https://users.cs.duke.edu/~brd/Teaching/Bio/asmb/current/Papers/Lit4Docking/Gold_dock.pdf

Development and validation of a genetic algorithm for flexible docking.

Flavonoids are nearly ubiquitous in plants and are recognized as the pigments responsible for the colors of leaves, especially in autumn. They are rich in seeds, citrus fruits, olive oil, tea, and red wine. They are low molecular weight compounds composed of a three-ring structure with various substitutions. This basic structure is shared by tocopherols (vitamin E). Flavonoids can be subdivided according to the presence of an oxy group at position 4, a double bond between carbon atoms 2 and 3, or a hydroxyl group in position 3 of the C (middle) ring. These characteristics appear to also be required for best activity, especially antioxidant and antiproliferative, in the systems studied. The particular hydroxylation pattern of the B ring of the flavonoles increases their activities, especially in inhibition of mast cell secretion. Certain plants and spices containing flavonoids have been used for thousands of years in traditional Eastern medicine. In spite of the voluminous literature available, however, Western medicine has not yet used flavonoids therapeutically, even though their safety record is exceptional. Suggestions are made where such possibilities may be worth pursuing.

The Effects of Plant Flavonoids on Mammalian Cells:Implications for Inflammation, Heart Disease, and Cancer

The past few years have seen the development of powerful statistical methods for detecting adaptive molecular evolution. These methods compare synonymous and nonsynonymous substitution rates in protein-coding genes, and regard a nonsynonymous rate elevated above the synonymous rate as evidence for darwinian selection. Numerous cases of molecular adaptation are being identified in various systems from viruses to humans. Although previous analyses averaging rates over sites and time have little power, recent methods designed to detect positive selection at individual sites and lineages have been successful. Here, we summarize recent statistical methods for detecting molecular adaptation, and discuss their limitations and possible improvements.

/pdf/statistical-methods-for-detecting-molecular-adaptation-3s1x47gbtt.pdf

Statistical methods for detecting molecular adaptation.

2.1.8. Michael Reaction 2245 2.1.9. Others 2247 2.2. Cyclization Reactions 2248 2.2.1. Carbon Diels−Alder Reactions 2248 2.2.2. Aza-Diels−Alder Reactions 2252 2.2.3. Other Hetero-Diels−Alder Reactions 2255 2.2.4. Ionic Diels−Alder Reaction 2256 2.2.5. 1,3-Dipolar Cycloadditions 2256 2.2.6. Other Cycloaddition Reactions 2258 2.2.7. Prins-type Cyclization 2259 2.3. Friedel−Crafts Acylation and Alkylation 2259 2.4. Baylis−Hillman Reaction 2263 2.5. Radical Addition 2264 2.6. Heterocycle Synthesis 2267 2.7. Diazocarbonyl Insertion 2270 3. C−X (X ) N, O, P, Etc.) Bond Formation 2271 3.1. Aromatic Nitration and Sulfonylation 2271 3.2. Michael Reaction 2272 3.3. Glycosylation 2273 3.4. Aziridination 2275 3.5. Diazocarbonyl Insertion 2276 3.6. Ring-Opening Reactions 2277 3.7. Other C−X Bond Formations 2280 4. Oxidation and Reduction 2280 4.1. Oxidation 2280 4.2. Reduction 2281 5. Rearrangement 2283 6. Protection and Deprotection 2285 6.1. Protection 2285 6.2. Deprotection 2288 7. Polymerization 2291 8. Miscellaneous Reactions 2291 9. Lanthanide(II) Triflates in Organic Synthesis 2295 10. Conclusion 2295 11. Acknowledgment 2295 12. References 2295

Rare-earth metal triflates in organic synthesis

10. Patented Literature 2616 10.1. Esterification 2616 10.2. Ether Formation 2619 10.2.1. Etherification without Cyclization 2619 10.2.2. Etherification with Cyclization 2624 10.3. N-Alkylation 2625 10.4. Other Reactions 2627 11. Summary and Outlook 2628 12. Note Added in Proof 2628 13. Abbreviations Used in This Review 2629 14. Acknowledgments 2629 15. Supporting Information Available 2630 16. References 2630

Mitsunobu and Related Reactions: Advances and Applications

https://febs.onlinelibrary.wiley.com/doi/pdf/10.1016/S0014-5793%2898%2901470-7

Identification of regions in which positive selection may operate in S-RNase of Rosaceae: implication for S-allele-specific recognition sites in S-RNase.

SDR Structure, Mechanism of Action, and Substrate Recognition

An interferon-induced endoribonuclease, ribonuclease L (RNase L), is implicated in both the molecular mechanism of action of interferon and the fundamental control of RNA stability in mammalian cells. RNase L is catalytically active only after binding to an unusual activator molecule containing a 5′-phosphorylated 2′,5′-linked oligoadenylate (2-5A), in the N-terminal half. Here, we report the crystal structure of the N-terminal ankyrin repeat domain (ANK) of human RNase L complexed with the activator 2-5A. This is the first structural view of an ankyrin repeat structure directly interacting with a nucleic acid, rather than with a protein. The ANK domain folds into eight ankyrin repeat elements and forms an extended curved structure with a concave surface. The 2-5A molecule is accommodated at a concave site and directly interacts with ankyrin repeats 2–4. Interestingly, two structurally equivalent 2-5A binding motifs are found at repeats 2 and 4. The structural basis for 2-5A recognition by ANK is essential for designing stable 2-5As with a high likelihood of activating RNase L.

/pdf/structural-basis-for-recognition-of-2-5-linked-26edhb81dl.pdf

Structural basis for recognition of 2′,5′-linked oligoadenylates by human ribonuclease L

The human malaria parasite Plasmodium falciparum is responsible for the deaths of more than a million people each year. Fosmidomycin has been proven to be efficient in the treatment of P. falciparum malaria by inhibiting 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR), an enzyme of the non-mevalonate pathway, which is absent in humans. However, the structural details of DXR inhibition by fosmidomycin in P. falciparum are unknown. Here, we report the crystal structures of fosmidomycin-bound complete quaternary complexes of PfDXR. Our study revealed that (i) an intrinsic flexibility of the PfDXR molecule accounts for an induced-fit movement to accommodate the bound inhibitor in the active site and (ii) a cis arrangement of the oxygen atoms of the hydroxamate group of the bound inhibitor is essential for tight binding of the inhibitor to the active site metal. We expect the present structures to be useful guides for the design of more effective antimalarial compounds.

/pdf/molecular-basis-of-fosmidomycin-s-action-on-the-human-32x2pttywj.pdf

Kazuo T. Nakamura

Papers

Identification of regions in which positive selection may operate in S-RNase of Rosaceae: implication for S-allele-specific recognition sites in S-RNase.

SDR Structure, Mechanism of Action, and Substrate Recognition

Structural basis for recognition of 2′,5′-linked oligoadenylates by human ribonuclease L

Molecular basis of fosmidomycin's action on the human malaria parasite Plasmodium falciparum

Vibrational spectra and structures of zinc carboxylates I. Zinc acetate dihydrate