Amit Sonkar - Academia.edu (original) (raw)

Papers by Amit Sonkar

<i>Fasciola gigantica</i> is the causative organism of fascioliasis and is responsibl... more <i>Fasciola gigantica</i> is the causative organism of fascioliasis and is responsible for major economic losses in livestock production globally. <i>F. gigantica</i> thioredoxin1 (FgTrx1) is an important redox-active enzyme involved in maintaining the redox homeostasis in the cell. To identify a potential anti-fasciolid compound, we conducted a structure-based virtual screening of natural compounds from the ZINC database (<i>n</i> = 1,67,740) against the FgTrx1 structure. The ligands were docked against FgTrx1 and 309 ligands were found to have better docking score. These compounds were evaluated for Lipinski and ADMET prediction, and 30 compounds were found to fit well for re-docking studies. After refinement by molecular docking and drug-likeness analysis, three potential inhibitors (ZINC15970091, ZINC9312362, and ZINC9312661) were identified. These three ligands were further subjected to molecular dynamics simulation (MDS) to compare the dynamics and stability of the protein structure after binding of the ligands. The binding free energy analyses were calculated to determine the intermolecular interactions. The results suggested that the two compounds had a binding free energy of –82.237, and –109.52 kJ.mol⁻¹ for compounds with IDs ZINC9312362 and ZINC9312661, respectively. These predicted compounds displayed considerable pharmacological and structural properties to be drug candidates. We concluded that these two compounds could be potential drug candidates to fight against <i>F. gigantica</i> parasites.

ABSTRACTFascioliasis is a neglected food-borne disease caused by liver flukes (genus Fasciola) an... more ABSTRACTFascioliasis is a neglected food-borne disease caused by liver flukes (genus Fasciola) and affects more than 200 million people worldwide. Despite technological advances, little is known about the molecular biology and biochemistry of the fluke. We present the draft genome of Fasciola gigantica for the first time. The assembled draft genome has a size of ~1.04 Gb with an N50 of 129 kb. A total of 20,858 genes were predicted. The de novo repeats identified in the draft genome were 46.85%. In pathway analysis, all the genes of glycolysis, Kreb’s cycle and fatty acid metabolism were found to be present, but the key genes for fatty acid production in fatty acid biosynthesis were missing. This indicates that the fatty acid required for the survival of the fluke may be acquired from the host bile. The genomic information will provide a comprehensive resource to facilitate the development of novel interventions for fascioliasis control.

ACS Omega, 2019

Intrinsically disordered proteins (IDPs) lack an ordered 3D structure. These proteins contain one... more Intrinsically disordered proteins (IDPs) lack an ordered 3D structure. These proteins contain one or more intrinsically disordered protein regions (IDPRs). IDPRs interact promiscuously with other proteins, which leads to their structural transition from a disordered to an ordered state. Such interaction-prone regions of IDPs are known as molecular recognition features. Recent studies suggest that IDPs provide structural plasticity and functional diversity to viral proteins that are involved in rapid replication and immune evasion within the host cells. In the present study, we evaluated the prevalence of IDPs and IDPRs in human T lymphotropic virus type 1 (HTLV-1) proteome. We also investigated the presence of MoRF regions in the structural and nonstructural proteins of HTLV-1. We found abundant IDPRs in HTLV-1 bZIP factor, p30, Rex, and structural nucleocapsid p15 proteins, which are involved in diverse functions such as virus proliferation, mRNA export, and genomic RNA binding. Our study analyzed the HTLV-1 proteome with the perspective of intrinsic disorder identification. We propose that the intrinsic disorder analysis of HTLV-1 proteins may form the basis for the development of protein disorderbased drugs.

International Journal of Biological Macromolecules, 2018

Peptidoglycan (PG) is the main constituent of the bacterial cell wall. The enzyme UDP-Nacetylgluc... more Peptidoglycan (PG) is the main constituent of the bacterial cell wall. The enzyme UDP-Nacetylglucosamine enolpyruvyl transferase (MurA) catalyzes the transfer of enolpyruvate from phosphoenolpyruvate to uridinediphospho-N-acetylglucosamine, which is the first committed step of PG biosynthesis. In this study, we have systematically examined the urea-induced unfolding of Acinetobacter baumannii MurA (AbMurA) using various optical spectroscopic techniques and molecular dynamic simulations. The urea-induced unfolding of AbMurA was a three-state process, where a metastable intermediate conformation state is populated between 3.0-4.0 M. Above 6.0 M urea, AbMurA gets completely unfolded. The transition from the native structure to the partially unfolded metastable state involves ~30% loss of native contacts but little change in the radius of gyration or core hydration properties. The intermediate-to-unfolded state transition was characterized by a large increase in the radius of gyration. Molecular dynamics trajectories simulated in different unfolding conditions suggest that urea destabilizes AbMurA structure weakening hydrophobic interactions and the hydrogen bond network. We observed a

International journal of biological macromolecules, 2018

Accurate chromosomal segregation is crucial for the maintenance of genomic integrity. Rna14 is a ... more Accurate chromosomal segregation is crucial for the maintenance of genomic integrity. Rna14 is a major component of the yeast pre-mRNA 3'-end processing factor, the cleavage factor IA complex, and is involved in cleavage and polyadenylation of mRNA in the nucleus. Rna14 is also essential for the maintenance of genomic integrity in fission yeast Schizosaccharomyces pombe. In the present study, we report that a non-homologous mutation, A394E that is present in the central intrinsic disordered region of Rna14 leads to chromosomal instability in fission yeast. This mutation was shown to disrupt chromosome segregation and 3'-end maturation, and also affects the pre-mRNA splicing in vivo at non-permissive temperatures. We observed that a significant part of Rna14 is intrinsically disordered, that includes the N- and C-terminal of Rna14, as well as the central region containing the HAT repeats and the mutation within amino acid residues 372-435. These regions are crucial for the fu...

Journal of biomolecular structure & dynamics, Jan 27, 2017

Opisthorchis felineus is the etiological agent of opisthorchiasis in humans. O. felineus cytochro... more Opisthorchis felineus is the etiological agent of opisthorchiasis in humans. O. felineus cytochrome P450 (OfCYP450) is an important enzyme in the parasite xenobiotic metabolism. To identify the potential anti-opisthorchid compound, we conducted a structure-based virtual screening of natural compounds from the ZINC database (n = 1,65,869) against the OfCYP450. The ligands were screened against OfCYP450 in four sequential docking modes that resulted in 361 ligands having better docking score. These compounds were evaluated for Lipinski and ADMET prediction, and 10 compounds were found to fit well with re-docking studies. After refinement by docking and drug-likeness analyses, four potential inhibitors (ZINC2358298, ZINC8790946, ZINC70707116, and ZINC85878789) were identified. These ligands with reference compounds (itraconazole and fluconazole) were further subjected to molecular dynamics simulation (MDS) and binding energy analyses to compare the dynamic structure of protein after li...

International Journal of Biological Macromolecules, 2017

We demonstrate the reversible fibrillation of a globular protein modulated by salt under physiolo... more We demonstrate the reversible fibrillation of a globular protein modulated by salt under physiological pH.  The enzyme self-assembles into a fibrillar structure in the absence of salt in vitro.  The mature fibrillar structure is dynamic and restores its structure as well as activity with the addition of salt.  The results indicate the balance between stabilizing forces and the localized electrostatic repulsions destabilizing the structure is adjusted via ion shielding.

Molecular genetics and genomics : MGG, Jan 31, 2017

Accurate segregation of chromosome during mitosis requires the coordinated action of several cell... more Accurate segregation of chromosome during mitosis requires the coordinated action of several cell cycle checkpoints that monitor replication of the genome and the attachment of sister chromatids to the mitotic spindle apparatus. Here we have characterized the fission yeast Ctf1, an ortholog of S. cerevisiae Rna15 in the maintenance of genomic integrity. The ctf1 is nonessential for the cell survival and its deletion strain exhibit cold sensitivity. The ctf1 deleted cells exhibit genetic interaction with spindle checkpoint protein Mad2 and Bub1. The deletion of ctf1 gene affects the chromosomal attachment to the mitotic spindle leading to the accumulation of Bub1-GFP foci. Ctf1 localizes to the nucleus and physically interacts with Rna14, a cleavage and polyadenylation factor.

