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Article ; Online: Drug-Repurposing Approach To Combat

Singh, Vishakha / Dhankhar, Poonam / Dalal, Vikram / Tomar, Shailly / Golemi-Kotra, Dasantila / Kumar, Pravindra

ACS omega

2022 Volume 7, Issue 43, Page(s) 38448–38458

Abstract: Staphylococcus ... ...

Abstract	Staphylococcus aureus
Language	English
Publishing date	2022-10-18
Publishing country	United States
Document type	Journal Article
ISSN	2470-1343
ISSN (online)	2470-1343
DOI	10.1021/acsomega.2c03671
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Article ; Online: Biochemical and structural basis for Moraxella catarrhalis enoyl-acyl carrier protein reductase (FabI) inhibition by triclosan and estradiol.

Katiki, Madhusudhanarao / Neetu, Neetu / Pratap, Shivendra / Kumar, Pravindra

Biochimie

2022 Volume 198, Page(s) 8–22

Abstract: The enoyl-acyl carrier protein reductase (ENR) is an established drug target and catalyzes the last reduction step of the fatty acid elongation cycle. Here, we report the crystal structures of FabI from Moraxella catarrhalis (McFabI) in the apo form, ... ...

Abstract	The enoyl-acyl carrier protein reductase (ENR) is an established drug target and catalyzes the last reduction step of the fatty acid elongation cycle. Here, we report the crystal structures of FabI from Moraxella catarrhalis (McFabI) in the apo form, binary complex with NAD+ and ternary complex with NAD
MeSH term(s)	Acyl Carrier Protein ; Enoyl-(Acyl-Carrier-Protein) Reductase (NADH)/metabolism ; Estradiol ; Moraxella catarrhalis ; Triclosan/pharmacology
Chemical Substances	Acyl Carrier Protein ; Triclosan (4NM5039Y5X) ; Estradiol (4TI98Z838E) ; Enoyl-(Acyl-Carrier-Protein) Reductase (NADH) (EC 1.3.1.9)
Language	English
Publishing date	2022-03-08
Publishing country	France
Document type	Journal Article
ZDB-ID	120345-9
ISSN	1638-6183 ; 0300-9084
ISSN (online)	1638-6183
ISSN	0300-9084
DOI	10.1016/j.biochi.2022.02.008
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Article ; Online: Quantum Mechanics/Molecular Mechanics Studies on the Catalytic Mechanism of a Novel Esterase (FmtA) of

Dalal, Vikram / Golemi-Kotra, Dasantila / Kumar, Pravindra

Journal of chemical information and modeling

2022 Volume 62, Issue 10, Page(s) 2409–2420

Abstract: FmtA is a novel esterase that shares the penicillin-binding protein (PBP) core structural folding but found to hydrolyze the removal of d-Ala from teichoic acids. Molecular docking, dynamics, and MM-GBSA of FmtA and its variants S127A, K130A, Y211A, ... ...

Abstract	FmtA is a novel esterase that shares the penicillin-binding protein (PBP) core structural folding but found to hydrolyze the removal of d-Ala from teichoic acids. Molecular docking, dynamics, and MM-GBSA of FmtA and its variants S127A, K130A, Y211A, D213A, and K130AY211A, in the presence or absence of wall teichoic acid (WTA), suggest that active site residues S127, K130, Y211, D213, N343, and G344 play a role in substrate binding. Quantum mechanics (QM)/molecular mechanics (MM) calculations reveal that during WTA catalysis, K130 deprotonates S127, and the nucleophilic S127 attacks the carbonyl carbon of d-Ala bound to WTA. The tetrahedral intermediate (TI) complex is stabilized by hydrogen bonding to the oxyanion holes. The TI complex displays a high energy gap and collapses to an energetically favorable acyl-enzyme complex.
MeSH term(s)	Catalysis ; Cell Wall/chemistry ; Cell Wall/metabolism ; Esterases/analysis ; Esterases/metabolism ; Molecular Docking Simulation ; Staphylococcus aureus/metabolism ; Teichoic Acids/analysis ; Teichoic Acids/chemistry ; Teichoic Acids/metabolism
Chemical Substances	Teichoic Acids ; Esterases (EC 3.1.-)
Language	English
Publishing date	2022-04-27
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	190019-5
ISSN	1549-960X ; 0095-2338
ISSN (online)	1549-960X
ISSN	0095-2338
DOI	10.1021/acs.jcim.2c00057
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Article ; Online: Biophysical and modeling-based approach for the identification of inhibitors against DOHH from Leishmania donovani.

