Orchestration and theranostic applications of synthetic genome with Hachimoji bases/building blocks.

Synthetic genomics is a novel field of chemical biology where the chemically modified genetic alphabets have been considered in central dogma of life. Tweaking of chemical compositions of natural nucleotide bases could be developed as novel building blocks of DNA/RNA. The modified bases (dP, dZ, dS, and dB etc.) have been demonstrated to be adaptable for replication, transcription and follow Darwinism law of evolution. With advancement of chemical biology especially nucleotide chemistry, synthetic genetic codes have been discovered and Hachimoji nucleotides are the most important and significant one among them. These additional nucleotide bases can form orthogonal base-pairing, and also follow Darwinian evolution and other structural features. In the Hachimoji base pairing, synthetic building blocks are formed using eight modified nucleotide (DNA/RNA) letters (hence the name "Hachimoji"). Their structural conformations, like polyelectrolyte backbones and stereo-regular building blocks favor thermodynamic stability and confirm Schrodinger aperiodic crystal. From the structural genomics aspect, these synthetic bases could be incorporated into the central dogma of life. Researchers have shown Hachimoji building blocks were transcribed to its RNA counterpart as a functional fluorescent Hachimoji aptamer. Apart from several unnatural nucleotide base pairs maneuvered into its in vitro and in vivo applications, this review describes future perspective towards the development and therapeutic utilization of the genetic codes, a primary objective of synthetic and chemical biology.

Divergent mutations of Delta and Omicron variants: key players behind differential viral attributes across the COVID-19 waves.

The third SARS-CoV-2 pandemic wave causing Omicron variant has comparatively higher replication rate and transmissibility than the second wave-causing Delta variant. The exact mechanism behind the differential properties of Delta and Omicron in respect to infectivity and virulence is not properly understood yet. This study reports the analysis of different mutations within the receptor binding domain (RBD) of spike glycoprotein and non-structural protein (nsp) of Delta and Omicron strains. We have used computational studies to evaluate the properties of Delta and Omicron variants in this work. Q498R, Q493R and S375F mutations of RBD showed better docking scores for Omicron compared to Delta variant of SARS-CoV-2, whereas nsp3_L1266I with PARP15 (7OUX), nsp3_L1266I with PARP15 (7OUX), and nsp6_G107 with ISG15 (1Z2M) showed significantly higher docking score. The findings of the present study might be helpful to reveal the probable cause of relatively milder form of COVID-19 disease manifested by Omicron in comparison to Delta variant of SARS-CoV-2 virus. Supplementary Information: The online version contains supplementary material available at 10.1007/s13337-023-00823-0.

Effect of deletions in the α-globin gene on the phenotype severity of ß-thalassemia.

Thalassemia is the most common inherited hemoglobinopathy worldwide. Variation of clinical symptoms in this hemoglobinopathy entails differences in disease-onset and transfusion requirements. The aim of this study was to investigate the role of α-globin gene deletions in modulating the clinical heterogeneity of ß-thalassemia (ß-thal) syndromes. A total number 270 ß-thal subjects were enrolled. Hematological parameters were recorded. ß-Globin mutations were determined by amplified refractory mutation system-polymerase chain reaction (ARMS-PCR), gap-PCR and Sanger sequencing. α-Globin gene deletions were determined by multiplex PCR. Out of 270 ß-thal subjects, 19 carried ß+/ß+, 74 had ß0/ß0 and 177 had the ß0/ß+ genotype. When we determined the severity of the different ß-thal subjects in coinherited with the α gene deletion, it was revealed that, 84.2% ß+/ß+ subjects carried a non severe phenotype and did not have an α gene deletion. Of the ß0/ß0 individuals, 95.9% presented a severe phenotype, irrespective of α-globin gene deletions. In cases with the ß0/ß+ genotype, 19.2% subjects also carried a deletion on the α gene. Of these, 61.8% presented a non severe phenotype and 38.2% were severely affected. Only in the ß0/ß+ category did α gene deletions make a significant contribution (p < 0.001) toward alleviation of clinical severity. Therefore, it can be stated that α-globin gene deletions play a role in ameliorating the phenotype in patients with a ß+/ß0 genotype.

