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Southwestern College at Winfield
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Hecht D.,Southwestern College at Winfield
Drug Development Research | Year: 2011

(Table Presented) In silico modeling of ADMET property models with QSAR and QSPR models has proven to be an effective approach for increasing the efficiency of small molecule drug discovery and development processes. Development of new, improved models and techniques is currently an active area of research. In recent years, there has been growing interest in adapting tools and techniques from the fields of computational intelligence and machine learning for use in drug discovery and development. This report reviews some of the more popular applications. © 2010 Wiley-Liss, Inc.

Ungar H.,Cabrillo College | Brown D.R.,Southwestern College at Winfield
Journal of Chemical Education | Year: 2010

ChemEd Bridges is an NSF-funded project that provides career and professional development opportunities for chemistry faculty members who teach at two-year colleges (2YCs). We broaden the interests and the horizons of these faculty members by building bridges between them and the broader community of chemical educators. In particular, we have increased the involvement of 2YC faculty in ACS national and regional activities, and we work to strengthen relations between the chemistry faculties of 2YCs and four-year colleges and universities. This report provides an overview of the 2YC student body and faculty, some recent ACS recommendations, and the resources and opportunities that ChemEd Bridges offers. © 2010 The American Chemical Society and Division of Chemical Education, Inc.

Wang C.C.N.,Asia University, Taiwan | Hecht D.A.,Southwestern College at Winfield | Sheu P.C.-Y.,University of California at Irvine | Tsai J.J.P.,Asia University, Taiwan
Proceedings - 2013 IEEE 7th International Conference on Semantic Computing, ICSC 2013 | Year: 2013

Computer-aided drug design methodologies have proven to be very effective, greatly enhancing the efficiency of drug discovery and development processes. In this paper we describe how to integrate complex drug discovery problems and computational solutions via a semantic interface. In particular we describe a Structured Natural Language approach to chemical similarity searches, quantitative structure activity relationship (QSAR) modeling and in silico protein-ligand docking. © 2013 IEEE.

Smith D.E.,San Diego State University | Marquez I.,San Diego State University | Lokensgard M.E.,San Diego State University | Rheingold A.L.,University of California at San Diego | And 2 more authors.
Angewandte Chemie - International Edition | Year: 2015

Many biologically active molecules exist as rapidly interconverting atropisomeric mixtures. Whereas one atropisomer inhibits the desired target, the other can lead to off-target effects. Herein, we study atropisomerism as a possibility to improve the selectivities of kinase inhibitors through the synthesis of conformationally stable pyrrolopyrimidines. Each atropisomer was isolated by HPLC on a chiral stationary phase and subjected to inhibitor profiling across a panel of 18 tyrosine kinases. Notably different selectivity patterns between atropisomers were observed, as well as improved selectivity compared to a rapidly interconverting parent molecule. Computational docking studies then provided insights into the structure-based origins of these effects. This study is one of the first examples of the intentional preorganization of a promiscuous scaffold along an atropisomeric axis to increase target selectivity, and provides fundamental insights that may be applied to other atropisomeric target scaffolds. Rigidified: A series of conformationally stable kinase inhibitors were synthesized, and the effect of atropisomerism on kinase selectivity was assessed. The use of these inhibitors was found to lead to improved selectivity compared with the rapidly interconverting parent compounds. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Hecht D.,Southwestern College at Winfield | Fogel G.B.,Natural Selection Inc.
Journal of Computer-Aided Molecular Design | Year: 2012

Plasmodium falciparum, the causal agent of malaria, continues to evolve resistance to frontline therapeutics such as chloroquine and sulfadoxine-pyrimethamine. Here we study the amino acid replacements in dihydrofolate reductase (DHFR) that confer resistance to pyrimethamine while still binding the natural DHFR substrate, 7,8-dihydrofolate, and cofactor, NADPH. The chain of amino acid replacements that has led to resistance can be inferred in a computer, leading to a broader understanding of the coevolution between the drug and target. This in silico approach suggests that only a small set of specific active site replacements in the proper order could have led to the resistant strains in the wild today. A similar approach can be used on any target of interest to anticipate likely pathways of future resistance for more effective drug development. © 2012 Springer Science+Business Media Dordrecht.