Journal of biomolecular structure & dynamics, Jan 19, 2017

Fasciola gigantica is the causative organism of fascioliasis and is responsible for major economi... more Fasciola gigantica is the causative organism of fascioliasis and is responsible for major economic losses in livestock production globally. F. gigantica thioredoxin1 (FgTrx1) is an important redox-active enzyme involved in maintaining the redox homeostasis in the cell. To identify a potential anti-fasciolid compound, we conducted a structure-based virtual screening of natural compounds from the ZINC database (n = 1,67,740) against the FgTrx1 structure. The ligands were docked against FgTrx1 and 309 ligands were found to have better docking score. These compounds were evaluated for Lipinski and ADMET prediction, and 30 compounds were found to fit well for re-docking studies. After refinement by molecular docking and drug-likeness analysis, three potential inhibitors (ZINC15970091, ZINC9312362 and ZINC9312661) were identified. These three ligands were further subjected to molecular dynamics simulation (MDS) to compare the dynamics and stability of the protein structure after binding o...

Journal of biomolecular structure & dynamics, Jan 12, 2017

Mycobacterium tuberculosis is the etiological agent of tuberculosis in humans and is responsible ... more Mycobacterium tuberculosis is the etiological agent of tuberculosis in humans and is responsible for more than two million deaths annually. M. tuberculosis isocitrate lyase (MtbICL) catalyzes the first step in the glyoxylate cycle, plays a pivotal role in the persistence of M. tuberculosis, which acts as a potential target for an anti-tubercular drug. To identify the potential anti-tuberculosis compound, we conducted a structure-based virtual screening of natural compounds from the ZINC database (n = 1,67,748) against the MtbICL structure. The ligands were docked against MtbICL in three sequential docking modes that resulted in 340 ligands having better docking score. These compounds were evaluated for Lipinski and ADMET prediction, and 27 compounds were found to fit well with re-docking studies. After refinement by molecular docking and drug-likeness analysis, three potential inhibitors (ZINC1306071, ZINC2111081, and ZINC2134917) were identified. These three ligands and the referen...

Biochemical and biophysical research communications, Aug 10, 2017

Mycobacterium tuberculosis isocitrate lyase (MtbICL) is a key enzyme of the glyoxylate cycle that... more Mycobacterium tuberculosis isocitrate lyase (MtbICL) is a key enzyme of the glyoxylate cycle that catalyzes the cleavage of isocitrate to succinate and glyoxylate and is a potential antituberculosis drug target. The aim of this research was to explore the structural alterations induced by L418A point mutation that caused the loss of enzyme activity. In-depth structural analyses were carried out for understanding the influence of L418A mutation using techniques, viz. molecular dynamics, principal component analysis, time-dependent secondary structure, residue interaction network and molecular docking. Since L418A mutation site is structurally far from the active site, it cannot influence the binding of the substrate directly. Our results showed that collective motions, residual mobility, and flexibility of the enzyme increased upon mutation. The mutated residue changed the global conformational dynamics of the system along with the residue-residue interaction network, leading to a lo...

