Water promoted, microwave-assisted oxidative novel deamination of N-aminoquinazolinones

A novel deamination of 2-alkyl/aryl 3-amino-4（3H）-quinazolinones series using aqueous KMnO4 under thermal condition and microwave irradiation is described. Compared to thermal condition, significantly higher yields in much shorter times were observed for reactions under microwave irradiation. A plausible mechanism has been proposed for the oxidative water-promoted deamination.

Insight into the deamination mechanism of 6-cyclopropylamino guanosine analogs for anti-HIV drug design

Deamination is a crucial step in the transformation of 6-cyclopropylamino guanosine prodrug to its active form. A convenient method using capillary electrophoresis （CE） without sample labeling was developed to analyze the deamination of a series of D-/L-6-cyclopropylamino guanosine analogs by mouse liver homogenate, mouse liver microsome, and adenosine deaminase （ADA）. A two-step process involving a 6-amino guanosine intermediate formed by oxidative N-dealkylation was demonstrated in the metabolism of 6-cyclopropylamino guanosine to 6-hydroxy guanosine. The results indicated that the transformation rates of different prodrugs to the active form varied greatly, which were closely correlated with the configuration of nucleosides and the structure of glycosyl groups. Most importantly, D-form analogs were metabolized much faster than their L-counterparts, thus clearly pointed out that compared to guanine, modification of glycosyl part might be a better choice for the development of L-Kuanosine analogs for the treatment of HIV,

Eucaryotic DNA Methylation and Gene Mutation

5-methylcytosine (m5C) as a rare base exists in eucaryotic genomes, it is a normal constituent of many eucaryotic DNA, whose existence is a character of eucaryotic DNA. In the regular physiological conditions, cytosine residue of eucaryotic DNA is methylated to be popular. Up to the present, many people consider that the m5C may be mutation hotspots by the m5C deamination leading to gene mutation. Our theoretical investigations indicated that the spontaneous mutation caused by the transition of G - C-A - T, in eukaryotic DNA, may be a result caused by the tautomer changing base pairs and may also be caused by other factor actions, however it could not be caused by the deamination of m5C.

Does intra-ruminal nitrogen recycling waste valuable resources? A review of major players and their manipulation

Nitrogenous emissions from ruminant livestock production are of increasing public concern and, together with methane, contribute to environmental pollution. The main cause of nitrogen-(N)-containing emissions is the inadequate provision of N to ruminants, leading to an excess of ammonia in the rumen, which is subsequently excreted. Depending on the size and molecular structure, various bacterial, protozoal and fungal species are involved in the ruminal breakdown of nitrogenous compounds(NC). Decelerating ruminal NC degradation by controlling the abundance and activity of proteolytic and deaminating microorganisms, but without reducing cellulolytic processes, is a promising strategy to decrease N emissions along with increasing N utilization by ruminants. Different dietary options, including among others the treatment of feedstuffs with heat or the application of diverse feed additives, as well as vaccination against rumen microorganisms or their enzymes have been evaluated. Thereby, reduced productions of microbial metabolites, e.g. ammonia, and increased microbial N flows give evidence for an improved N retention. However, linkage between these findings and alterations in the rumen microbiota composition, particularly NC-degrading microbes, remains sparse and contradictory findings confound the exact evaluation of these manipulating strategies, thus emphasizing the need for comprehensive research. The demand for increased sustainability in ruminant livestock production requests to apply attention to microbial N utilization efficiency and this will require a better understanding of underlying metabolic processes as well as composition and interactions of ruminal NC-degrading microorganisms.

