J. Phillip Bowen

Design, synthesis, and biological evaluation of angiogenesis inhibitors: aromatic enone and dienone analogues of curcumin

The quest to find new antitumor compounds is an ongoing research endeavor in many laboratories around the world. The use of small-molecule angiogenesis inhibitors promises to be a potentially effective method for cancer treatment and possible prevention. Many antiangiogenic compounds are in various stages of laboratory evaluations and clinical trials. Curcumin is a natural product that has exhibited potent antiangiogenic properties. Based on a simple pharmacophore model, using standard drug design concepts, aromatic enone and aromatic dienone analogues of curcumin were prepared and/or obtained commercially. These compounds were screened for antiangiogenic properties via an in vitro SVR assay and were found to inhibit cell proliferation.

Novel furano analogues of duocarmycin C1 and C2: design, synthesis, and biological evaluation of seco-iso-Cyclopropylfurano[2,3-e]indoline (seco-iso-CFI) and seco-Cyclopropyltetrahydrofurano[2,3-f]quinoline (seco-CFQ) analogues

The design, synthesis and biological evaluation of novel seco-iso-cyclopropylfurano[2,3-e]indoline (seco-iso-CFI) and the seco-cyclopropyltetrahydrofurano[2,3-f]quinoline (seco-CFQ) analogues of the duocarmycins are described. These novel analogues (4-7) were designed on the premise that the lone pair of electrons on the furano-oxygen atom could enter into conjugation with the isocyclopropylfurano[e]indolone (iso-CFI) alkylating moiety, formed from the loss of HCl in compounds 4-7. The seco-iso-CFI DNA alkylating pharmacophore was synthesized through a well precedented approach of 5-exo-trig aryl radical cyclization with a vinyl chloride. In our studies, in addition to the formation of the seco-iso-CFI product, an equal amount of an unexpected seco-CFQ product was also generated during the radical cyclization reaction. Like CC-1065 and adozelesin, using Taq DNA polymerase stop and thermal cleavage assays, the seco-iso-CFI compounds (4 and 6) and the seco-CFQ compounds (5 and 7) were shown to preferentially alkylate the adenine-N3 position within the minor groove of long stretches of A residues. A MM2 energy optimized molecular model of a 1:1 complex of compound 6 with DNA reveals that the iso-CFI compound fits snugly within the minor groove. Using a MTT based experiment, the cytotoxicity of compounds 4-7 were determined against the growth of murine leukemia (L1210), mastocytoma (P815) and melanoma (B16) cell lines. The concentrations of compounds required to inhibit the growth of these tumor cells by 50% is in the range of 10(-8)M. These compounds were also tested against a panel of human cancer cells by the National Cancer Institute, demonstrating that the compounds exhibited a high level of activity against selected solid tumors. At a concentration of 0.0084 microM (based on the IC(50) of compound 17 (seco-CBI-TMI) against the growth L1210 cells), while compounds 4 and 17 were toxic against murine bone marrow cells as judged by a colony forming study of freshly isolated murine progenitor hematopoeitic cells, compound 5, a seco-CFQ compound, was significantly less toxic. Flow cytometric analysis of P815 cells that had been incubated for 24h with compounds 4 and 5 at their cytotoxic IC(50) concentrations indicated the induction of apoptosis in a large percentage of cells, thereby suggesting that this might be the mechanism by which the iso-CFI compounds kill cells.

