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Article: Author Reply Re: Jena R, Sharma AP, Madhavan K, Sridhar AN, Parmar K, Shrivastava N. What should urologists know about pseudojournals and open access publishing? A narrative review of the literature. Indian J Urol 2022;38:184-90.

Jena, Rahul / Sharma, Aditya Prakash / Madhavan, Kumar

Indian journal of urology : IJU : journal of the Urological Society of India

2022 Volume 39, Issue 1, Page(s) 78–79

Language	English
Publishing date	2022-12-29
Publishing country	India
Document type	Journal Article
ZDB-ID	639268-4
ISSN	1998-3824 ; 0970-1591
ISSN (online)	1998-3824
ISSN	0970-1591
DOI	10.4103/iju.iju_366_22
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Article ; Online: Binding of Nucleotide Inhibitors to the NS5 RdRp of the ZIKA Virus in the Replication Initiation State.

Pant, S / Jena, N R

Current medicinal chemistry

2024

Abstract: Introduction: The bindings of several ribonucleoside triphosphate (NTP) inhibitors to the RNA-dependent RNA polymerase (RdRp) of the Zika virus (ZIKV) are studied herein to identify potential drug-like candidates that can inhibit the replication of the ... ...

Abstract	Introduction: The bindings of several ribonucleoside triphosphate (NTP) inhibitors to the RNA-dependent RNA polymerase (RdRp) of the Zika virus (ZIKV) are studied herein to identify potential drug-like candidates that can inhibit the replication of the viral genome by RdRp. Method: In this study, a guanosine triphosphate (GTP) bound RdRp structure is generated to model the replication initiation state of RdRp. Subsequently, the bindings of 30 NTP inhibitors to the GTP binding site of RdRp are studied in detail by using the molecular docking method. Based on the docking scores, four NTP inhibitors, such as 2'-Cmethyl- adenosine-5'-triphosphate (mATP), 7-deaza-2'-C-methyladenosine-TP (daza-- mATP), 1-N6-Ethenoadenosine-5'-triphosphate (eATP), and Remdesivir-5'-triphosphate (RTP) are shortlisted for further analysis by employing molecular dynamics simulations and binding free-energy methods. Results: These inhibitors are found to bind to RdRp quite strongly, as evident from their relative binding free energies that lie between -31.54±4.54 to -89.46±4.58 kcal/- mol. As the binding of RTP to the GTP site of RdRp generates the most stable complex, which is about 45 kcal/mol more stable than the binding of GTP to RdRp, it is most likely that RTP may inhibit the replication of the Zika viral genome efficiently. Conclusion: However, experimental studies are required to measure the potency of RTP and other drugs before their clinical use.
Language	English
Publishing date	2024-02-12
Publishing country	United Arab Emirates
Document type	Journal Article
ZDB-ID	1319315-6
ISSN	1875-533X ; 0929-8673
ISSN (online)	1875-533X
ISSN	0929-8673
DOI	10.2174/0109298673259914231213052438
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Article ; Online: Rare Tautomers of Artificially Expanded Genetic Letters and their Effects on the Base Pair Stabilities.

Jena, N R

Chemphyschem : a European journal of chemical physics and physical chemistry

2022 Volume 23, Issue 6, Page(s) e202100908

Abstract: In order to expand the existing genetic letters, it is necessary to design robust nucleotides that can function naturally in living cells. Therefore, it is desirable to examine the roles of recently-proposed second-generation artificially genetic letters ...

Abstract	In order to expand the existing genetic letters, it is necessary to design robust nucleotides that can function naturally in living cells. Therefore, it is desirable to examine the roles of recently-proposed second-generation artificially genetic letters in producing stable duplex DNA. Herein, a reliable dispersion-corrected density functional theory method is used to shed light on the electronic structures and properties of different rare tautomers of proposed expanded genetic letters and their effects on the base pair stabilities in the duplex DNA. It is found that the rare tautomers are not only stable in the aqueous medium but can also pair with natural bases to produce stable mispairs. Except for J and V, all of the artificial genetic letters are found to produce mispairs that are about 1-7 kcal mol
MeSH term(s)	Base Pairing ; DNA/chemistry ; DNA/genetics ; Isomerism ; Nucleotides/chemistry ; Static Electricity ; Thermodynamics
Chemical Substances	Nucleotides ; DNA (9007-49-2)
Language	English
Publishing date	2022-01-28
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2025223-7
ISSN	1439-7641 ; 1439-4235
ISSN (online)	1439-7641
ISSN	1439-4235
DOI	10.1002/cphc.202100908
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Article ; Online: Discovery of a Plasmodium falciparum glucose-6-phosphate dehydrogenase 6-phosphogluconolactonase inhibitor (R,Z)-N-((1-ethylpyrrolidin-2-yl)methyl)-2-(2-fluorobenzylidene)-3-oxo-3,4-dihydro-2H-benzo[b][1,4]thiazine-6-carboxamide (ML276) that reduces parasite growth in vitro.

