AI-assisted generation and in-depth in-silico evaluation of potential inhibitor targeting aurora kinase A (AURKA): An anticancer discovery exploiting synthetic lethality approach.

Genetic alterations are lead causative agents behind the complex pathologies of cancers which render all treatments unarmed. Such alterations in oncogenes can be treated by direct inhibition by specific drugs while alteration in tumor suppressor genes mediating loss of function is challenging to treat. Identification of synthetic lethal partners to specific tumor suppressor genes and mediating their inhibition can be a potential approach to deal with loss of function mutations. Aurora kinase A (AURKA) has been established as an effective synthetic lethal partner of several tumor suppressor genes and is overexpressed in cancerous conditions, mediating adverse pathologies. The present AI-assisted study deals with the generation of novel inhibitor compounds against AURKA and the exhaustive evaluation of the best compound using molecular docking, molecular dynamic simulation, MM/PBSA, and QM/MMGBSA-based analysis. Out of the 200 novel compounds generated using features of ATP binding pocket of AURKA and previously reported inhibitor, compound 1 (4-{5-fluoro-6-[(1Z)-3-hydrazinyl-3-oxo-2-phenylprop-1-en-1-yl]pyridin-2-yl}benzoic acid) was identified as the most potent candidate with high negative binding energy of -10.4 kcal/mol in molecular docking analysis. The molecular dynamic simulation analysis resulted in major conformational changes in the conserved DFG motif and loop 277-291 of AURKA in the apo-AURKA compared to AURKA-compound 1 complex thus maintaining open ATP binding cavity in apo-form and inhibiting the entry of ATP to its binding site in complex form. The free energy landscape displayed a persistence of folded states of the enzyme in complex form. The MM/PBSA revealed effective Gibb's free energy of binding of -11 kcal/mol for compound 1 inhibiting AURKA. The QM/MMGBSA analysis resulted in a significantly high negative binding energy of -13.98 kcal/mol proving significant inhibition potential of compound 1 against AURKA. Therefore, further in-vitro investigation can provide a novel effective, and safe treatment against a wide range of cancers by targeting a well-established cancer target AURKA.

Copper-Catalyzed Thiolation of Hydrazones with Sodium Sulfinates: A Straightforward Synthesis of Benzylic Thioethers.

A facile and sustainable protocol for the thiolation of hydrazones with sodium sulfinates has been developed in the presence of CuBr2 and DBU in DMF to afford diverse benzylic thioethers. Control experiments reveal a radical pathway involving a thiyl radical as a key intermediate.

Multi-omics approach reveals elevated potential of bacteria for biodegradation of imidacloprid.

The residual imidacloprid, a widely used insecticide is causing serious environmental concerns. Knowledge of its biodegradation will help in assessing its residual mass in soil. In view of this, a soil microcosm-based study was performed to test the biodegradation potential of Agrobacterium sp. InxBP2. It achieved ∼88% degradation in 20 days and followed the pseudo-first-order kinetics (k = 0.0511 day-1 and t1/2=7 days). Whole genome sequencing of Agrobacterium sp. InxBP2 revealed a genome size of 5.44 Mbp with 5179 genes. Imidacloprid degrading genes at loci K7A42_07110 (ABC transporter substrate-binding protein), K7A42_07270 (amidohydrolase family protein), K7A42_07385 (ABC transporter ATP-binding protein), K7A42_16,845 (nitronate monooxygenase family protein), and K7A42_20,660 (FAD-dependent monooxygenase) having sequence and functional similarity with known counterparts were identified. Molecular docking of proteins encoded by identified genes with their respective degradation pathway intermediates exhibited significant binding energies (-6.56 to -4.14 kcal/mol). Molecular dynamic simulation discovered consistent interactions and binding depicting high stability of docked complexes. Proteome analysis revealed differential protein expression in imidacloprid treated versus untreated samples which corroborated with the in-silico findings. Further, the detection of metabolites proved the bacterial degradation of imidacloprid. Thus, results provided a mechanistic link between imidacloprid and associated degradative genes/enzymes of Agrobacterium sp. InxBP2. These findings will be of immense significance in carrying out the lifecycle analysis and formulating strategies for the bioremediation of soils contaminated with insecticides like imidacloprid.