Parameter analysis and refinement toolkit system and its application in MM3 parameterization for phosphine and its derivatives

The multiparameter multistep relaxation (MPMSR) method, a routine within a new suite of parameterization programs entitled parameter analysis and refinement toolkit system (PARTS), was developed to assist in the development of molecular mechanics (MM3 and MM2) force field parameters and represents an ongoing effort in our laboratories to generate more accurate force fields in shorter times. In contrast to other computerized parameterization approaches, this method simulates intuition guided trial‐and‐error and has been used successfully within our laboratories to develop MM2 and MM3 force fields. The primary aim of this approach is to minimize human inspection time and effort, with simultaneous improvement in the efficiency and accuracy of the parameterization process. In an effort to validate the generality of the MPMSR method, a well parameterized data set of phosphine derivatives was reexamined. With the identical set of training molecules used in the original MM3 phosphine parameterization and with minimal human intervention, MPMSR shortened the process from several months to approximately five days. Although the previous phosphine force field is well parameterized, the newly generated MPMSR set of parameters has achieved an overall better fit to the experimentally observed data and ab initio calculations.

Ab initio calculations and molecular mechanics (MM3) force field development for sulfonamide and its alkyl derivatives

Abstract Sulfonamide and eight of its alkyl derivatives were studied with ab initio calculations ( gaussian 94) at the MP2/6–31 + G∗ level of theory. Based on the theoretically calculated geometries and vibrational spectra, and on torsional energy profiles, MM3 force field parameters have been developed that accurately simulate the behavior of this class of compound. The Parameter Analysis and Refinement Toolkit System (PARTS) has been shown to provide a convenient approach for molecular mechanics parameterization and is used in this study to quickly generate MM3 parameters. Using this new set of parameters, MM3 reproduces well the ab initio results for all nine molecules within the training set in terms of both geometrical data and vibrational frequencies.

Comparative molecular field analysis and molecular modeling studies of 20-(S)- camptothecin analogs as inhibitors of DNA topoisomerase I and anticancer/antitumor agents

Conformational studies and comparative molecular field analysis (CoMFA) were undertakenfor a series of camptothecin (CPT) analogs to correlate topoisomerase I inhibition with thesteric and electrostatic properties of 32 known compounds. The resulting CoMFA modelshave been used to make predictions on novel CPT derivatives. Using the newly derived MM3parameters, a molecular database of the 32 CPT analogs was created. Various point atomiccharges were generated and assigned to the MM3 minimized structures, which were used inpartial least-squares analyses. Overall, CoMFA models with the greatest predictive validitywere obtained when both the R- and S-isomers were included in the data set, andsemiempirical charges were calculated for MM3 minimized low-energy lactone structures. Across-validated R2 of 0.758 and a non-cross-validated R2 of 0.916 were obtained for MM3minimized structures with PM3 ESP charges for the 32 CPT analogs. The derived QSARequations were used to assign topoisomerase I inhibition values for compounds in this studyand compounds not included in the original data set. Prior to its appearance in the literature,an IC50 of 103 nM was predicted for the 10,11-oxazole derivative. This CoMFA predictedvalue compared favorably with the recently reported value of 150 nM. The CoMFA modelwas also evaluated by predicting the activities of recently reported 11-aza CPT and trionederivatives. The predicted activity (IC50 = 249 nM) for 11-aza CPT compared well with thereported value of 383 nM.

An efficient synthesis of 2-aryl and 2-alkenyl-3-alkoxy-cyclohexenones by a modified Stille reaction

Abstract A general direct procedure for the synthesis of 2-aryl and 2-alkenyl-3-alkoxy-cyclohexenones using a modified Stille coupling is described.

MOLECULAR MECHANICS STUDIES OF ACYL HALIDES : I. MOLECULAR STRUCTURES AND CONFORMATIONAL ANALYSIS

A new molecular mechanics (MM3) force field has been developed based on various experimental data as well as ab initio calculations. Computer‐generated molecular structures and energy values were compared with experimentally determined data. The acyl halides studied were formyl halides, acetyl halides, propionyl halides, n‐butyryl halides, 2‐methylpropionyl halides, and 2,2‐dimethylpropionyl halides. The rms deviations were 0.005 Å and 1.06° for bond lengths and bond angles, respectively. MM3 was in good overall agreement with the available structural, conformational, and thermodynamic data. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1370–1386, 1998

