2.25 +/- 0.03, 2.33 +/- 0.03, and 1.84 +/- 0.05 for RTX, RTX-amide, and phorbol 12,13-dibenzoate 20-homovanillylamide, respectively, indicating that both new compounds induced apparent positive cooperativity among vanilloid binding sites.(ABSTRACT TRUNCATED AT 250 WORDS)

Conformational changes of small molecules binding to proteins

Flexible molecules change their conformation upon binding to a protein. This was shown by the analysis of small molecules whose structures have been determined by X-ray crystallography of both the pure compound and the compound bound to a protein. Thirty-three compounds present both in the Cambridge Structural Database and the Brookhaven Protein Data Bank were analyzed, and both were compared with the global energy minimum conformation calculated by the molecular mechanics program CHARMm. It was found that the conformation bound to the protein differs from that in the crystal structure and also from that of the global energy minimum, and the degree of deformation depends upon the number of freely rotatable bonds in the molecule. Analysis of the conformational energies of the flexible molecules showed that, for most of those compounds, both the crystal and the protein-bound conformations are energetically well above the global minimum, and, in many cases, not even in any local energy minimum. Semi-empirical calculations performed for a select number of structures, using both the AM1 and PM3 hamiltonians, confirmed these results. These findings are discussed as to their impact upon contemporary methods of drug design.

The discovery of novel, structurally diverse protein kinase C agonists through computer 3D-database pharmacophore search. Molecular modeling studies

A computer protein kinase C (PK-C) pharmacophore search on 206,876 nonproprietary structures in the NCI 3D-database led to the discovery of five compounds which were found to possess PK-C binding affinities in the low micromolar range and six others having detectable, but marginal, binding affinities. Molecular modeling studies showed that in addition to the presence of the defined pharmacophore, hydrophobicity and conformational energy are the two other important factors determining the PK-C binding affinity of a compound. The modeling results were confirmed by synthetic modification of two inactive compounds, producing two active derivatives. These newly discovered, structurally diverse lead compounds are being used as the basis for further synthetic modifications aimed at more potent PK-C ligands that will compete with the phorbol esters.

Graph theory and group contributions in the estimation of boiling points

Estimation of normal boiling points of organic compounds using a group contribution method is known to be unsatisfactory and an attempt has been made to improve the accuracy of the estimations by including chemical graph information in the regressions. This leads to a measurable improvement in the results obtained for both a set of 63 alcohols and also a set of 541 structurally diverse organic compounds. This new approach was found to have better predictive ability than the group contribution approach both in the cross-validation tests and in predicting the normal boiling points for 32 new compounds.

National Cancer Institute Drug Information System 3D database

A searcheable database of three-dimensional structures has been developed from the chemistry database of the NCI Drug Information System (DIS), a file of about 450,000 primarily organic compounds which have been tested by NCI for anticancer activity. The DIS database is very similar in size and content to the proprietary databases used in the pharmaceutical industry; its development began in the 1950s; and this history led to a number of problems in the generation of 3D structures.

Protein kinase C. Modeling of the binding site and prediction of binding constants

A detailed examination of the mode of binding of phorbol esters to protein kinase C led to a model of the phorbol binding site in the enzyme. The efficacy with which various synthetic diacylglycerol analogs and ribonolactones are able to bind to this site was determined by means of semiempirical quantum mechanical calculations using PM3, and an estimate of the binding energy was made in each case. Sixteen synthetic analogs of 1,2-diacylglycerol and two natural products were studied, and their calculated energies of binding to this model were correlated with the measured Ki values. The binding energies calculated for this receptor model, together with solubility and entropy considerations, allow prediction through regressive fit of free energies of binding which correlate very well with the measured binding constants.

Applications of computers to toxicological research

Computers are used in toxicology in two ways. They are able to manage and manipulate large amounts of data, and it is because of this that they are used quite commonly to search toxicity databases. The mechanical ability of computers has led a number of organizations to pursue their use in regulatory compliance. The cost-benefit aspect of this issue being what it is, much more effort can be expected in this area. The other major use of computers has been to support efforts to predict or estimate toxicity properties. This task has proven to be very difficult, as was expected, and progress has been mixed. Developers of systems, testing their own development, report impressive accuracy, as has been seen. The "real world" view is less felicitous. In a highly publicized, head-to-head test of some of the computer methods against human experts, accurate prediction of carcinogenicity by computer was achieved for 49-59% of the compounds, depending upon the method used. The humans, on the other hand, scored between 65% and 84%. A conclusion that could be drawn from this experiment is that with compounds which "obviously" are or are not carcinogenic, both computers and humans score well. Once obviousness recedes however, both are at a disadvantage, but humans can improvise more effectively. As research continues, the computer methods will develop better learning sets, and so there will be incremental improvements in their performance.(ABSTRACT TRUNCATED AT 250 WORDS)

Chem-X and CAMBRIDGE. Comparison of computer generated chemical structures with X-ray crystallographic data

The structures of a number of molecules as determined by X-ray crystallography have been compared with the structures for the same molecules as calculated by the 3D structure generation program, Chem-X. In the group of molecules examined, ChemModel produced structures that were essentially identical to those based upon X-ray data in 57% of the cases. The corresponding figure for the widely used alternative model builder, CONCORD, was 38%. The superior performance of ChemModel was due entirely to that program's ability to generate multiple structures covering the entire conformational space.

QSAR of conformationally flexible molecules: comparative molecular field analysis of protein-tyrosine kinase inhibitors

Comparative Molecular Field Analysis (CoMFA) has been applied to a study of quantitative structure-activity relationships (QSAR) of conformationally flexible molecules. The relationship between three-dimensional structure and activity of 20 styrene derivatives which inhibit protein-tyrosine kinase was determined. A technique was developed that allows accurate prediction of the inhibitory activity of these molecules and identification in each case of the active conformation. The problem of multiple energetically acceptable conformations was approached in an iterative procedure. Use was made of the varying degrees of symmetry among the molecules. First, CoMFA QSAR models were developed using only those compounds that possess a symmetrical substituent pattern on the phenyl ring. These CoMFA models were then used to select the active conformers of the less symmetrical compounds in the set. Allowing multiple conformers for each compound in the dataset yielded higher crossvalidated r2 values and better predictivity of the QSAR models. Different probe atoms (C+, O-, neutral C) were explored, the O- probe atom exhibiting the highest selectivity in the conformer selection process.

A ring-enlarged oxetanocin A analogue as an inhibitor of HIV infectivity

Two ring-expanded analogues (compounds 2 and 3) of the anti-HIV fermentation product oxetanocin A (1) were synthesized from commercially available diacetone D-glucose. Antiviral testing against HIV in ATH8 cells revealed that the ring-expanded analogue 2 possessed a similar activity profile as oxetanocin A. Neither compound, however, was capable of providing full protection to the cells against HIV infection. The isomeric ring-expanded analogue 3 was totally devoid of anti-HIV activity. Molecular modeling suggested that while oxetanocin A and compounds 2 and 3 share a large common substructure with the potent anti-HIV drug, dideoxyadenosine (ddA), the extra hydroxymethyl substituent may contribute negatively to the binding of these molecules to a critical enzyme. The negative contribution may be less important in oxetanocin and isomer 2 than in isomer 3. From these studies it would appear that both oxetane and tetrahydrofuran rings are equivalent templates to support the adenine base in terms of anti-HIV activity.

The NCI Drug Information System. 3. The DIS Chemistry Module

The Chemistry Module of the Drug Information System (DIS) handles a database of 400,000 structures. New or modified records are created in this database on a daily basis and are merged into the file promptly. The Chemistry database is searchable in a wide variety of ways and provides novel methods for both input and output of chemical structures.

The NCI Drug Information System. 2. DIS Pre-Registry

The Pre-Registry Module of the Drug Information System (DIS) is a staging area through which all new compounds are passed prior to acquisition and testing. Several methods are available for the entry of structures into the Pre-Registry; all involve built-in data validation. Newly entered structures are examined by computer programs for structural novelty and potential for anticancer activity. For those compounds that proceed to acquisition, the various acquisition steps, such as letter writing and record updating, are performed automatically. When a sample is obtained, the entire Pre-Registry record is updated and moved forward into the permanent DIS chemistry files.

The NCI Drug Information System. 4. Inventory and Shipping Modules

The Inventory/Shipping package of the NCI Drug Information System (DIS) is designed to support all inventory and shipping operations associated with the testing by the NCI of large numbers of chemicals for anticancer activity. Two major databases, an Inventory database and a Shipping History database, contain all of the data associated with these operations. Software that supports the operations in an online interactive manner also provides for the accessing and updating of these databases as necessary. Special hardware in the form of barcode reader/printers and digital balances is also interfaced to the system to improve the efficiency of the operations.

The NCI Drug Information System. 6. System maintenance

The NCI Drug Information System (DIS) is a collection of 24 interactively searchable databases which contain all the data associated with NCI's drug screening program. Data flow into all of these databases upon a daily basis, and maintenance procedures have been developed which provide a high degree of currency to the files. An extensive security system controls both write access and read access to the DIS and matches both to the authorization possessed by each specific user. Detailed usage statistics are collected automatically. The cost of the overall system in terms of both manpower and machine time is discussed briefly.

The NCI Drug Information System. 5. DIS Biology Module

The NCI drug screening program tests over 10,000 chemicals per year for activity against cancer. The associated Drug Information System (DIS) captures all the raw testing data and provides for its validation. The large quantity of numeric data gathered during testing is maintained within the DIS in a database that is interactively searchable and automatically updated at regular intervals.

The NCI Drug Information System. 1. System overview

An interactive computer system has been designed to handle all the data associated with the National Cancer Institute's (NCI) drug screening program. The system resides on the NIH DEC System 10 computers and allows interactive access to the entire NCI screening data system. This contains over 20 separate databases, including a chemistry file of about 400,000 structures and a biology file of approximately 1.5 million test records. New compounds and test data are added daily to the files, and the system also controls and records all the daily operations of the screening program, such as acquisition, shipping, and biological testing of chemicals.

Toxicities derived from anti-tumor screening data

A recent study published by the National Academy of Sciences emphasized an acute shortage of data on the toxic effects of chemicals in man and animals. This shortage makes risk assessment difficult and impacts seriously on the development of a sound environmental policy. The National Cancer Institute, in its search for effective anti-cancer agents, has determined quantitative as well as qualitative toxicities for a large number of chemicals. Probit analysis was used to derive lethalities (LD50s) from data obtained in the process of testing anti-cancer agents in mice. These data were compared with those derived from testing those same agents in normal mice and it was found that a correlation exists between the two toxicities. Toxicities derived from NCI testing in normal animals were compared with published values and a similar correlation was found. LD50s were derived for all compounds tested in normal mice as well as those tested in mice bearing L1210 and P388 lymphocytic leukemias. Over 32,000 LD50s were derived for 22,597 unique compounds.

Development of a chemical information system

The 10-year history of the development of the NIH-EPA Chemical Information System is described. The System grew from the cooperative efforts of several agencies of the federal government and now is publicly available on a fee-for-service basis on computers in the private sector.

Environmental uses of the NIH-EPA chemical information system

A publicly accessible computer system for chemical information has been developed jointly by a number of agencies of the U.S. government. The system contains spectroscopic, crystallographic, toxicological, and regulatory data for more than 200,000 chemicals. The entire data base may be searched for a particular chemical structure or substructure, whose properties may then be retrieved. Alternatively, searching with numeric properties data is possible, permitting the identification of chemicals. Access is by local telephone call, and the system is used on a fee-for-service basis by organizations in over 20 countries. An important application of the system is to problems of chemical pollution.

A computer-based toxicology search system

An interactive computer search system, based on the National Institute for Occupational Safety and Health's Registry of Toxic Effects of Chemicals (NIOSH-RTECS) has been developed. This system permits the location and retrieval of specified toxicity data defined by test animal, dosage method, toxicity level, and compound identity. All available toxicity data for a given chemical substance, identified by name or structure, may be retrieved using either the Chemical Abstracts Service (CAS) Registry Number or the RTECS Accession Number for that compound. The search system is running upon an international computer network, and may be used by anyone interested on a fee-for-service basis.

Mass spectra of some specifically deuterated tryptamines

The mass spectra of the four tryptamine derivatives, N-acetyl-5-methoxytryptamine (melatonin), N-acetyl-5-hydroxytryptamine (N-acetyl-serotonin), N,N-dimethyl-5-hydroxtryptamine (bufotenine) and N,N-dimethyl-5-methoxytryptamine (O-methylbufotenine), with specifically labeled [D4] aminoethyl sidechains have been measured. Comparison of these spectra with those of the unlabeled compounds enable the major fragmentations of the compounds to be defined.