Katiki, Madhusudhanarao / Sharma, Monica / Neetu, Neetu / Rentala, Madhubala / Kumar, Pravindra

Briefings in functional genomics

2022 Volume 22, Issue 2, Page(s) 217–226

Abstract: The amino acid hypusine (Nε-4-amino-2-hydroxybutyl(lysine)) occurs only in isoforms of eukaryotic translation factor 5A (eIF5A) and has a role in initiating protein translation. Hypusinated eIF5A promotes translation and modulates mitochondrial function ... ...

Abstract	The amino acid hypusine (Nε-4-amino-2-hydroxybutyl(lysine)) occurs only in isoforms of eukaryotic translation factor 5A (eIF5A) and has a role in initiating protein translation. Hypusinated eIF5A promotes translation and modulates mitochondrial function and oxygen consumption rates. The hypusination of eIF5A involves two enzymes, deoxyhypusine synthase and deoxyhypusine hydroxylase (DOHH). DOHH is the second enzyme that completes the synthesis of hypusine and the maturation of eIF5A. Our current study aims to identify inhibitors against DOHH from Leishmania donovani (LdDOHH), an intracellular protozoan parasite causing Leishmaniasis in humans. The LdDOHH protein was produced heterologously in Escherichia coli BL21(DE3) cells and characterized biochemically. The three-dimensional structure was predicted, and the compounds folic acid, scutellarin and homoarbutin were selected as top hits in virtual screening. These compounds were observed to bind in the active site of LdDOHH stabilizing the structure by making hydrogen bonds in the active site, as observed by the docking and molecular dynamics simulation studies. These results pave the path for further investigation of these molecules for their anti-leishmanial activities.
MeSH term(s)	Humans ; Leishmania donovani
Language	English
Publishing date	2022-06-30
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2540916-5
ISSN	2041-2657 ; 2041-2649 ; 2041-2647
ISSN (online)	2041-2657
ISSN	2041-2649 ; 2041-2647
DOI	10.1093/bfgp/elac014
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Article: Emerging SARS-CoV-2 Variants: Genetic Variability and Clinical Implications

Dubey, Aakriti / Choudhary, Shweta / Kumar, Pravindra / Tomar, Shailly

Current microbiology. 2022 Jan., v. 79, no. 1

2022

Abstract: The sudden rise in COVID-19 cases in 2020 and the incessant emergence of fast-spreading variants have created an alarming situation worldwide. Besides the continuous advancements in the design and development of vaccines to combat this deadly pandemic, ... ...

Abstract	The sudden rise in COVID-19 cases in 2020 and the incessant emergence of fast-spreading variants have created an alarming situation worldwide. Besides the continuous advancements in the design and development of vaccines to combat this deadly pandemic, new variants are frequently reported, possessing mutations that rapidly outcompeted an existing population of circulating variants. As concerns grow about the effects of mutations on the efficacy of vaccines, increased transmissibility, immune escape, and diagnostic failures are few other apprehensions liable for more deadly waves of COVID-19. Although the phenomenon of antigenic drift in new variants of SARS-CoV-2 is still not validated, it is conceived that the virus is acquiring new mutations as a fitness advantage for rapid transmission or to overcome immunological resistance of the host cell. Considerable evolution of SARS-CoV-2 has been observed since its first appearance in 2019, and despite the progress in sequencing efforts to characterize the mutations, their impacts in many variants have not been analyzed. The present article provides a substantial review of literature explaining the emerging variants of SARS-CoV-2 circulating globally, key mutations in viral genome, and the possible impacts of these new mutations on prevention and therapeutic strategies currently administered to combat this pandemic. Rising infections, mortalities, and hospitalizations can possibly be tackled through mass vaccination, social distancing, better management of available healthcare infrastructure, and by prioritizing genome sequencing for better serosurveillance studies and community tracking.
Keywords	COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; antigenic variation ; evolution ; health services ; infrastructure ; pandemic ; vaccination ; viral genome ; viruses
Language	English
Dates of publication	2022-01
Size	p. 20.
Publishing place	Springer US
Document type	Article
Note	Review
ZDB-ID	134238-1
ISSN	1432-0991 ; 0343-8651
ISSN (online)	1432-0991
ISSN	0343-8651
DOI	10.1007/s00284-021-02724-1
Database	NAL-Catalogue (AGRICOLA)

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Article: Biochemical and structural basis for Moraxella catarrhalis enoyl-acyl carrier protein reductase (FabI) inhibition by triclosan and estradiol