Computer‐Assisted Molecular Modeling: Indispensable Tools for Molecular Pharmacology

Ball‐and‐stick mechanical models, typically associated with chemists, have been helpful in understanding structural problems and the relationship between structure and biologic activity. With progress in computer speed, graphics performance, and software innovation, molecules of biological interest can be subjected to rigorous calculations. Computational chemistry and biology are rooted in the belief that theoretical physics can be used to calculate accurate molecular structures. Although in its infancy, computer‐assisted molecular modeling is gaining attention and acceptability as an increasing number of researchers turn their attention toward rational molecular design. The trend to use theoretical methods can be traced to the greater availability of computer graphics workstations, decreasing computer costs, faster central processing units, more robust algorithms, and “user‐friendly” software codes. Every major pharmaceutical company has invested in these resources to reduce the time it takes to design and develop pharmaceutical agents. Because of the vast financial and manpower investments needed to introduce a single drug, medicinal chemists and pharmacologists are interested in understanding and predicting drug action at the molecular level. Although drug action is still poorly understood, molecular modeling should reduce some of the labor in the development of pharmaceutical agents.

Solenopsin A and analogs exhibit ceramide-like biological activity

Background(−)-Solenopsin A is a piperidine alkaloid that is a component of the venom of the fire ant Solenopsis invicta. Previously, we have demonstrated that solenopsin exhibit anti-angiogenic activity and downregulate phosphoinositol-3 kinase (PI3K) in the p53 deficient renal cell carcinoma cell line 786-O. Solenopsin has structural similarities to ceramide, a major endogenous regulator of cell signaling and cancer therapy induced apoptosis.MethodsDifferent analogs of solenopsin were synthesized in order to explore structure-activity relationships. The anti-proliferative effect of solenopsin and analogs was tested on six different cell lines, including three tumor cell lines, two normal cutaneous cell lines, and one immortalized hyperproliferative cell line. FRET-based reporters were used to study the affect of solenopsin and analogs on Akt activity and PDK1 activation and sucrose density gradient fractionation was performed to examine recruitment of PTEN to membrane rafts. Western-blotting was used to evaluate the affect of solenopsin and analogs on the Akt and the MAPK 44/42 pathways in three different tumor cell lines. Measurement of cellular oxygen consumption rate together with autophagy staining was performed to study mitochondrial function. Finally, the affect of solenopsin and analogs on ROS production was investigated.ResultsIn this paper we demonstrate that solenopsin analogs with potent anti-proliferative effects can be synthesized from inexpensive dimethylpyridines. To determine whether solenopsin and analogs act as ceramide analogs, we examined the effect of solenopsin and analogs on two stereotypic sites of ceramide activity, namely at lipid rafts and mitochondria. We found that native solenopsin, (−)-solenopsin A, inhibits functional Akt activity and PDK1 activation in lipid rafts in a similar fashion as ceramide. Both cis and trans analogs of solenopsin reduce mitochondrial oxygen consumption, increase reactive oxygen, and kill tumor cells with elevated levels of Akt phosphorylation. However, only solenopsin induces mitophagy, like ceramide.ConclusionsThe requirements for ceramide induced mitophagy and inhibition of Akt activity and PDK1 activation in lipid rafts are under strict stereochemical control. The naturally occurring (−)-solenopsin A mimic some of the functions of ceramide and may be therapeutically useful in the treatment of hyperproliferative and malignant disorders of the skin, even in the presence of elevated levels of Akt.

The Impact of Ionization States of Matrix Metalloproteinase Inhibitors on Docking-Based Inhibitor Design

The influence of ionization states of hydroxamates and retrohydroxamates and the presence of zinc ions in the active site were investigated using the wild-type and E402Q mutant of MMP-9. The deprotonated hydroxamates showed a significantly enhanced enrichment factor in the presence of zinc ions. A pharmacophore model was developed based on the deprotonated compounds and was used to identify four structurally diverse compounds with antiproliferative activities.