Intensity of estrus expression - valuable obvious determinant of fertility in Bos indicus cows.

This study aimed to characterize estrus response and to establish relationships between intensity of estrus, preovulatory follicle (POF) size and estradiol (E2) concentrations on day of AI, luteal profiles and pregnancy outcome in lactating Hariana breed of cows. 200 cyclic cows were subjected to Ovsynch (n = 54) and Pre-OV treatment (n = 146). Ovsynch: Buserelin acetate (BA; 10 µg), Cloprostenol (500 µg) and BA (10 µg) were injected i.m. on day 0, 7 and 9, respectively, irrespective of treatment. Pre-OV: BA (10 µg) and Cloprostenol (500 µg) was also injected i.m. simultaneously 7 days prior to initiate Ovsynch. On the basis of estrus behavior, the cows were classified into three groups: weak, moderate and intense. Artificial insemination performed at 18-24 hours after 2nd BA of Ovsynch in both treatments. The average duration of estrus did not differ (p > 0.05) between Ovsynch and Pre-OV treatment. A positive correlation was observed between estrus response and POF size, concentration of E2 on day of AI and luteal profiles on day 12 post-AI. First service conception rate was higher in cows exhibited intense (45.46%) and moderate (42.56%) estrus response than weak (28.57%) estrus response. In conclusion, intensity of estrus expression could be considered as important determinant for deciding pregnancy outcomes in Bos indicus cows.

Detection of the ß-lactoglobulin genotype in zebu cattle (Gangatiri) milk using high-resolution accurate mass spectroscopy.

We studied the genetic polymorphism of beta-lactoglobulin (ß-Lg) whey protein in Gangatiri zebu cows for this Research Communication. The polymorphic nature of milk protein fractions and their association with milk production traits, composition and quality has attracted several efforts in evaluating the allelic distribution of protein locus as a potential dairy trait marker. Genetic variants of ß-Lg have highly significant effects on casein number (B > A) and protein recovery (B > A) and also determine the yield of cheese dry matter (B > A). Molecular techniques of polyacrylamide gel electrophoresis and high-resolution accurate mass-spectroscopy were applied to characterize the ß-Lg protein obtained from the Gangatiri breed milk. Sequence analysis of ß-Lg showed the presence of variant B having UniProt database accession number P02754, coded on the PAEP gene. Our study can provide reference and guidance for the selection of superior milk (having ß-LgB) from this indigenous breed that could potentially give a good yield of ß-Lg for industrial applications.

Proteomics-based milk whey proteome profiling of Indian Jersey crossbreed cows followed by chromosomal mapping.

BACKGROUND: Milk contains a massive class of minor proteins that are known for their various biological and molecular functions. Many whey proteins transfer the host defense mechanism to the human body. In this assay, electrophoresis followed by a high-resolution mass spectrometry-based proteomic approach has been applied to identify the whey proteome of Indian Jersey crossbreed bovines. RESULTS: Two search engines, MS Amanda and Sequest HT, have shown more than 29 minor proteins. Chromosomal mapping revealed that chromosomes 5 and 9 are expressing maximum proteins in the whey proteome. The principal component analysis, outlier plots, scree plots, score plots, and loading plots were generated to further assess the results. CONCLUSION: The majorly expressed ones are glycosylation-dependent cell adhesion molecule-1, ubiquitin, desmoglein, annexin, glycoprotein, arginase, histones, peroxiredoxin, vimentin, desmin, catenin, peripherin, and 70 kDa heat shock protein. © 2023 Society of Chemical Industry.

5d CIDR-Heatsynch improves the circulatory estradiol levels, estrus expression and conception rate in anestrus buffalo (Bubalus bubalis).

