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Article ; Online: Forecasting the Problem of Excessive Oil Entrainment in a Desalter Using Spinning Drop Method.

Sharma, Ekta / Shown, Biswajit / Sulakhe, Swapnil / Naik, Vijay M / Thaokar, Rochish M / Juvekar, Vinay A

ACS omega

2024 Volume 9, Issue 11, Page(s) 12768–12778

Abstract: Frequent desalter upsets in the refineries processing opportunity crude oils are often triggered by a rapid and uncontrollable buildup of the rag layer, a thick water-in-oil emulsion, at the oil-brine interface. This is caused by spontaneous ... ...

Abstract	Frequent desalter upsets in the refineries processing opportunity crude oils are often triggered by a rapid and uncontrollable buildup of the rag layer, a thick water-in-oil emulsion, at the oil-brine interface. This is caused by spontaneous emulsification of brine in oil. This study investigates a unique observation from a spinning drop (SD) tensiometer, revealing the low apparent interfacial tension and rigidity of SD caused by spontaneous emulsification. Fine droplets of brine generated through spontaneous emulsification decorate the SD surface and form a stable, low-energy bilayer. Simulated rag layers using the brines from upset incidences exhibit similar behavior, indicating that spontaneous emulsification is driven by chemical species in brine, which promote osmotic water transport. The rate of rag layer buildup correlates with the rate of spontaneous emulsification, with the temperature coefficient of interfacial tension reduction serving as a sensitive indicator. An imminent upset in the operation can be forecasted by measuring this temperature coefficient, enabling preventive measures.
Language	English
Publishing date	2024-03-11
Publishing country	United States
Document type	Journal Article
ISSN	2470-1343
ISSN (online)	2470-1343
DOI	10.1021/acsomega.3c08554
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Article ; Online: Soil carbon-nutrient cycling, energetics, and carbon footprint in calcareous soils with adoption of long-term conservation tillage practices and cropping systems diversification.

Pramanick, Biswajit / Kumar, Mritunjay / Naik, Banavath Mahesh / Singh, Santosh Kumar / Kumar, Mukesh / Singh, Shiv Vendra

The Science of the total environment

2023 Volume 912, Page(s) 169421

Abstract: Calcareous soils, comprising vast areas in northern and eastern parts of India, are characterized by low soil organic carbon (SOC) with high free ... ...

Abstract	Calcareous soils, comprising vast areas in northern and eastern parts of India, are characterized by low soil organic carbon (SOC) with high free CaCO
Language	English
Publishing date	2023-12-19
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2023.169421
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Zs.A 949: Show issues

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Article ; Online: Identification of FDA-approved drugs with triple targeting mode of action for the treatment of monkeypox: a high throughput virtual screening study.

Srivastava, Varshita / Naik, Biswajit / Godara, Priya / Das, Dorothy / Mattaparthi, Venkata Satish Kumar / Prusty, Dhaneswar

Molecular diversity

2023

Abstract: According to the Center for Disease Control and Prevention, as of August 23, 94 countries had confirmed 42,954 Monkeypox Virus cases. As specific monkeypox drugs are not yet developed, the treatment depends on repurposed FDA-approved drugs. According to ... ...

Abstract	According to the Center for Disease Control and Prevention, as of August 23, 94 countries had confirmed 42,954 Monkeypox Virus cases. As specific monkeypox drugs are not yet developed, the treatment depends on repurposed FDA-approved drugs. According to a recent study, the Monkeypox outbreak is caused by a strain with a unique mutation, raising the likelihood that the virus will develop resistance to current drugs by acquiring mutations in the targets of currently used drugs. The probability of multiple mutations in two or more drug targets at a time is always low than mutation in a single drug target. Therefore, we identified 15 triple-targeting FDA-approved drugs that can inhibit three viral targets, including topoisomerase1, p37, and thymidylate kinase, using high throughput virtual screening approach. Further, the molecular dynamics simulation analysis of the top hits such as Naldemedine and Saquinavir with their respective targets reveals the formation of stable conformational changes of the ligand-protein complexes inside the dynamic biological environment. We suggest further research on these triple-targeting molecules to develop an effective therapy for the currently spreading Monkeypox.
Language	English
Publishing date	2023-04-20
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1376507-3
ISSN	1573-501X ; 1381-1991
ISSN (online)	1573-501X
ISSN	1381-1991
DOI	10.1007/s11030-023-10636-4
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Zs.A 4946: Show issues

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Article ; Online: Peptide-ligand conjugate based immunotherapeutic approach for targeted dismissal of non-structural protein 1 of dengue virus: A novel therapeutic solution for mild and severe dengue infections.

Srivastava, Varshita / Godara, Priya / Jena, Sudip Prasad / Naik, Biswajit / Singh, Satyendra / Prajapati, Vijay Kumar / Prusty, Dhaneswar

International journal of biological macromolecules

2024 Volume 260, Issue Pt 2, Page(s) 129562

Abstract: Dengue virus infection has significantly increased, with reported cases soaring from 505,430 in 2000 to 2,809,818 in 2022, emphasizing the need for effective treatments. Among the eleven structural and non-structural proteins of DENV, Non-structural ... ...

Abstract	Dengue virus infection has significantly increased, with reported cases soaring from 505,430 in 2000 to 2,809,818 in 2022, emphasizing the need for effective treatments. Among the eleven structural and non-structural proteins of DENV, Non-structural protein 1 (NS1) has emerged as a promising target due to its diverse role in modulating the immune response, inducing vascular leakage, and facilitating viral replication and assembly. Monoclonal antibodies are the sole therapeutics to target NS1, but concerns about their cross-reactivity persist. Given these concerns, our study focuses on designing a novel Peptide Ligand Conjugate (PLC) as a potential alternative immunotherapeutic agent against NS1. This PLC aims to mediate the immune elimination of soluble NS1 and NS1-presenting DENV-infected host cells by pre-existing vaccine-induced immunity. By employing the High Throughput Virtual Screening (HTVS) method, QikProp analysis, and Molecular Dynamics studies, we identified three hits from Asinex Biodesigned Ligands out of 220,177 compounds that show strong binding affinity towards the monoclonal binding site of NS1 protein. After a rigorous analysis of physicochemical characteristics, antigenicity, allergenicity, and toxicity using various servers, we selected two peptides: the minimum epitopic region of the Diphtheria and Tetanus toxins as the peptide components of the PLCs. A non-cleavable, non-reactive oxime linker connected the ligand with the peptide through oxime and amide bonds. DPT vaccine is widely used in dengue-endemic countries, and it has been reported that antibodies titer against MER of Diphtheria toxin and Tetanus toxins persist lifelong in DPT-vaccinated people. Therefore, once the rationally designed PLCs bind to NS1 through the ligands, the peptide will induce an immune response against NS1 by triggering pre-existing DPT antibodies and activating memory cells. This orchestrated immune response will destroy soluble NS1 and NS1-expressing DENV-infected cells, thereby reducing the illness of severe dengue hemorrhagic fever and the DENV infection, respectively. Given the increasing demand for new therapeutics for DENV treatment, further investigation into this novel immune-therapeutic strategy may offer a new avenue for treating mild and severe dengue infections.
MeSH term(s)	Humans ; Dengue Virus ; Dengue/therapy ; Dengue/diagnosis ; Severe Dengue ; Ligands ; Tetanus Toxin ; Peptides ; