Chemoinformatics methods for systematic comparison of molecules from natural and synthetic sources and design of hybrid libraries

Evaluation of Antimicrobial and Antioxidant Potential of Oxalis corymbosa Extracts

This work aimed to assess the antioxidant and antimicrobial properties of Oxalis corymbosa extracts. Biochemical analyses were conducted on various plant parts, utilizing enzymatic and non-enzymatic assays. Parameters such as total soluble protein, chlorophyll, and carotenoid contents were also evaluated to elucidate the role of bioactive chemical compounds. The antimicrobial screening of extracts was performed against the bacterial and fungal strains Escherichia coli, Staphylococcus aureus, and Candida albicans, respectively. Results indicated that chlorophyll a, chlorophyll b, total chlorophyll, carotenoid content, anthocyanin content, catalase, peroxidase, and superoxide dismutase were most abundant in the O. corymbosa leaves. Moreover, total ascorbate peroxidase content, total phenolic content, and total flavonoid content were found to be higher in the roots compared to other parts. High-performance liquid chromatography analysis identified chlorogenic acid as the major component, followed by gallic acid, caffeic acid, quercetin, and salicylic acid. Regarding antibacterial potential, each extract exhibited significant activity, with methanolic and ethyl acetate extracts demonstrating the maximum inhibition zone against S. aureus and E. coli, respectively. These findings highlight the substantial antioxidant and antibacterial potential of different parts of O. corymbosa, suggesting their promising applications as ingredients in various nutraceutical products.

Synthesis of Spiro[indazole-3,3'-indolin]-2'-ones via [3 + 2] Dipolar Cycloaddition of Arynes with 3-Diazoindolin-2-ones and Indazolo[2,3-c]quinazolin-6(5H)-ones by Subsequent Thermal Isomerization

An efficient protocol for facile construction of spiro[indazole-3,3'-indolin]-2'-ones was developed via [3 + 2] dipolar cycloaddition of arynes with 3-diazoindolin-2-ones under mild conditions in excellent yields. Subsequent thermal isomerization of the spiro[indazole-3,3'-indolin]-2'-ones readily afforded indazolo[2,3-c]quinazolin-6(5H)-ones.

An efficient system for heterologous expression of secondary metabolite genes in Aspergillus nidulans

Fungal secondary metabolites (SMs) are an important source of medically valuable compounds. Genome projects have revealed that fungi have many SM biosynthetic gene clusters that are not normally expressed. To access these potentially valuable, cryptic clusters, we have developed a heterologous expression system in Aspergillus nidulans . We have developed an efficient system for amplifying genes from a target fungus, placing them under control of a regulatable promoter, transferring them into A. nidulans , and expressing them. We have validated this system by expressing nonreducing polyketide synthases of Aspergillus terreus and additional genes required for compound production and release. We have obtained compound production and release from six of these nonreducing polyketide synthases and have identified the products. To demonstrate that the procedure allows transfer and expression of entire secondary metabolite biosynthetic pathways, we have expressed all the genes of a silent A. terreus cluster and demonstrate that it produces asperfuranone. Further, by expressing the genes of this pathway in various combinations, we have clarified the asperfuranone biosynthetic pathway. We have also developed procedures for deleting entire A. nidulans SM clusters. This allows us to remove clusters that might interfere with analyses of heterologously expressed genes and to eliminate unwanted toxins.

Information properties of naturally-occurring proteins: Fourier analysis and complexity phase plots

In previous work from this lab, the information in natural proteins was investigated with Ribonuclease A (RNase A) serving as the source. The signature traits were investigated at three structure levels: primary through tertiary. The present paper travels further by charting the primary structure information of about half a million molecules. This was feasible given abundant sequence archives for both living and viral systems. Notably, a method is presented for evaluating primary structure information, based on Fourier analysis and spectral complexity. Significantly, the results show certain complexity traits to be universal for living sources. Viruses, by contrast, encode protein collections which are case-specific and complexity-divergent. The results have ramifications for discriminating collections on the basis of sequence information. This discrimination offers new strategies for selecting drug targets.

On the information expressed in enzyme structure: more lessons from ribonuclease A

Brownian computations were directed at Ribonuclease A (RNase A) and variants in folded states so as to quantify information of the statistical type at the atom/covalent bond level. This advanced the research reported in this journal last year on the information properties of enzyme primary structure. Brownian computation data are illustrated for a sixteen-member library. The results identify signature traits that distinguish the folded wild type (WT) molecule from variants. The distinctions are explainable in terms of correlated information and dispersion energy. The Brownian tools used for this study can be directed at other protein families (e.g., kinases, isomerases, etc.) in rapid screening, QSAR, and design applications.

Chemoinformatics as a Theoretical Chemistry Discipline

Here, chemoinformatics is considered as a theoretical chemistry discipline complementary to quantum chemistry and force-field molecular modeling. These three fields are compared with respect to molecular representation, inference mechanisms, basic concepts and application areas. A chemical space, a fundamental concept of chemoinformatics, is considered with respect to complex relations between chemical objects (graphs or descriptor vectors). Statistical Learning Theory, one of the main mathematical approaches in structure-property modeling, is briefly reviewed. Links between chemoinformatics and its "sister" fields - machine learning, chemometrics and bioinformatics are discussed.

Rapid synthesis of the indole-indolone scaffold via [3+2] annulation of arynes by methyl indole-2-carboxylates

The reaction of methyl indole-2-carboxylates and arynes affords a very efficient, high yielding synthesis of a novel indole-indolone ring system, which tolerates considerable functionality, is broad in scope and proceeds under mild reaction conditions.

How good is your screening library?

Efficient library design is an ongoing challenge for investigators seeking novel ligands for proteins, whether for drug discovery or chemical biology. Strategies that add neglected chemistry or exclude unproductive compounds are two dominant recent themes, as is a growing awareness of molecular complexity and its implications. The choice of how complex molecules in screening libraries should be often amounts to how big they should be. Small, simple molecules have lower affinities and must be screened at high concentration, but they will also have higher hit rates. Larger compounds, on the other hand, will often more closely resemble final drugs, but because they are more highly functionalized and specific, they will have much lower hit rates. The best general-purpose screening libraries may well be those of intermediate complexity that are free of artifact-causing nuisance compounds.