The present study aimed to investigate whether increasing estradiol (E2) during preovulatory period would increase estrous expression, luteal profiles and conception rate in 5d CIDR based timed AI protocol. A total 156 anestrus buffalo allocated (78 per group) to either 5d CIDR-Cosynch (d-5: CIDR + GnRH; d0: PGF2α+CIDR removal; 72 h post-CIDR removal: GnRH) or 5d CIDR-Heatsynch (d-5: CIDR + GnRH; d0: PGF2α+CIDR removal; 24 h post-CIDR removal: estradiol benzoate) group. All the buffaloes inseminated at 72 and 84 h post-CIDR removal. A subset of buffalo (n = 58) were subjected to examination of the follicle diameter and luteal profile during protocol, post-AI on days 5 and 12. The buffalo in 5d CIDR-Heatsynch had greater (p < .05) E2 concentrations, estrus induction and increasing trend (p < .08) for conception rate (57.7% vs. 43.6%) than 5d CIDR-Cosynch. The percentage of pregnant buffalo that exhibited estrus signs was greater (p < .01) in 5d CIDR-Heatsynch than 5d CIDR-Cosynch. Positive correlation (p < .01) was observed between POF and E2 concentrations; POF and CL diameter, CL diameter and P4 concentrations. Estrus response and P4 concentrations were indicators of probability of pregnancy. In conclusion, 5d CIDR-Heatsynch tended to improve conception rate. The estrus expression and P4 concentrations (d5 and 12 post-first-AI) is the indicator of probability of pregnancy in buffalo.

In silico structural inhibition of ACE-2 binding site of SARS-CoV-2 and SARS-CoV-2 omicron spike protein by lectin antiviral dyad system to treat COVID-19.

Spike glycoprotein of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) binds angiotensin-converting enzyme-2 (ACE-2) receptors via its receptor-binding domain (RBD) and mediates virus-to-host cell fusion. Recently emerged omicron variant of SARS-CoV-2 possesses around 30 mutations in spike protein where N501Y tremendously increases viral infectivity and transmission. Lectins interact with glycoproteins and mediate innate immunity displaying antiviral, antibacterial, and anticarcinogenic properties. In this study, we analyzed the potential of lectin, and lectin-antibody (spike-specific) complex to inhibit the ACE-2 binding site of wild and N501Y mutated spike protein by utilizing in silico molecular docking and simulation approach. Docking of lectin at reported ACE-2 binding spike-RBD residues displayed the ZDock scores of 1907 for wild and 1750 for N501Y mutated spike-RBD. Binding of lectin with antibody to form proposed dyad complex gave ZDock score of 1174 revealing stable binding. Docking of dyad complex with wild and N501Y mutated spike-RBD, at lectin and antibody individually, showed high efficiency binding hence, effective structural inhibition of spike-RBD. MD simulation of 100 ns of each complex proved high stability of complexes with RMSD values ranging from 0.2 to 1.5 nm. Consistent interactions of lead ACE-2 binding spike residues with lectin during simulation disclosed efficient structural inhibition by lectin against formation of spike RBD-ACE-2 complex. Hence, lectins along with their ability to induce innate immunity against spike glycoprotein can structurally inhibit the spike-RBD when given as lectin-antibody dyad system and thus can be developed into a dual effect treatment against COVID-19. Moreover, the high binding specificity of this system with spike-RBD can be exploited for development of diagnostic and drug-delivery systems.

Presynchronization with simultaneous administration of GnRH and prostaglandin F2α (PGF2α) 7 days prior to Ovsynch improves reproductive profile in Hariana zebu cow.

This study is aimed at assessing the impact of simultaneous administration of GnRH and prostaglandin F2α (PGF2α) 7 days prior to Ovsynch in Hariana cow. Two hundred cyclic cows (> 4 months postpartum) were assigned to control (n = 54) and pre-OV (n = 146). As per Ovsynch protocol, buserelin acetate (10 µg), cloprostenol (500 µg), and buserelin acetate (10 µg) were injected i.m. on days 0, 7, and 9, respectively, in cows irrespective of treatment. But in pre-OV cows, buserelin acetate (10 µg) and cloprostenol (500 µg) were also injected i.m. simultaneously 7 days prior to initiate the Ovsynch protocol. Artificial insemination was performed between 18 and 24 h after the 2nd GnRH of Ovsynch in both treatments. Ultrasonography and blood sampling for hormonal analysis were done on each day of treatment, on day of AI, and 12 days post-AI. Pre-OV treatment resulted to increased (45.20% vs 29.62%; P < 0.05) pregnancy outcomes and higher (P < 0.01) ovulation rate to first GnRH of Ovsynch than control. Cows showing complete luteolysis in response to PGF2α of Ovsynch were also higher (P < 0.05) in pre-OV than control. Greater (P < 0.05) synchronization rate was recorded in pre-OV than control (86.76% and 68.75%). The circulating concentrations of estradiol on day of AI and progesterone on day 12 post-AI were higher (P < 0.01) in cows diagnosed pregnant than non-pregnant in both control and pre-OV treatment. In conclusion, simultaneous administration of GnRH and PGF2α 7 days before Ovsynch improved the synchronization rate and luteal profile in terms of CL area and hence resulted in higher conception rate in Hariana zebu cow.

Visible-Light-Induced Photocatalytic Oxidative Decarboxylation of Cinnamic Acids to 1,2-Diketones.

A concerted metallophotoredox catalysis has been realized for the efficient decarboxylative functionalization of α,ß-unsaturated carboxylic acids with aryl iodides in the presence of perylene bisimide dye to afford 1,2-diketones.

Maternal transmission of mitochondrial diseases.

Given the major role of the mitochondrion in cellular homeostasis, dysfunctions of this organelle may lead to several common diseases in humans. Among these, maternal diseases linked to mitochondrial DNA (mtDNA) mutations are of special interest due to the unclear pattern of mitochondrial inheritance. Multiple copies of mtDNA are present in a cell, each encoding for 37 genes essential for mitochondrial function. In cases of mtDNA mutations, mitochondrial malfunctioning relies on mutation load, as mutant and wild-type molecules may co-exist within the cell. Since the mutation load associated with disease manifestation varies for different mutations and tissues, it is hard to predict the progeny phenotype based on mutation load in the progenitor. In addition, poorly understood mechanisms act in the female germline to prevent the accumulation of deleterious mtDNA in the following generations. In this review, we outline basic aspects of mitochondrial inheritance in mammals and how they may lead to maternally-inherited diseases. Furthermore, we discuss potential therapeutic strategies for these diseases, which may be used in the future to prevent their transmission.

Triazino indole-quinoline hybrid: a novel approach to antileishmanial agents.

A novel series of 1,2,4-triazino-[5,6b]indole-3-thione covalently linked to 7-chloro-4-aminoquinoline have been synthesized and evaluated for their in vitro activity against extracellular promastigote and intracellular amastigote form of Leishmania donovani. Among all tested compounds, compounds 7a and 7b were found to be the most active with IC50 values 1.11, 0.36µM and selectivity index (SI) values 67, >1111, respectively, against amastigote form of L. donovani which is several folds more potent than the standard drugs, miltefosine (IC50=8.10µM, SI=7) and sodium stibo-gluconate (IC50=54.60µM, SI⩾7).

Biodegradation of acetaminophen: Microcosm centric genomic-proteomic-metabolomics evidences.

Acetaminophen (APAP) is a frequently used, over-the-counter analgesic and antipyretic medication. Considering increase in global consumption, its ubiquity in environment with potential toxic impacts has become a cause of great concern. Hence, bioremediation of this emerging contaminant is of paramount significance. The present study incorporates a microcosm centric omics approach to gain in-depth insights into APAP degradation by Paracoccus sp. APAP_BH8. It can metabolize APAP (300 mg kg-1) within 16 days in soil microcosms. Genome analysis revealed potential genes capable of mediating degradation includes M20 aminoacylase family protein, guanidine deaminase, 4-hydroxybenzoate 3-monooxygenase, and 4-hydroxyphenylpyruvate dioxygenase. Whole proteome analysis showed differential expression of enzymes and bioinformatics provided evidence for stable binding of intermediates at the active site of considered enzymes. Metabolites identified were 4-aminophenol, hydroquinone, and 3-hydroxy-cis, cis-muconate. Therefore, Paracoccus sp. APAP_BH8 with versatile enzymatic and genetic attributes can be a promising candidate for formulating improved in situ APAP bioremediation strategies.

Insights into the biodegradation of fipronil through soil microcosm-omics analyses of Pseudomonas sp. FIP_ A4.

