Biomedical subjects

Richard Kho

Publications and source records attributed to Richard Kho.

5 recordsLinked to original sources

PubMed2005

Ring systems in mutagenicity databases.

The distribution of ring systems in public mutagenicity databases is analyzed. An automated enumeration of substructures permits determination of the occurrence of different scaffolds in data sets. The counts are used to perform population analysis via proportions and odds ratios of mutagenic compounds. Pairwise calculations of odds ratios between scaffolds allow comparison of ring systems for isostere replacement studies. These findings are presented in tables that readily show which scaffold is likely to occur in mutagenic compounds. Also, rings identified in public domain mutagenicity data sets are compared to rings in drugs data sets; unfortunately, public mutagenicity data sets do not reflect the types of scaffolds in drugs and those typically used in medicinal chemistry. The findings bring into question the utility of predictive models that were derived from public domain data sets. The automated ring identification and statistical approaches used here can be applied to other pharmacological properties to yield information about chemical scaffolds.

Confidence Intervals↗

PubMed2004

Systems-based design of bi-ligand inhibitors of oxidoreductases: filling the chemical proteomic toolbox.

Genomics-driven growth in the number of enzymes of unknown function has created a need for better strategies to characterize them. Since enzyme inhibitors have traditionally served this purpose, we present here an efficient systems-based inhibitor design strategy, enabled by bioinformatic and NMR structural developments. First, we parse the oxidoreductase gene family into structural subfamilies termed pharmacofamilies, which share pharmacophore features in their cofactor binding sites. Then we identify a ligand for this site and use NMR-based binding site mapping (NMR SOLVE) to determine where to extend a combinatorial library, such that diversity elements are directed into the adjacent substrate site. The cofactor mimic is reused in the library in a manner that parallels the reuse of cofactor domains in the oxidoreductase gene family. A library designed in this manner yielded specific inhibitors for multiple oxidoreductases.

Animals↗

PubMed2003

A path from primary protein sequence to ligand recognition.

A novel method to organize protein structural information based solely on sequence is presented. The method clusters proteins into families that correlate with the three-dimensional protein structure and the conformation of the bound ligands. This procedure was applied to nicotinamide adenine dinucleotide [NAD(P)]-utilizing enzymes to identify a total of 94 sequence families, 53 of which are structurally characterized. Each of the structurally characterized proteins within a sequence family correlates to a single protein fold and to a common bound conformation of NAD(P). A wide range of structural folds is identified that recognize NAD(P), including Rossmann folds and beta/alpha barrels. The defined sequence families can be used to identify the type and prevalence of NAD(P)-utilizing enzymes in the proteomes of sequenced organisms. The proteome of Mycobacterium tuberculosis was mined to generate a proteome-wide profile of NAD(P)-utilizing enzymes coded by this organism. This enzyme family comprises approximately 6% of the open reading frames, with the largest subgroup being the Rossmann fold, short-chain dehydrogenases. The preponderance of short-chain dehydrogenases correlates strongly with the phenotype of M. tuberculosis, which is characterized as having one of the most complex prokaryotic cell walls.

Amino Acid Sequence↗

PubMed2001

Efficient Photocatalytic Degradation of Environmental Pollutants with Mass-Produced ZnS Nanocrystals.

Photocatalytic degradation of water pollutants using nanometersized semiconductor colloids is an emerging area of environmental remediation. The synthesis of semiconductor nanocrystals (NCs), however, can be costly and result in low product yields. For large-scale photocatalytic application in environmental remediation, cost-effective production of the semiconductor NCs would be ideal. Demonstrated in this report is the efficient photocatalytic degradation of p-nitrophenol (pNP) and Acid Orange 7 (AO7) using ZnS nanocrystals ( approximately 3 to 5 nm diameter) produced in gram quantities with >50% product yield. The pNP half-life in ZnS nanocrystal photocatalyzed reactions was about 1.95 to 2.45 min, whereas in comparable TiO(2) reactions, the pNP half-lives were in the range of 12 to 15 min. Absorption spectra of the photocatalysis reactions suggested the decolorization of pNP without any noticeable formation of phenolic intermediates, implying a mechanism that involves a pNP ring opening via a radical mediated attack. Likewise, the degradation of AO7 was suggested to occur via an oxidative pathway involving hydroxyl radicals formed at the photocatalyst/liquid interface. Optimum conditions for AO7 degradation such as pH, photocatalyst-to-AO7 ratio, and photocatalyst surface passivation were similar to those for pNP. By demonstrating efficient mineralization of these model pollutants using mass-produced ZnS nanocrystals, we hope to lay the foundations necessary for development of large-scale, field-applicable systems. Copyright 2001 Academic Press.

Journal Article↗

PubMedDate not supplied

Genome-wide profile of oxidoreductases in viruses, prokaryotes, and eukaryotes.

Enzymes that utilize nicotinamide adenine dinucleotide (NAD) or its 2'-phosphate derivative (NADP) are found throughout the kingdoms of life. These enzymes are fundamental to many biochemical pathways, including central intermediary metabolism and mechanisms for cell survival and defense. The complete genomes of 25 organisms representing bacteria, protists, fungi, plants, and animals, and 811 viruses, were mined to identify and classify NAD(P)-dependent enzymes. An average of 3.4% of the proteins in these genomes was categorized as NAD(P)-utilizing proteins, with highest prevalence in the medium-chain oxidoreductase and short-chain oxidoreductase families. In general, the distribution of these enzymes by oxidoreductase family was correlated to the number of different catalytic mechanisms in each family. Organisms with smaller genomes encoded a larger proportion of NAD(P)-dependent enzymes in their proteome (approximately 6%) as compared to the larger genomes of eukaryotes (approximately 3%). Among viruses, those with large, double-strand DNA genomes were shown to encode oxidoreductases. Gram-positive and gram-negative bacteria showed some differences in the distribution of NAD(P)-dependent proteins. Several organisms such as M. tuberculosis, P. falciparum, and A. thaliana showed unique distributions of oxidoreductases corresponding to some phenotypic features.

Animals↗