International Journal of Biological Macromolecules, 2017

Peroxides are one of the most important radicals that cause oxidative stress. Certain Glutathione... more Peroxides are one of the most important radicals that cause oxidative stress. Certain Glutathione Stransferases (GSTs) have been reported to show peroxidase activity. We report a novel peroxidase activity of Synechocystis GST-sll1545. The recombinant protein was purified to homogeneity and characterized. Low Km (0.109 M) and high Vmax (0.663 mol min −1) values suggest a high preference of sll1545 for cumenehydroperoxide. Disc inhibition assay confirmed the ability of the enzyme to protect cells against peroxide-induced damage. sll1545 has very low sequence and structural similarity with theta and alpha class GSTs that exhibit glutathione-dependent peroxidase activity. Recent data from our laboratory shows that sll1545 is also strongly active against dichloroacetate (DCA), which is a characteristic of zeta class GST. Interestingly, sll1545 shows less than 20% sequence identity with zeta class GST. Molecular dynamic simulation results show that sll1545 was much more structurally different from alpha/theta classes. Our results suggest that sll1545 shows structural variation from zeta, theta/alpha classes of GSTs but have related enzymatic activity. Phylogenetic analysis reveal that sll1545 is evolutionally very distinct from the known GSTs. Overall, the data suggest that Synechocystis sll1545 does not belong to any known GST class and represent a novel GST class, which we have named rho.

Journal of Genetics, 2016

Spliceosome and 3-end processing complexes are necessary for the precursor mRNA (pre-mRNA) matura... more Spliceosome and 3-end processing complexes are necessary for the precursor mRNA (pre-mRNA) maturation. Spliceosome complex removes noncoding introns, while 3-end processing involves in cleavage and addition of poly(A) tails to the nascent transcript. Rna14 protein in budding yeast has been implicated in cleavage and polyadenylation of mRNA in the nucleus but their role in the pre-mRNA splicing has not been studied. Here, we report the isolation of a mutant allele of rna14 in fission yeast, Schizosaccharomyces pombe that exhibits reduction in protein level of Chk1 at the nonpermissive temperature, primarily due to the defects in posttranscriptional processing. Reverse transcriptase-polymerase chain reaction analysis reveals defective splicing of the chk1 + transcript at the nonpermissive temperature. Apart from chk1 + , the splicing of some other genes were also found to be defective at the nonpermissive temperature suggesting that Rna14 might be involved in pre-mRNA splicing. Subsequently, genetic interaction of Rna14 with prp1 and physical interactions with Prp28 suggest that the Rna14 might be part of a larger protein complex responsible for the pre-mRNA maturation.

Biochimica et biophysica acta, Jan 12, 2015

Faithful segregation of chromosomes is essential for the maintenance of genome integrity. In a ge... more Faithful segregation of chromosomes is essential for the maintenance of genome integrity. In a genetic screen to identify genes related to checkpoint function, we have characterized the role of rna14, an essential gene in the maintenance of chromosome dynamics. We demonstrate that Rna14 localizes in the nucleus and in the absence of functional Rna14, the cells exhibit chromosomal segregation defects. The mutant allele of rna14 exhibits genetic interaction with key kinetochore components and spindle checkpoint proteins. Inactivation of rna14 leads to accumulation of Bub1-GFP foci, a protein required for spindle checkpoint activation that could be due to the defects in the attachment of mitotic spindle to the chromosome. Consistently, the double mutant of rna14-11 and bub1 knockout exhibits high degree of chromosome mis-segregation. At restrictive condition, the rna14-11 mutant cells exhibit defects in cell cycle progression with high level of septation. The orthologs of Rna14 in Sacc...

Management of Microbial Resources in the Environment, 2013

ABSTRACT

Scientific Reports, 2017

Isocitrate lyase (ICL), a potential anti-tubercular drug target, catalyzes the first step of the ... more Isocitrate lyase (ICL), a potential anti-tubercular drug target, catalyzes the first step of the glyoxylate shunt. In the present investigation, we studied the conformational flexibility of MtbICL to better understand its stability and catalytic activity. Our biochemical results showed that a point mutation at Phe345, which is topologically distant (>10 Å) to the active site signature sequence (189KKCGH193), completely abolishes the activity of the enzyme. In depth computational analyses were carried out for understanding the structural alterations using molecular dynamics, time-dependent secondary structure and principal component analysis. The results showed that the mutated residue increased the structural flexibility and induced conformational changes near the active site (residues 170–210) and in the C-terminal lid region (residues 411–428). Both these regions are involved in the catalytic activity of MtbICL. Upon mutation, the residual mobility of the enzyme increased, resu...