Katiki, Madhusudhanarao / Neetu, Neetu / Pratap, Shivendra / Kumar, Pravindra

Biochimie. 2022 July, v. 198

2022

Abstract	The enoyl-acyl carrier protein reductase (ENR) is an established drug target and catalyzes the last reduction step of the fatty acid elongation cycle. Here, we report the crystal structures of FabI from Moraxella catarrhalis (McFabI) in the apo form, binary complex with NAD+ and ternary complex with NAD ⁺ -triclosan (TCL) determined at 2.36, 2.12 and 2.22 Å resolutions, respectively. The comparative study of these three structures revealed three different conformational states for the substrate-binding loop (SBL), including an unstructured intermediate, a structured intermediate and a closed conformation in the apo, binary and ternary complex forms, respectively; indicating the flexibility of SBL during the ligand binding. Virtual screening has suggested that estradiol cypionate may be a potential inhibitor of McFabI. Subsequently, estradiol (EST), the natural form of estradiol cypionate, was assessed for its FabI-binding and -inhibition properties. In vitro studies demonstrated that TCL and EST bind to McFabI with high affinity (KD = 0.038 ± 0.004 and 5 ± 0.06 μM respectively) and inhibit its activity (Kᵢ = 62.93 ± 3.95 nM and 25.97 ± 1.93 μM respectively) and suppress the growth of M. catarrhalis. These findings reveal that TCL and EST inhibit the McFabI activity and thereby affect cell growth. This study suggests that estradiol may be exploited as a novel scaffold for the designing and development of more potential FabI inhibitors.
Keywords	Moraxella catarrhalis ; cell growth ; comparative study ; drugs ; estradiol ; fatty acids ; ligands ; oxidoreductases ; triclosan
Language	English
Dates of publication	2022-07
Size	p. 8-22.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	120345-9
ISSN	0300-9084
ISSN	0300-9084
DOI	10.1016/j.biochi.2022.02.008
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Article ; Online: Characterization of AICAR transformylase/IMP cyclohydrolase (ATIC) bifunctional enzyme from Candidatus Liberibacer asiaticus.

Lonare, Sapna / Rode, Surabhi / Verma, Preeti / Verma, Shalja / Kaur, Harry / Alam, Md Shahid / Wangmo, Padma / Kumar, Pravindra / Roy, Partha / Sharma, Ashwani Kumar

Biochimica et biophysica acta. Proteins and proteomics

2024 Volume 1872, Issue 4, Page(s) 141015

Abstract: The bifunctional enzyme, 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) transformylase/inosine monophosphate (IMP) cyclohydrolase (ATIC) is involved in catalyzing penultimate and final steps of purine de novo biosynthetic pathway crucial for the ... ...

Abstract	The bifunctional enzyme, 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) transformylase/inosine monophosphate (IMP) cyclohydrolase (ATIC) is involved in catalyzing penultimate and final steps of purine de novo biosynthetic pathway crucial for the survival of organisms. The present study reports the characterization of ATIC from Candidatus Liberibacer asiaticus (CLasATIC) along with the identification of potential inhibitor molecules and evaluation of cell proliferative activity. CLasATIC showed both the AICAR Transformylase (AICAR TFase) activity for substrates, 10-f-THF (K
Language	English
Publishing date	2024-04-12
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2918798-9
ISSN	1878-1454 ; 1570-9639
ISSN (online)	1878-1454
ISSN	1570-9639
DOI	10.1016/j.bbapap.2024.141015
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Article ; Online: Structural insights at acidic pH of dye-decolorizing peroxidase from Bacillus subtilis.

Dhankhar, Poonam / Dalal, Vikram / Sharma, Ashwani Kumar / Kumar, Pravindra

Proteins

2022 Volume 91, Issue 4, Page(s) 508–517

Abstract: Dye-decolorizing peroxidases (DyPs), a type of heme-containing oxidoreductase enzymes, catalyze the peroxide-dependent oxidation of various industrial dyes as well as lignin and lignin model compounds. In our previous work, we have recently reported the ... ...