Comparative Efficacy and Safety Between Deferiprone and Deferasirox with Special Reference to Serum Ferritin Level and Cardiac Function in Bengali ß-Thalassemia Major Children.

Deferiprone (DFP) and deferasirox (DFX) are the most well-known, efficacious and safe chelators to reduce the serum ferritin (SF) level in multi transfused thalassemic children, although there are few reports available for assessing the efficacy between DFP and DFX. We compared the efficacy of DFP vs. DFX as iron chelating drugs in ß-thalassemia major (ß-TM) patients. Pediatric patients diagnosed to carry ß-TM, aged between 2 and 10 years, were recruited. A suitable data collection form and questionnaire were used. Paired and unpaired t-tests were used to compare the safety and efficacy of the chelating drugs DFP and DFX. The mean SF level at the 12th month was found to be 3016.73 ± 670.04 ng/mL (p = 0.002) in the DFX-treated group, which was quite significant in contrast to DFP response, where the value was 3204.06 ± 690.15 ng/mL (p = 0.14). There is no statistically significant (p = 0.15) difference on relative changes of the left ventricular ejection fraction (LVEF), between these two groups. The adverse effects were transient and none of them required stoppage of therapy. Deferasirox is more effective when compared to DFP in reducing chelating drug-related complications and iron overload specially in multiple transfusion dependent ß-TM patients.

Drug Repurposing: Hydroxyurea Therapy Improves the Transfusion-Free Interval in HbE/Beta-Thalassemia-Major Patients with the XmnI Polymorphism.

Aims: HbE/ß-thalassemia is the most prevalent form of severe ß-thalassemia in Asian countries. Hydroxyurea (HU) is the most common drug used for the management of sickle-cell anemia but not thalassemia. In this study, we aimed to assess clinical HU response among the Bengali HbE/ß-thalassemia patients with respect to the XmnI γGglobin polymorphism and elucidate the association between this polymorphism and HU response efficacy. Materials and Methods: We enrolled 49 transfusion-dependent patients with HbE/ß-thalassemia. Fetal hemoglobin levels were measured using high-performance liquid chromatography and complete blood counts were determined pre- and post-HU therapy. Polymerase chain reaction-restriction fragment length polymorphism analyses were performed for genotyping the XmnI γGglobin polymorphism. Results: A total of 30 (61.22%) patients were found to be responders, whereas the remaining 19 (38.78%) were nonresponders. We found 33 patients with the heterozygous (C/T) and three with the homozygous mutant (T/T) genotype status. We obtained a statistically significant correlation (p < 0.001) between the XmnI polymorphism genotype and transfusion-free interval. Patients with the XmnI polymorphism were found to be good responders for HU therapy and showed increased hemoglobin levels. Conclusions: Our findings indicate that HU is a potential drug candidate for thalassemia management, particularly for HbE/ß-thalassemia. These results hold implications in repurposing HU as an effective and efficient therapy for HbE/ß-thalassemia.

The Prevalence of HBB Mutations among the Transfusion-Dependent and Non Transfusion-Dependent Hb E/ß-Thalassemia Children in a Tertiary Center of West Bengal, India.

Hb E (HBB: c.79G>A)/ß-thalassemia (Hb E/ß-thal) is responsible for nearly half of all the different kinds of severe ß-thal. This disorder is characterized by a wide range of clinical variability ranging from mild, asymptomatic non transfusion-dependent thalassemia (NTDT) to severe transfusion-dependent thalassemia (TDT). The aim of the present study was to determine the prevalence of different ß-globin gene (HBB) mutations in Hb E/ß-thal subjects and their potential role in transfusion dependence. One hundred and ten consecutive children with Hb E/ß-thal attending the Pediatric Department of Burdwan Medical College, Burdwan, West Bengal, India were enrolled. Based on hemoglobin (Hb) electrophoresis or high-performance liquid chromatography (HPLC), patients were recruited and later ß-globin gene sequencing was done to find out the prevalence of different HBB mutations. Transfusion-dependent thalassemia was seen in 42 children (38.2%), while NTDT was seen in 68 children (61.8%). A total of 10 different ß-globin mutant alleles were characterized. The most frequent mutation on the ß-globin gene was IVS-I-5 (G>C) (HBB: c0.92+5G>C) in both groups. The ß-globin gene mutations alone cannot determine transfusion dependence among the Hb E/ß-thal patients.