Preuss, Janina / Maloney, Patrick / Peddibhotla, Satyamaheshwar / Hedrick, Michael P / Hershberger, Paul / Gosalia, Palak / Milewski, Monika / Li, Yujie Linda / Sugarman, Eliot / Hood, Becky / Suyama, Eigo / Nguyen, Kevin / Vasile, Stefan / Sergienko, Eduard / Mangravita-Novo, Arianna / Vicchiarelli, Michael / McAnally, Danielle / Smith, Layton H / Roth, Gregory P /

Diwan, Jena / Chung, Thomas D Y / Jortzik, Esther / Rahlfs, Stefan / Becker, Katja / Pinkerton, Anthony B / Bode, Lars

Journal of medicinal chemistry

2012 Volume 55, Issue 16, Page(s) 7262–7272

Abstract: ... flux, they depend on the G6PD activity of PfGluPho. The lead compound identified from this effort, (R,Z ... N-((1-ethylpyrrolidin-2-yl)methyl)-2-(2-fluorobenzylidene)-3-oxo-3,4-dihydro-2H-benzo[b][1,4 ...

Abstract	A high-throughput screen of the NIH's MLSMR collection of ∼340000 compounds was undertaken to identify compounds that inhibit Plasmodium falciparum glucose-6-phosphate dehydrogenase (PfG6PD). PfG6PD is important for proliferating and propagating P. falciparum and differs structurally and mechanistically from the human orthologue. The reaction catalyzed by glucose-6-phosphate dehydrogenase (G6PD) is the first, rate-limiting step in the pentose phosphate pathway (PPP), a key metabolic pathway sustaining anabolic needs in reductive equivalents and synthetic materials in fast-growing cells. In P. falciparum , the bifunctional enzyme glucose-6-phosphate dehydrogenase-6-phosphogluconolactonase (PfGluPho) catalyzes the first two steps of the PPP. Because P. falciparum and infected host red blood cells rely on accelerated glucose flux, they depend on the G6PD activity of PfGluPho. The lead compound identified from this effort, (R,Z)-N-((1-ethylpyrrolidin-2-yl)methyl)-2-(2-fluorobenzylidene)-3-oxo-3,4-dihydro-2H-benzo[b][1,4]thiazine-6-carboxamide, 11 (ML276), is a submicromolar inhibitor of PfG6PD (IC(50) = 889 nM). It is completely selective for the enzyme's human isoform, displays micromolar potency (IC(50) = 2.6 μM) against P. falciparum in culture, and has good drug-like properties, including high solubility and moderate microsomal stability. Studies testing the potential advantage of inhibiting PfG6PD in vivo are in progress.
MeSH term(s)	Antimalarials/chemical synthesis ; Antimalarials/chemistry ; Antimalarials/pharmacology ; Carboxylic Ester Hydrolases/antagonists & inhibitors ; Drug Stability ; Glucosephosphate Dehydrogenase/antagonists & inhibitors ; High-Throughput Screening Assays ; Multienzyme Complexes/antagonists & inhibitors ; Parasitic Sensitivity Tests ; Plasmodium falciparum/drug effects ; Plasmodium falciparum/enzymology ; Small Molecule Libraries ; Stereoisomerism ; Structure-Activity Relationship ; Thiazines/chemical synthesis ; Thiazines/chemistry ; Thiazines/pharmacology
Chemical Substances	Antimalarials ; Multienzyme Complexes ; N-((1-ethylpyrrolidin-2-yl)methyl)-2-(2-fluorobenzylidene)-3-oxo-3,4-dihydro-2H-benzo(b)(1,4)thiazine-6-carboxamide ; Small Molecule Libraries ; Thiazines ; glucose-6-phosphate dehydrogenase-6-phosphogluconolactonase, Plasmodium falciparum ; Glucosephosphate Dehydrogenase (EC 1.1.1.49) ; Carboxylic Ester Hydrolases (EC 3.1.1.-)
Language	English
Publishing date	2012-08-06
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	218133-2
ISSN	1520-4804 ; 0022-2623
ISSN (online)	1520-4804
ISSN	0022-2623
DOI	10.1021/jm300833h
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Article ; Online: Repurposing of antiparasitic drugs against the NS2B-NS3 protease of the Zika virus.