<i>Fasciola gigantica</i> is the causative organism of fascioliasis and is responsibl... more <i>Fasciola gigantica</i> is the causative organism of fascioliasis and is responsible for major economic losses in livestock production globally. <i>F. gigantica</i> thioredoxin1 (FgTrx1) is an important redox-active enzyme involved in maintaining the redox homeostasis in the cell. To identify a potential anti-fasciolid compound, we conducted a structure-based virtual screening of natural compounds from the ZINC database (<i>n</i> = 1,67,740) against the FgTrx1 structure. The ligands were docked against FgTrx1 and 309 ligands were found to have better docking score. These compounds were evaluated for Lipinski and ADMET prediction, and 30 compounds were found to fit well for re-docking studies. After refinement by molecular docking and drug-likeness analysis, three potential inhibitors (ZINC15970091, ZINC9312362, and ZINC9312661) were identified. These three ligands were further subjected to molecular dynamics simulation (MDS) to compare the dynamics and stability of the protein structure after binding of the ligands. The binding free energy analyses were calculated to determine the intermolecular interactions. The results suggested that the two compounds had a binding free energy of –82.237, and –109.52 kJ.mol⁻¹ for compounds with IDs ZINC9312362 and ZINC9312661, respectively. These predicted compounds displayed considerable pharmacological and structural properties to be drug candidates. We concluded that these two compounds could be potential drug candidates to fight against <i>F. gigantica</i> parasites.

ABSTRACTFascioliasis is a neglected food-borne disease caused by liver flukes (genus Fasciola) an... more ABSTRACTFascioliasis is a neglected food-borne disease caused by liver flukes (genus Fasciola) and affects more than 200 million people worldwide. Despite technological advances, little is known about the molecular biology and biochemistry of the fluke. We present the draft genome of Fasciola gigantica for the first time. The assembled draft genome has a size of ~1.04 Gb with an N50 of 129 kb. A total of 20,858 genes were predicted. The de novo repeats identified in the draft genome were 46.85%. In pathway analysis, all the genes of glycolysis, Kreb’s cycle and fatty acid metabolism were found to be present, but the key genes for fatty acid production in fatty acid biosynthesis were missing. This indicates that the fatty acid required for the survival of the fluke may be acquired from the host bile. The genomic information will provide a comprehensive resource to facilitate the development of novel interventions for fascioliasis control.

ACS Omega, 2019

Intrinsically disordered proteins (IDPs) lack an ordered 3D structure. These proteins contain one... more Intrinsically disordered proteins (IDPs) lack an ordered 3D structure. These proteins contain one or more intrinsically disordered protein regions (IDPRs). IDPRs interact promiscuously with other proteins, which leads to their structural transition from a disordered to an ordered state. Such interaction-prone regions of IDPs are known as molecular recognition features. Recent studies suggest that IDPs provide structural plasticity and functional diversity to viral proteins that are involved in rapid replication and immune evasion within the host cells. In the present study, we evaluated the prevalence of IDPs and IDPRs in human T lymphotropic virus type 1 (HTLV-1) proteome. We also investigated the presence of MoRF regions in the structural and nonstructural proteins of HTLV-1. We found abundant IDPRs in HTLV-1 bZIP factor, p30, Rex, and structural nucleocapsid p15 proteins, which are involved in diverse functions such as virus proliferation, mRNA export, and genomic RNA binding. Our study analyzed the HTLV-1 proteome with the perspective of intrinsic disorder identification. We propose that the intrinsic disorder analysis of HTLV-1 proteins may form the basis for the development of protein disorderbased drugs.