Cross-Sectional Study for the Detection of Mutations in the Beta-Globin Gene Among Patients with Hemoglobinopathies in the Bengali Population.

AIMS: Thalassemia is a common autosomal recessive blood disorder, which is most prevalent in South East Asian and Mediterranean populations. It is considered as a major health burden in the Indian population. The aims of the present study were to investigate the common, as well as uncommon, mutations responsible for thalassemia in the Bengali population. METHODS: The Bengali state was divided into four sampling zones. Mutation detection was done using Sanger sequencing of the HBB gene. RESULTS: A total of 14 different mutations were observed, including rare mutations IVS1-130(G>C), IVS1-129(A>C), -90(T>C), CD16(-C), -30(T>C), CD15(-T), and a novel mutation CD53(C>T). The frequencies of IVS1-5(G>C) and CD26(G>A) mutations were higher than other mutations. There were also some silent polymorphisms found in the studied group, CD3(T>C), CD10(C>A), IVSII-16(G>C), IVSII-74(T>G), -42(C>G). CONCLUSION: The present study is the first attempt to screen for ß-thalassemia-causing mutations by direct sequencing in different districts of West Bengal. The information obtained from the present study may be helpful for thalassemia management and prenatal mutation detection.

Hb Midnapore [ß53(D4)Ala→Val; HBB: c.161C>T]: A Novel Hemoglobin Variant with a Structural Abnormality Associated with IVS-I-5 (G>C) (HBB: c.92+5G>C) Found in a Bengali Indian Family.

We describe a novel C>T substitution at codon 53 of the HBB gene (HBB: c.161C>T). The proband was a transfusion-dependent ß-thalassemia major (ß-TM) patient. DNA was extracted and subsequently, DNA sequencing was done to detect the mutations on the HBB gene. Capillary zone electrophoresis (CZE) revealed the presence of an unknown peak. She inherited this mutation from her grandmother through her mother. This mutation exists in cis with the common ß0 mutation IVS-I-5 (G>C) (HBB: c.92+5G>C). The proband is homozygous for HBB: c.92+5G>C and needs monthly transfusions. On the other hand, her grandmother, mother and sister all possess this novel mutation cis with the heterozygous HBB: c.92+5G>C. They are carriers not thalassemic. This mutation produces the substitution ß53(D4)Ala→Val; HBB: c.161C>T, a new structural hemoglobin (Hb) variant. As this variant was identified in a Bengali family from Paschim Midnapore district of West Bengal, India, it has been designated as Hb Midnapore. This variant has now been reported to the HbVar database.

Association of a Zn(2+) containing metallo ß-lactamase with the anticancer antibiotic mithramycin.

Pathogenic bacteria that are resistant to ß-lactam antibiotics mostly utilize serine ß-lactamases to degrade the antibiotics. Current studies have shown that different subclasses of metallo ß-lactamases (E[MBL]) are involved in the defense mechanism of drug resistant bacteria. Here we report that the Zn(2+) containing subclass B1 E[MBL] from Bacillus cereus binds to a naturally occurring anti-cancer drug mithramycin (MTR). Spectroscopic (CD and fluorescence) and isothermal titration calorimetry studies show that MTR forms a high affinity complex with the Zn(2+) ion containing E[MBL]. Abolished interaction of MTR with apo E[MBL] suggests that the formation of this high affinity complex occurs due to the potential of MTR to bind bivalent metal ions like Zn(2+). Furthermore, CD spectroscopy, dynamic light scattering and differential scanning calorimetry studies indicate that the strong association with sub-micromolar dissociation constant leads to an alteration in the enzyme conformation at both secondary and tertiary structural levels. The enzyme activity decreases as a consequence to this conformational disruption arising from the formation of a ternary complex involving MTR, catalytic Zn(2+) and the enzyme. Our results suggest that the naturally occurring antibiotic MTR, a generic drug, has the potential as an E[MBL] inhibitor.