Pant, S / Jena, N R

Journal of biomolecular structure & dynamics

2023 , Page(s) 1–13

Abstract: To date, no approved drugs are available to treat the Zika virus (ZIKV) infection. Therefore, it is necessary to urgently identify potential drugs against the ZIKV infection. Here, the repurposing of 30 antiparasitic drugs against the NS2B-NS3 protease ... ...

Abstract	To date, no approved drugs are available to treat the Zika virus (ZIKV) infection. Therefore, it is necessary to urgently identify potential drugs against the ZIKV infection. Here, the repurposing of 30 antiparasitic drugs against the NS2B-NS3 protease of the ZIKV has been carried out by using combined docking and molecular dynamics- (MD) simulations. Based on the docking results, 5 drugs, such as Amodiaquine, Primaquine, Paromomycin, Dichlorophene, and Ivermectin were screened for further analysis by MD simulations and free energy calculations. Among these drugs, Amodiaquine and Dichlorophen are found to produce the most stable complexes and possess relative binding free energies of about -44.3 ± 3.7 kcal/mol and -41.1 ± 5.3 kcal/mol respectively. Therefore, they would act as potent small-molecule inhibitors of the ZIKV protease.However, evaluations of biological and safety activities of these drugs against the ZIKV protease are required before their clinical use.Communicated by Ramaswamy H. Sarma.
Language	English
Publishing date	2023-09-25
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2255648
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Article ; Online: Peptide inhibitors derived from the nsp7 and nsp8 cofactors of nsp12 targeting different substrate binding sites of nsp12 of the SARS-CoV-2.

Jena, N R / Pant, Suyash

Journal of biomolecular structure & dynamics

2023 , Page(s) 1–13

Abstract: SARS-COV-2 is responsible for the COVID-19 pandemic, which has infected more than 767 million people worldwide including about 7 million deaths till 5 June 2023. Despite the emergency use of certain vaccines, deaths due to COVID-19 have not yet stopped ... ...

Abstract	SARS-COV-2 is responsible for the COVID-19 pandemic, which has infected more than 767 million people worldwide including about 7 million deaths till 5 June 2023. Despite the emergency use of certain vaccines, deaths due to COVID-19 have not yet stopped completed. Therefore, it is imperative to design and develop drugs that can be used to treat patients suffering from COVID-19. Here, two peptide inhibitors derived from nsp7 and nsp8 cofactors of nsp12 have been shown to block different substrate binding sites of nsp12 that are mainly responsible for the replication of the viral genome of SARS-CoV-2. By using the docking, molecular dynamics (MD), and MM/GBSA techniques, it is shown that these inhibitors can bind to multiple binding sites of nsp12, such as the interface of nsp7 and nsp12, interface of nsp8 and nsp12, RNA primer entry site, and nucleoside triphosphate (NTP) entry site. The relative binding free energies of the most stable protein-peptide complexes are found to lie between ∼-34.20 ± 10.07 to -59.54 ± 9.96 kcal/mol. Hence, it is likely that these inhibitors may bind to different sites of nsp12 to block the access of its cofactors and the viral genome, thereby affecting the replication. It is thus proposed that these peptide inhibitors may be further developed as potential drug candidates to suppress the viral loads in COVID-19 patients.Communicated by Ramaswamy H. Sarma.
Language	English
Publishing date	2023-07-11
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2235012
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Article ; Online: Structure and stability of different triplets involving artificial nucleobases: clues for the formation of semisynthetic triple helical DNA.