Reducing SARS-CoV-2 pathological protein activity with small molecules

Coronaviruses are dangerous human and animal pathogens.The newly identified coronavirus SARS-CoV-2 is the causative agent of COVID-19 outbreak,which is a real threat to human health and life.The world has been struggling with this epidemic for about a year,yet there are still no targeted drugs and effective treatments are very limited.Due to the long process of developing new drugs,reposition of existing ones is one of the best ways to deal with an epidemic of emergency infectious diseases.Among the existing drugs,there are candidates potentially able to inhibit the SARS-CoV-2 replication,and thus inhibit the infection of the virus.Some therapeutics target several proteins,and many diseases share molecular paths.In such cases,the use of existing pharmaceuticals for more than one purpose can reduce the time needed to design new drugs.The aim of this review was to analyze the key targets of viral infection and potential drugs acting on them,as well as to discuss various strategies and therapeutic approaches,including the possible use of natural products.We highlighted the approach based on increasing the involvement of human deaminases,particularly APOBEC deaminases in editing of SARS-CoV-2 RNA.This can reduce the cytosine content in the viral genome,leading to the loss of its integrity.We also indicated the nucleic acid technologies as potential approaches for COVID-19 treatment.Among numerous promising natural products,we pointed out curcumin and cannabidiol as good candidates for being antiSARS-CoV-2 agents.

The Pattern of Occurrence of Cytosine in the Genetic Code Minimizes Deleterious Mutations and Favors Proper Function of the Translational Machinery

The standard genetic code consists of 64 combinations of base triplets made from four different bases. The research aim of this study was to investigate the pattern of occurrence of cytosine in the genetic code. By exploring the base composition and sequence of all 64 codons, the author found some important features based on the instability of cytosine. Because cytosine undergoes spontaneous deamination that converts it into uracil, it is evolutionarily favorable to exclude cytosine from codons critical to the initiation and termination of translation. For amino acids that have one to three synonymous codons (also called synonyms), the frequency of occurrence of C in the first and second positions of their mRNA codons is significantly lower than the frequencies of A, U, and G. For mRNA codons that encode amino acids with four synonyms, the trend of base composition is opposite to those encoding amino acids with one to three synonyms;the instability of C could be inhibited or reduced via formation of hydrogen bonds with a G and/or with a protonated C, and the secondary structure of the resultant mRNA could be adjusted via the multiple synonymous alternates at the third position of their codons to facilitate the translation process. The overall pattern of occurrence for C in the genetic code not only minimizes deleterious mutations and favors proper function of the translational machinery by excluding C from certain positions within codons, but also allows the occurrence of genetic diversity via mutation by including C in less-critical positions.

The Earliest Discovery of the Role of Magnesium Ions on Stabilizing the Tertiary Structure of the Transfer RNA and Its Biological Significance —A Short Memoir

In early of 1960s, I was a graduate student studying on tRNA biochemistry. In the course of the research, the magnesium ions stabilized the tertiary structure of tRNA, resulting in its resistance to enzymatic degradation was discovered independently. The experiment of deaminated (denatured) tRNA obtained from native tRNA was designed and conducted and further proved the validity of this finding. It was found that magnesium ions could stabilize the tertiary structure of the natrive tRNA but could not stabilize structure of the deaminated tRNA. In term of the methodology, this stabilization technique has been widely applied in sequencing analysis of RNA and has greatly promoted the progress in the study of primary structure of RNA. More importantly, the stabilization of the tertiary structure of RNA by magnesium ions plays a key role both in the processing of messenger RNAs and the ribozyme activity. After our first article in Chinese was published in 1963, a paper of Nishimura & Novelli came into our note. The received date of their paper was March 22 of 1963, only 4 days earlier than that of our first paper. Thus, we and Nishimura & Novelli made almost at the same time the earliest discovery of the role of magnesium ions on stabilizing the tertiary structure of the transfer RNA and thus resulted in resistance of tRNA degradation by enzymes. However, this discovery was not initially appreciated for a period of time but was finally “visualized” and proved by X-ray crystal structure of yeast phenylalanine tRNA, which has provided more accurate information on the geometry of the magnesium-binding sites in tRNA.

Scoping Antifungal Activities of Various Forms of Chitosan Oligomers and Their Potential Fixation in Wood

Chitosan oligomers （average Dp-4） are known for their antifungal activity and wood decay resistance. These oligomers are susceptible to moisture, and promote yeast growth upon air exposure after a sufficient length of time. Chitosan oligomers of three different states viz. completely dried, freshly prepared and highly viscous form, were prepared to compare their in-vitro antifungal activities against three brown-rot fungi, two sapstain and one mould fungus using agar nutrient medium. Additionally, a mixture of chitosan oligomers and boric acid was used for wood treatment. The nutrient medium bioassay results show that all states of chitosan oligomers inhibited the growth of tested basidiomycetes fungi, but not sapstain and mould fungi. Subsequently, wood decay results confirm antifungal activity of chitosan oligomers plus boron against basidiomycetes, but highlighted their leachability upon water exposure.