International Journal of Biological Macromolecules, 2018

Peptidoglycan (PG) is the main constituent of the bacterial cell wall. The enzyme UDP-Nacetylgluc... more Peptidoglycan (PG) is the main constituent of the bacterial cell wall. The enzyme UDP-Nacetylglucosamine enolpyruvyl transferase (MurA) catalyzes the transfer of enolpyruvate from phosphoenolpyruvate to uridinediphospho-N-acetylglucosamine, which is the first committed step of PG biosynthesis. In this study, we have systematically examined the urea-induced unfolding of Acinetobacter baumannii MurA (AbMurA) using various optical spectroscopic techniques and molecular dynamic simulations. The urea-induced unfolding of AbMurA was a three-state process, where a metastable intermediate conformation state is populated between 3.0-4.0 M. Above 6.0 M urea, AbMurA gets completely unfolded. The transition from the native structure to the partially unfolded metastable state involves ~30% loss of native contacts but little change in the radius of gyration or core hydration properties. The intermediate-to-unfolded state transition was characterized by a large increase in the radius of gyration. Molecular dynamics trajectories simulated in different unfolding conditions suggest that urea destabilizes AbMurA structure weakening hydrophobic interactions and the hydrogen bond network. We observed a

International journal of biological macromolecules, 2018

Accurate chromosomal segregation is crucial for the maintenance of genomic integrity. Rna14 is a ... more Accurate chromosomal segregation is crucial for the maintenance of genomic integrity. Rna14 is a major component of the yeast pre-mRNA 3'-end processing factor, the cleavage factor IA complex, and is involved in cleavage and polyadenylation of mRNA in the nucleus. Rna14 is also essential for the maintenance of genomic integrity in fission yeast Schizosaccharomyces pombe. In the present study, we report that a non-homologous mutation, A394E that is present in the central intrinsic disordered region of Rna14 leads to chromosomal instability in fission yeast. This mutation was shown to disrupt chromosome segregation and 3'-end maturation, and also affects the pre-mRNA splicing in vivo at non-permissive temperatures. We observed that a significant part of Rna14 is intrinsically disordered, that includes the N- and C-terminal of Rna14, as well as the central region containing the HAT repeats and the mutation within amino acid residues 372-435. These regions are crucial for the fu...

Journal of biomolecular structure & dynamics, Jan 27, 2017

Opisthorchis felineus is the etiological agent of opisthorchiasis in humans. O. felineus cytochro... more Opisthorchis felineus is the etiological agent of opisthorchiasis in humans. O. felineus cytochrome P450 (OfCYP450) is an important enzyme in the parasite xenobiotic metabolism. To identify the potential anti-opisthorchid compound, we conducted a structure-based virtual screening of natural compounds from the ZINC database (n = 1,65,869) against the OfCYP450. The ligands were screened against OfCYP450 in four sequential docking modes that resulted in 361 ligands having better docking score. These compounds were evaluated for Lipinski and ADMET prediction, and 10 compounds were found to fit well with re-docking studies. After refinement by docking and drug-likeness analyses, four potential inhibitors (ZINC2358298, ZINC8790946, ZINC70707116, and ZINC85878789) were identified. These ligands with reference compounds (itraconazole and fluconazole) were further subjected to molecular dynamics simulation (MDS) and binding energy analyses to compare the dynamic structure of protein after li...

International Journal of Biological Macromolecules, 2017

We demonstrate the reversible fibrillation of a globular protein modulated by salt under physiolo... more We demonstrate the reversible fibrillation of a globular protein modulated by salt under physiological pH.  The enzyme self-assembles into a fibrillar structure in the absence of salt in vitro.  The mature fibrillar structure is dynamic and restores its structure as well as activity with the addition of salt.  The results indicate the balance between stabilizing forces and the localized electrostatic repulsions destabilizing the structure is adjusted via ion shielding.

Molecular genetics and genomics : MGG, Jan 31, 2017

Accurate segregation of chromosome during mitosis requires the coordinated action of several cell... more Accurate segregation of chromosome during mitosis requires the coordinated action of several cell cycle checkpoints that monitor replication of the genome and the attachment of sister chromatids to the mitotic spindle apparatus. Here we have characterized the fission yeast Ctf1, an ortholog of S. cerevisiae Rna15 in the maintenance of genomic integrity. The ctf1 is nonessential for the cell survival and its deletion strain exhibit cold sensitivity. The ctf1 deleted cells exhibit genetic interaction with spindle checkpoint protein Mad2 and Bub1. The deletion of ctf1 gene affects the chromosomal attachment to the mitotic spindle leading to the accumulation of Bub1-GFP foci. Ctf1 localizes to the nucleus and physically interacts with Rna14, a cleavage and polyadenylation factor.

Journal of biomolecular structure & dynamics, Jan 19, 2017

Fasciola gigantica is the causative organism of fascioliasis and is responsible for major economi... more Fasciola gigantica is the causative organism of fascioliasis and is responsible for major economic losses in livestock production globally. F. gigantica thioredoxin1 (FgTrx1) is an important redox-active enzyme involved in maintaining the redox homeostasis in the cell. To identify a potential anti-fasciolid compound, we conducted a structure-based virtual screening of natural compounds from the ZINC database (n = 1,67,740) against the FgTrx1 structure. The ligands were docked against FgTrx1 and 309 ligands were found to have better docking score. These compounds were evaluated for Lipinski and ADMET prediction, and 30 compounds were found to fit well for re-docking studies. After refinement by molecular docking and drug-likeness analysis, three potential inhibitors (ZINC15970091, ZINC9312362 and ZINC9312661) were identified. These three ligands were further subjected to molecular dynamics simulation (MDS) to compare the dynamics and stability of the protein structure after binding o...

Journal of biomolecular structure & dynamics, Jan 12, 2017

Mycobacterium tuberculosis is the etiological agent of tuberculosis in humans and is responsible ... more Mycobacterium tuberculosis is the etiological agent of tuberculosis in humans and is responsible for more than two million deaths annually. M. tuberculosis isocitrate lyase (MtbICL) catalyzes the first step in the glyoxylate cycle, plays a pivotal role in the persistence of M. tuberculosis, which acts as a potential target for an anti-tubercular drug. To identify the potential anti-tuberculosis compound, we conducted a structure-based virtual screening of natural compounds from the ZINC database (n = 1,67,748) against the MtbICL structure. The ligands were docked against MtbICL in three sequential docking modes that resulted in 340 ligands having better docking score. These compounds were evaluated for Lipinski and ADMET prediction, and 27 compounds were found to fit well with re-docking studies. After refinement by molecular docking and drug-likeness analysis, three potential inhibitors (ZINC1306071, ZINC2111081, and ZINC2134917) were identified. These three ligands and the referen...

Biochemical and biophysical research communications, Aug 10, 2017

Mycobacterium tuberculosis isocitrate lyase (MtbICL) is a key enzyme of the glyoxylate cycle that... more Mycobacterium tuberculosis isocitrate lyase (MtbICL) is a key enzyme of the glyoxylate cycle that catalyzes the cleavage of isocitrate to succinate and glyoxylate and is a potential antituberculosis drug target. The aim of this research was to explore the structural alterations induced by L418A point mutation that caused the loss of enzyme activity. In-depth structural analyses were carried out for understanding the influence of L418A mutation using techniques, viz. molecular dynamics, principal component analysis, time-dependent secondary structure, residue interaction network and molecular docking. Since L418A mutation site is structurally far from the active site, it cannot influence the binding of the substrate directly. Our results showed that collective motions, residual mobility, and flexibility of the enzyme increased upon mutation. The mutated residue changed the global conformational dynamics of the system along with the residue-residue interaction network, leading to a lo...