Fipronil, a phenylpyrazole insecticide, is used to kill insects resistant to conventional insecticides. Though its regular and widespread use has substantially reduced agricultural losses, it has also caused its accumulation in various environmental niches. The biodegradation is an effective natural process that helps in reducing the amount of residual insecticides. This study deals with an in-depth investigation of fipronil degradation kinetics and pathways in Pseudomonas sp. FIP_A4 using multi-omics approaches. Soil-microcosm results revealed ∼87% degradation within 40 days. The whole genome of strain FIP_A4 comprises 4.09 Mbp with 64.6% GC content. Cytochrome P450 monooxygenase and enoyl-CoA hydratase-related protein, having 30% identity with dehalogenase detected in the genome, can mediate the initial degradation process. Proteome analysis revealed differential enzyme expression of dioxygenases, decarboxylase, and hydratase responsible for subsequent degradation. Metabolome analysis displayed fipronil metabolites in the presence of the bacterium, supporting the proposed degradation pathway. Molecular docking and dynamic simulation of each identified enzyme in complex with the specific metabolite disclosed adequate binding and high stability in the enzyme-metabolite complex. This study provides in-depth insight into genes and their encoded enzymes involved in the fipronil degradation and formation of different metabolites during pollutant degradation. The outcome of this study can contribute immensely to developing efficient technologies for the bioremediation of fipronil-contaminated soils.

Synthesis of perspicamide A and related diverse analogues: their bioevaluation as potent antileishmanial agents.

The first protocol for the synthesis of perspicamide A and related diverse analogues has been developed from economical and readily available starting materials. Furthermore, a few synthesized analogues, 24a, 24b, 24c, 24d, and 24l, exhibited potent activity against Leishmania donovani with IC(50) values ranging from 3.75 to 10.37 µM and a selectivity index (SI) ranging from 9.58 to 53.12, which is improved compared to the standard drug Miltefosine (IC(50) 12.4 µM and SI 4.1).

Impact of norgestomet supplementation during early luteal phase on subsequent luteal profiles and conception rate in buffalo: a preliminary study.

The current study was aimed to establish the impact of progesterone supplementation (norgestomet progestagen) between days 4 to 10 post-ovulation on subsequent luteal profile and conception rate in buffaloes. The 28 Murrah buffaloes of second to fourth parity, having normal reproductive organs, were estrus synchronized by double PGF(2α) protocol at 11 days apart. The buffaloes were inseminated during mid- to late estrus and thereafter repeated at 24 h interval. The buffaloes were randomly assigned into two groups: (1) control (no treatment, n = 14) and (2) treatment group (CRESTAR ear implant, n = 14). The CRESTAR ear implant (3 mg, norgestomet progestagen) was inserted subcutaneous between days 4 to 10 post-ovulation. The ovaries were scanned at estrus and thereafter on days 4, 10, 16, 21, and 40 post-ovulation to examine the preovulatory follicle (POF) and corpus luteum (CL) diameter. Each ultasonography was followed by blood sample collection for analysis of plasma progesterone concentrations following ovulation. The conception rate was similar (p > 0.05) between treated and control buffaloes. The pregnant buffalo of the control group had larger (p < 0.05) POF diameter than nonpregnant counterparts. The CL diameter was similar (p > 0.05) in both treated and untreated control as well as in their pregnant and nonpregnant buffaloes of the respective groups. The plasma progesterone concentrations were higher (p < 0.05) in the treatment group on the day 10 post-ovulation as compared to the control buffaloes. It is concluded that norgestomet supplementation had no impact on conception rate and CL diameter but enhances the plasma progesterone concentrations following treatment in buffaloes.

Genome sequencing and in silico analysis of isoprene degrading monooxygenase enzymes of Sphingobium sp. BHU LFT2.