Jena, N R / Shukla, P K

Scientific reports

2023 Volume 13, Issue 1, Page(s) 19246

Abstract: A triple helical DNA can control gene expression, help in homologous recombination, induce mutations to facilitate DNA repair mechanisms, suppress oncogene formations, etc. However, the structure and function of semisynthetic triple helical DNA are not ... ...

Abstract	A triple helical DNA can control gene expression, help in homologous recombination, induce mutations to facilitate DNA repair mechanisms, suppress oncogene formations, etc. However, the structure and function of semisynthetic triple helical DNA are not known. To understand this, various triplets formed between eight artificial nucleobases (P, Z, J, V, B, S, X, and K) and four natural DNA bases (G, C, A, and T) are studied herein by employing a reliable density functional theoretic (DFT) method. Initially, the triple helix-forming artificial nucleobases interacted with the duplex DNA containing GC and AT base pairs, and subsequently, triple helix-forming natural bases (G and C) interacted with artificial duplex DNA containing PZ, JV, BS, and XK base pairs. Among the different triplets formed in the first category, the C-JV triplet is found to be the most stable with a binding energy of about - 31 kcal/mol. Similarly, among the second category of triplets, the Z-GC and V-GC triplets are the most stable. Interestingly, Z-GC and V-GC are found to be isoenergetic with a binding energy of about - 30 kcal/mol. The C-JV, and Z-GC or V-GC triplets are about 12-14 kcal/mol more stable than the JV and GC base pairs respectively. Microsolvation of these triplets in 5 explicit water molecules further enhanced their stability by 16-21 kcal/mol. These results along with the consecutive stacking of the C-JV triplet (C-JV/C-JV) data indicate that the synthetic nucleobases can form stable semisynthetic triple helical DNA. However, consideration of a full-length DNA containing one or more semisynthetic bases or base pairs is necessary to understand the formation of semisynthetic DNA in living cells.
MeSH term(s)	Nucleic Acid Conformation ; DNA/genetics ; DNA/chemistry ; Base Pairing
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2023-11-07
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-46572-4
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Article ; Online: Role of different tautomers in the base-pairing abilities of some of the vital antiviral drugs used against COVID-19.

Jena, N R

Physical chemistry chemical physics : PCCP

2020 Volume 22, Issue 48, Page(s) 28115–28122

Abstract: Repurposed drugs are now considered as attractive therapeutics against COVID-19. It is shown that Remdesivir, a nucleoside drug that was originally invented for the Ebola virus, is effective in suppressing the replication of SARS-CoV-2 that causes COVID- ... ...

Abstract	Repurposed drugs are now considered as attractive therapeutics against COVID-19. It is shown that Remdesivir, a nucleoside drug that was originally invented for the Ebola virus, is effective in suppressing the replication of SARS-CoV-2 that causes COVID-19. Similarly, Galidesivir, Favipiravir, Ribavirin, N4-hydroxycytidine (EIDD-1931), and EIDD-2801 (a prodrug of EIDD-1931) were also found to be effective against COVID-19. However, the mechanisms of action of these drugs are not yet fully understood. For example, in some experimental studies, these drugs were proposed to act as a RNA-chain terminator, while in other studies, these were proposed to induce base-pair mutations above the error catastrophe limit to stall the replication of the viral RNA. To understand the mutagenic effects of these drugs, the role of different tautomers in their base-pairing abilities is studied here in detail by employing a reliable dispersion-corrected density functional theoretic method. It is found that Remdesivir and Galidesivir can adopt both amino and imino tautomeric conformations to base-pair with RNA bases. While the insertions of G and U are preferred against the amino tautomers of these drugs, the insertion of C is mainly possible against the imino tautomers. However, although Favipiravir and Ribavirin can make stable base pair interactions by using their keto and enol tautomers, the formation of the latter pairs would be less probable due to the endothermic nature of the products. Interestingly, the insertions of all of the RNA bases are found to be possible against the keto tautomer of Favipiravir, while the keto tautomer of Ribavirin has a clear preference for G. Remarkably, due to the negligible difference in the stability of EIDD-2801 and EIDD-1931, these tautomers would coexist in the biological environment. The insertion of G is found to be preferred against EIDD-1931 and the incorporations of U, A, and G are preferred opposite EIDD-2801. These findings suggest that base-pair mutations are the main causes of the antiviral properties of these drugs.
MeSH term(s)	Antiviral Agents/chemistry ; Base Pairing ; COVID-19/drug therapy ; Density Functional Theory ; Isomerism ; Models, Chemical ; Mutagens/chemistry ; Nucleosides/chemistry ; RNA/chemistry ; SARS-CoV-2/drug effects ; Thermodynamics
Chemical Substances	Antiviral Agents ; Mutagens ; Nucleosides ; RNA (63231-63-0)
Language	English
Publishing date	2020-12-08
Publishing country	England
Document type	Journal Article
ZDB-ID	1476244-4
ISSN	1463-9084 ; 1463-9076
ISSN (online)	1463-9084
ISSN	1463-9076
DOI	10.1039/d0cp05297c
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Article ; Online: Correction to: Complementary base pair interactions between different rare tautomers of the second‑generation artificial genetic alphabets.