International Journal of Biological Macromolecules, 2017

Peroxides are one of the most important radicals that cause oxidative stress. Certain Glutathione... more Peroxides are one of the most important radicals that cause oxidative stress. Certain Glutathione Stransferases (GSTs) have been reported to show peroxidase activity. We report a novel peroxidase activity of Synechocystis GST-sll1545. The recombinant protein was purified to homogeneity and characterized. Low Km (0.109 M) and high Vmax (0.663 mol min −1) values suggest a high preference of sll1545 for cumenehydroperoxide. Disc inhibition assay confirmed the ability of the enzyme to protect cells against peroxide-induced damage. sll1545 has very low sequence and structural similarity with theta and alpha class GSTs that exhibit glutathione-dependent peroxidase activity. Recent data from our laboratory shows that sll1545 is also strongly active against dichloroacetate (DCA), which is a characteristic of zeta class GST. Interestingly, sll1545 shows less than 20% sequence identity with zeta class GST. Molecular dynamic simulation results show that sll1545 was much more structurally different from alpha/theta classes. Our results suggest that sll1545 shows structural variation from zeta, theta/alpha classes of GSTs but have related enzymatic activity. Phylogenetic analysis reveal that sll1545 is evolutionally very distinct from the known GSTs. Overall, the data suggest that Synechocystis sll1545 does not belong to any known GST class and represent a novel GST class, which we have named rho.

Journal of Genetics, 2016

Spliceosome and 3-end processing complexes are necessary for the precursor mRNA (pre-mRNA) matura... more Spliceosome and 3-end processing complexes are necessary for the precursor mRNA (pre-mRNA) maturation. Spliceosome complex removes noncoding introns, while 3-end processing involves in cleavage and addition of poly(A) tails to the nascent transcript. Rna14 protein in budding yeast has been implicated in cleavage and polyadenylation of mRNA in the nucleus but their role in the pre-mRNA splicing has not been studied. Here, we report the isolation of a mutant allele of rna14 in fission yeast, Schizosaccharomyces pombe that exhibits reduction in protein level of Chk1 at the nonpermissive temperature, primarily due to the defects in posttranscriptional processing. Reverse transcriptase-polymerase chain reaction analysis reveals defective splicing of the chk1 + transcript at the nonpermissive temperature. Apart from chk1 + , the splicing of some other genes were also found to be defective at the nonpermissive temperature suggesting that Rna14 might be involved in pre-mRNA splicing. Subsequently, genetic interaction of Rna14 with prp1 and physical interactions with Prp28 suggest that the Rna14 might be part of a larger protein complex responsible for the pre-mRNA maturation.

Biochimica et biophysica acta, Jan 12, 2015

Faithful segregation of chromosomes is essential for the maintenance of genome integrity. In a ge... more Faithful segregation of chromosomes is essential for the maintenance of genome integrity. In a genetic screen to identify genes related to checkpoint function, we have characterized the role of rna14, an essential gene in the maintenance of chromosome dynamics. We demonstrate that Rna14 localizes in the nucleus and in the absence of functional Rna14, the cells exhibit chromosomal segregation defects. The mutant allele of rna14 exhibits genetic interaction with key kinetochore components and spindle checkpoint proteins. Inactivation of rna14 leads to accumulation of Bub1-GFP foci, a protein required for spindle checkpoint activation that could be due to the defects in the attachment of mitotic spindle to the chromosome. Consistently, the double mutant of rna14-11 and bub1 knockout exhibits high degree of chromosome mis-segregation. At restrictive condition, the rna14-11 mutant cells exhibit defects in cell cycle progression with high level of septation. The orthologs of Rna14 in Sacc...

Management of Microbial Resources in the Environment, 2013

ABSTRACT

Scientific Reports, 2017

Isocitrate lyase (ICL), a potential anti-tubercular drug target, catalyzes the first step of the ... more Isocitrate lyase (ICL), a potential anti-tubercular drug target, catalyzes the first step of the glyoxylate shunt. In the present investigation, we studied the conformational flexibility of MtbICL to better understand its stability and catalytic activity. Our biochemical results showed that a point mutation at Phe345, which is topologically distant (>10 Å) to the active site signature sequence (189KKCGH193), completely abolishes the activity of the enzyme. In depth computational analyses were carried out for understanding the structural alterations using molecular dynamics, time-dependent secondary structure and principal component analysis. The results showed that the mutated residue increased the structural flexibility and induced conformational changes near the active site (residues 170–210) and in the C-terminal lid region (residues 411–428). Both these regions are involved in the catalytic activity of MtbICL. Upon mutation, the residual mobility of the enzyme increased, resu...