The whole genome sequencing of a novel isoprene degrading strain of Sphingobium sp. BHU LFT2, its in silico analysis for identifying and characterizing enzymes, especially isoprene monooxygenases (IsoMO), which initiate the degradation process, and in vitro validation with cell extract of optimal temperature and pH and analysis for utilizing isoprene as the preferential substrate, were conducted. The most efficient monooxygenase was identified through comparative analyses using molecular docking followed by molecular dynamics simulation approach. The in silico results revealed high thermostability for most of the monooxygenases. Most potent monooxygenase with locus ID JQK15_20300 exhibiting high sequence similarity with known monooxygenases of isoprene-degrading Rhodococcus sp. LB1 and SC4 strains was identified. Interaction energy of -17.25 kJ/mol for JQK15_20300 with isoprene, was almost similar as that analysed for above-mentioned similar known counterparts, was exhibited by the molecular docking. Molecular dynamic simulation of 100 ns and free energy analysis of JQK15_20300 in the complex with isoprene gave persistent interaction of isoprene with JQK15_20300 during the simulation with high average binding energy of -47.13 kJ/mol thus proving higher affinity of JQK15_20300 for isoprene. The study revealed that the highly efficient isoprene degrading strain of Sphingobium sp. BHU LFT2 having effective monooxygenase could be utilized for large-scale applications including detoxification of air contaminated with isoprene in closed working systems.Communicated by Ramaswamy H. Sarma.

Microcosm-omics centric investigation reveals elevated bacterial degradation of imidacloprid.

Imidacloprid, a broad-spectrum insecticide, is widely used against aphids and other sucking insects. As a result, its toxic effect is becoming apparent in non-targeted organisms. In-situ bioremediation of residual insecticide from the environment utilizing efficient microbes would be helpful in reducing its load. In the present work, in-depth genomics, proteomics, bioinformatics, and metabolomics analyses were employed to reveal the potential of Sphingobacterium sp. InxBP1 for in-situ degradation of imidacloprid. The microcosm study revealed ∼79% degradation with first-order kinetics (k = 0.0726 day-1). Genes capable of mediating oxidative degradation of imidacloprid and subsequent decarboxylation of intermediates were identified in the bacterial genome. Proteome analysis demonstrated significant overexpression of the enzymes coded by these genes. Bioinformatic analysis revealed significant affinity and binding of the identified enzymes for their respective substrates (the degradation pathway intermediates). The nitronate monooxygenase (K7A41 01745), amidohydrolase (K7A41 03835 and K7A41 07535), FAD-dependent monooxygenase (K7A41 12,275), and ABC transporter enzymes (K7A41 05325, and K7A41 05605) were found to be effective in facilitating the transport and intracellular degradation of imidacloprid. The metabolomic study identified the pathway intermediates and validated the proposed mechanism and functional role of the identified enzymes in degradation. Thus, the present investigation provides an efficient imidacloprid degrading bacterial species as evidenced by its genetic attributes which can be utilized or further improved to develop technologies for in-situ remediation.

Synthesis of unsymmetrical ketones via dual catalysed cross-coupling of α,ß-unsaturated carboxylic acids with aryldiazonium salts.

A visible light-enabled synthesis of unsymmetrical ketones has been accomplished by the cross-coupling of α,ß-unsaturated carboxylic acids and aryldiazonium salts embracing a synergistic eosin Y and Co(OAc)2·4H2O catalysis. The reaction involves decarboxylative aerobic CC bond cleavage, and is endowed with the creation of new C-C and C-O bonds with good substrate scope.

Silver nanoparticle as an alternate to antibiotics in cattle semen during cryopreservation.

The proposed study was to determine if the silver nanoparticles can be used as potential antimicrobial agents and can replace the use of conventional antibiotics in semen without affecting the motility and fertility of semen. The silver nanoparticles prepared by chemical reduction method were confirmed by determination of the wavelength of surface plasmon resonance peak and further characterized using Zetasizer by determining their size, polydispersity index, and zeta potential. The nanoparticles were assessed for antibacterial activity and their concentration was optimized for use in semen extender for cryopreservation. Cryopreserved semen was further evaluated for seminal parameters, antioxidant parameter, and microbial load. Prepared silver NPs showed a plasmon resonance peak at 417 nm wavelength. NPs were found to possess antibacterial activity and were supplemented in semen extender @ 125 and 250 µg/ml for semen cryopreservation. There was a significant increase in pre and post-freezing motility and other seminal parameters. The microbial load of frozen-thawed semen of control and supplemented groups were well within the permissible limits. Lipid peroxidation levels were reduced in NPs supplemented groups, and reactive oxygen species (ROS) levels were significantly reduced in semen supplemented with 125 µg/ml NPs. Thus it can be conclude that silver NPs can be successfully used as a substitute for antibiotics in cattle bull semen cryopreservation with good antimicrobial activity and no adverse effects on sperm characteristics.