Hecht D.,Southwestern College at Winfield | Fogel G.B.,Natural Selection Inc.
2012 IEEE Symposium on Computational Intelligence and Computational Biology, CIBCB 2012 | Year: 2012

The evolution of drug resistance in malaria continues to be a widespread concern. Many of these drugs target key proteins such as dihydrofolate reductase (DHFR). However in malaria, the structural plasticity of DHFR allows it to maintain its active site and catalytic activity, while resisting drug binding. One way to better understand this process is through the appreciation of DHFR structural evolution in general, and then use in silico evolution to model both the drug docking and the likely amino acid changes in DHFR that will occur as a result. Using a comprehensive phylogenetic analysis of DHFR, we have generated a method that generates variant DHFR proteins and sequentially scores the docking of the natural cofactor NADPH and the known anti-malarial drug pyrimethamine in order to determine fitness. Iteration of this process allows the opportunity to model the coevolutionary processes involved with drug resistance and to predict responses to pharmaceuticals in advance of their use in the field. © 2012 IEEE.

Hecht D.,Southwestern College at Winfield | Tran J.,Brown University | Fogel G.B.,Natural Selection Inc.
Molecular Phylogenetics and Evolution | Year: 2011

The evolution of dihydrofolate reductase (DHFR) was studied through a comprehensive structural-based analysis. An amino acid sequence alignment was generated from a superposition of experimentally determined X-ray crystal structures of wild-type (wt) DHFR from the Protein Data Bank (PDB). Using this structure-based alignment of DHFR, a metric was generated for the degree of conservation at each alignment site - not only in terms of amino acid residue, but also secondary structure, and residue class. A phylogenetic tree was generated using the alignment that compared favorably with the canonical phylogeny. This structure-based alignment was used to confirm that the degree of conservation of active-site residues in terms of both sequence as well as structure was significantly greater than non-active site residues. These results can be used in helping to understand the likely future evolution of DHFR in response to novel therapies. © 2011 Elsevier Inc.

Brown D.R.,Southwestern College at Winfield | Bushey M.,Trinity University
Journal of Chemical Education | Year: 2010

Two-year colleges (2YCs) provide a significant amount of chemical education to undergraduates in the United States. By design, the charge of the 2YCs is to provide coursework at the lower-division level. Nonetheless, general chemistry courses in 2YCs can be enhanced with content to prepare future chemistry majors for upper-division education. The use of instrumentation in the laboratory is particularly well-suited to introduce students to upper-division concepts and ideas. This article illustrates the use of infrared spectroscopy in general chemistry as a means to prepare 2YC students for upper-division experiences they may encounter at their transfer institutions. © 2010 The American Chemical Society and Division of Chemical Education, Inc.

Van Stone M.,Southwestern College at Winfield
Proceedings of the International Astronomical Union | Year: 2011

Examining Ancient Maya notions about prophecies and their calendar cycles, we find that they predicted no 'end of the Maya calendar'. Indeed, surviving texts and art indicate that they seem to have expected no change in the status quo whatever, for at least 4000 years into the future. This search also turned up evidence that different local schools of calendar-priests differed significantly from each other; it is entirely possible that priests in one city expected the End of the World, while their peers elsewhere believed the opposite. © International Astronomical Union 2011.

Agency: NSF | Branch: Standard Grant | Program: | Phase: PROJECTS | Award Amount: 150.00K | Year: 2011

Project iLASER (investigations with Light And Sustainable Energy Resources) will engage children, youth and adults in the Southwest United States in public science education and hands-on activities. The Project iLASER team will visit communities in Chula Vista, CA; El Centro/Brawley, CA; Yuma, AZ; Nogales, AZ; Las Cruces, NM; El Paso, TX; McAllen, TX; and Harlingen, TX. Each two-day or three-day visit will include activities in light and solar energy. Numerous local partners, including Boys and Girls Clubs, YMCAs, science museums, two year colleges, chemistry clubs and individuals will assist. Two particularly critical partners are the Nanoscale Informal Science Education Network (NISE Net) and CCI Solar, a basic research center centered at Caltech. Public lectures on the science and impacts of CCI Solar research will be offered in each community.

Project iLASER is supported by the Division of Chemistry and the Division of Research on Learning, Lifelong Learning Cluster, as part of the celebration of the International Year of Chemistry.

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