Jena, N R / Das, P / Shukla, P K

Journal of molecular modeling

2023 Volume 29, Issue 5, Page(s) 157

Language	English
Publishing date	2023-04-25
Publishing country	Germany
Document type	Published Erratum
ZDB-ID	1284729-X
ISSN	0948-5023 ; 1610-2940
ISSN (online)	0948-5023
ISSN	1610-2940
DOI	10.1007/s00894-023-05563-y
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Article ; Online: Electron and hole interactions with P, Z, and P:Z and the formation of mutagenic products by proton transfer reactions.

Jena, N R

Physical chemistry chemical physics : PCCP

2019 Volume 22, Issue 2, Page(s) 919–931

Abstract: P and Z have recently been identified as promiscuous artificial nucleobases, which can behave as G and C, respectively, in duplex DNA. These nucleobases have been shown to participate in the replication reaction and can form stable B-DNA. A short ... ...

Abstract	P and Z have recently been identified as promiscuous artificial nucleobases, which can behave as G and C, respectively, in duplex DNA. These nucleobases have been shown to participate in the replication reaction and can form stable B-DNA. A short sequence of DNA containing P and Z has also been shown to help in the diagnosis of diseases. However, the behavior of P and Z exposed to radiation has not been explored. As electrons and holes are created during the interaction of radiation with DNA bases, it is desirable to understand the electron or hole trapping abilities of P and Z in duplex DNA. To unravel these abilities, electron affinities (EAs) and ionization potentials (IPs) of P and Z in bare and microhydrated complexes are computed and compared with those of G and C by using the B3LYP-D3 dispersion-corrected density functional theory method and the IEFPCM method to account for the bulk solvation in water. The computed EA and IP values of P and Z are found to be largely positive and hence their anions (P˙- and Z˙-) and cations (P˙+ and Z˙+) would be stable in DNA. It is further found that the electron trapping ability of Z is significantly higher than that of P, G, and C. However, the hole trapping ability of P is slightly higher than that of Z, but less than that of G. To account for the proton transfer abilities of Z, Z˙+, and Z˙-, the stabilities of different proton transferred products and their tautomers are also explored. It is found that among the different products, the one formed by the transfer of the N3 proton would be the most stable. However, the N3 proton transfer from Z to P in the P:Z and P:Z˙- complexes would be unfeasible due to the high barrier and endothermic nature of the reaction. Remarkably, the same reaction in the P:Z˙+ complex is found to be exothermic with a low barrier energy. Hence, the conversion of Z to Z˙+ would facilitate N3 proton transfer from Z to P in the P:Z complex. As the proton transferred products were suggested to induce genetic mutations, we propose that the formations of Z(N3 - H)˙ and P(N1 + H)+ in DNA would be mutagenic. These results are expected to help in the understanding of the radiation biology of P and Z in single-stranded and double-stranded DNA.
MeSH term(s)	Base Pairing ; DNA/chemistry ; DNA/genetics ; Electrons ; Mutagenesis/genetics ; Protons ; Quantum Theory
Chemical Substances	Protons ; DNA (9007-49-2)
Language	English
Publishing date	2019-12-17
Publishing country	England
Document type	Journal Article
ZDB-ID	1476244-4
ISSN	1463-9084 ; 1463-9076
ISSN (online)	1463-9084
ISSN	1463-9076
DOI	10.1039/c9cp05367k
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