Effective gene editing by high-fidelity base editor 2 in mouse zygotes

Targeted point mutagenesis through homologous recombination has been widely used in genetic studies and holds considerable promise for repairing disease- causing mutations in patients. However, problems such as mosaicism and low mutagenesis efficiency continue to pose challenges to clinical applicaUon of such approaches. Recently, a base editor （BE） system built on cytidine （C） deaminase and CRISPR/Cas9 technology was developed as an alternative method for targeted point mutagenesis in plant, yeast, and human cells. Base editors convert C in the deamination window to thymidine （T） efficiently, however, it remains unclear whether targeted base editing in mouse embryos is feasible. In this report, we generated a modified high- fidelity version of base editor 2 （HF2-BE2）, and investigated its base editing efficacy in mouse embryos. We found that HF2-BE2 could convert C to T efficiently, with up to 100% biallelic mutation efficiency in mouse embryos. Unlike BE3, HF2-BE2 could convert C to T on both the target and non-target strand, expanding the editing scope of base editors. Surprisingly, we found HF2-BE2 could also deaminate C that was proximal to the gRNA-binding region. Taken together, our work demonstrates the feasibility of generating point mutations in mouse by base editing, and underscores the need to carefully optimize base editing systems in order to eliminate proximal-site deamination.

APOBEC deaminases-mutases with defensive roles for immunity

In recent years, tremendous progress has been made in the elucidation of the biological roles and molecular mechanisms of the apolioprotein B mRNA-editing enzyme catalytic polypeptide (APOBEC) family of enzymes. The APOBEC family of cytidine deaminases has important functional roles within the adaptive and innate immune system. Activation induced cytidine deaminase (AID) plays a central role in the biochemical steps of somatic hypermutation and class switch recombination during antibody maturation, and the APOBEC 3 enzymes are able to inhibit the mobility of retroelements and the replication of retroviruses and DNA viruses, such as the human immunodeficiency virus type-1 and hepatitis B virus. Recent advances in structural and functional studies of the APOBEC enzymes provide new biochemical insights for how these enzymes carry out their biological roles. In this review, we provide an overview of these recent advances in the APOBEC field with a special emphasis on AID and APOBEC3G.

The crystal structure of Ac-AChBP in complex with α-conotoxin LvlA reveals the mechanism of its selectivity towards different nAChR subtypes

The a3＊ nAChRs, which are considered to be promising drug targets for problems such as pain, addiction, cardiovascular function, cognitive disorders etc., are found throughout the central and peripheral nervous system. The α-conotoxin （α-CTx） LvlA has been identified as the most selective inhibitor of α3β2 nAChRs known to date, and it can distinguish the α3132 nAChR subtype from the α6/α3β2β3 and α3β4 nAChR subtypes. However, the mechanism of its selectivity towards α3132, α6/α3β2β3, and α3β4 nAChRs remains elusive. Here we report the co-crystal structure of LvlA in complex with Aplysia californica acetylcholine binding protein （Ac-AChBP） at a resolution of 3.4 A. Based on the structure of this complex, together with homology modeling based on other nAChR subtypes and binding affinity assays, we conclude that Asp-11 of LvlA plays an important role in the selectivity of LvlA towards α3132 and α31o6132133 nAChRs by making a salt bridge with Lys-155 of the rat α3 subunit. Asn-9 lies within a hydrophobic pocket that is formed by Met-36, Thr-59, and Phe-119 of the rat β2 subunit in the α3β2 nAChR model, revealing the reason for its more potent selectivity towards the a3β2 nAChR subtype. These results provide molecular insights that can be used to design ligands that selectively target α3β2 nAChRs, with significant implications for the design of new therapeutic a-CTxs.