Abstract	Dye-decolorizing peroxidases (DyPs), a type of heme-containing oxidoreductase enzymes, catalyze the peroxide-dependent oxidation of various industrial dyes as well as lignin and lignin model compounds. In our previous work, we have recently reported the crystal structures of class A-type DyP from Bacillus subtilis at pH 7.0 (BsDyP7), exposing the location of three binding sites for small substrates and high redox-potential substrates. The biochemical studies revealed the optimum acidic pH for enzyme activity. In the present study, the crystal structure of BsDyP at acidic pH (BsDyP4) reveals two-monomer units stabilized by intermolecular salt bridges and a hydrogen bond network in a homo-dimeric unit. Based on the monomeric structural comparison of BsDyP4 and BsDyP7, minor differences were observed in the loop regions, that is, LI (Ala64-Gln71), LII (Glu96-Lys108), LIII (Pro117-Leu124), and LIV (Leu295-Asp303). Despite these differences, BsDyP4 adopts similar heme architecture as well as three substrate-binding sites to BsDyP7. In BsDyP4, a shift in Asp187, heme pocket residue discloses the plausible reason for optimal acidic pH for BsDyP activity. This study provides insight into the structural changes in BsDyP at acidic pH, where BsDyP is biologically active.
MeSH term(s)	Peroxidase/metabolism ; Bacillus subtilis ; Coloring Agents/metabolism ; Lignin/chemistry ; Peroxidases/chemistry ; Peroxidases/metabolism ; Hydrogen-Ion Concentration ; Heme/metabolism
Chemical Substances	Peroxidase (EC 1.11.1.7) ; Coloring Agents ; Lignin (9005-53-2) ; Peroxidases (EC 1.11.1.-) ; Heme (42VZT0U6YR)
Language	English
Publishing date	2022-11-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	806683-8
ISSN	1097-0134 ; 0887-3585
ISSN (online)	1097-0134
ISSN	0887-3585
DOI	10.1002/prot.26444
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Article ; Online: Structural Insights into Dihydroxylation of Terephthalate, a Product of Polyethylene Terephthalate Degradation.

Mahto, Jai Krishna / Neetu, Neetu / Sharma, Monica / Dubey, Monika / Vellanki, Bhanu Prakash / Kumar, Pravindra

Journal of bacteriology

2022 Volume 204, Issue 3, Page(s) e0054321

Abstract: Biodegradation of terephthalate (TPA) is a highly desired catabolic process for the bacterial utilization of this polyethylene terephthalate (PET) depolymerization product, but to date, the structure of terephthalate dioxygenase (TPDO), a Rieske ... ...

Abstract	Biodegradation of terephthalate (TPA) is a highly desired catabolic process for the bacterial utilization of this polyethylene terephthalate (PET) depolymerization product, but to date, the structure of terephthalate dioxygenase (TPDO), a Rieske oxygenase (RO) that catalyzes the dihydroxylation of TPA to a
MeSH term(s)	Dioxygenases/chemistry ; Oxygenases/genetics ; Phthalic Acids/metabolism ; Plastics ; Polyethylene Terephthalates/metabolism
Chemical Substances	Phthalic Acids ; Plastics ; Polyethylene Terephthalates ; terephthalic acid (6S7NKZ40BQ) ; Oxygenases (EC 1.13.-) ; Dioxygenases (EC 1.13.11.-)
Language	English
Publishing date	2022-01-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2968-3
ISSN	1098-5530 ; 0021-9193
ISSN (online)	1098-5530
ISSN	0021-9193
DOI	10.1128/JB.00543-21
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Article ; Online: Biochemical and molecular insights on the bioactivity and binding interactions of Bacillus australimaris NJB19 L-asparaginase.

Chakravarty, Namrata / Sharma, Monica / Kumar, Pravindra / Singh, R P

International journal of biological macromolecules

2022 Volume 215, Page(s) 1–11

Abstract: L-asparaginase, an antileukemic enzyme, is indispensable to the treatment of Acute Lymphoblastic Leukemia (ALL). However, the intrinsic glutaminase activity entails various side effects to the patients; thus, an improved version of the enzyme lacking ... ...

Abstract	L-asparaginase, an antileukemic enzyme, is indispensable to the treatment of Acute Lymphoblastic Leukemia (ALL). However, the intrinsic glutaminase activity entails various side effects to the patients; thus, an improved version of the enzyme lacking glutaminase activity would be a requisite for effective treatment management of ALL. The present study highlights the biochemical and molecular characteristics of the recombinant glutaminase-free L-asparaginase from Bacillus australimaris NJB19 (BaAsp). Investigation of the active site architecture of the protein unraveled the binding interactions of BaAsp with its substrate. Comparative analysis of the L-asparaginase sequences revealed few substitutions of key amino acids in the BaAsp that could construe its substrate selectivity and specificity. The purified heterologously expressed protein (42 kDa) displayed maximum L-asparaginase activity at 35-40 °C and pH 8.5-9, with no observed L-glutaminase activity. The kinetic parameters, Km and Vmax, were determined as 45.6 μM and 0.16 μmoles min
MeSH term(s)	Antineoplastic Agents/chemistry ; Asparaginase/chemistry ; Bacillus ; Humans ; Precursor Cell Lymphoblastic Leukemia-Lymphoma/drug therapy ; Substrate Specificity ; Zinc
Chemical Substances	Antineoplastic Agents ; Asparaginase (EC 3.5.1.1) ; Zinc (J41CSQ7QDS)
Language	English
Publishing date	2022-06-16
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2022.06.110
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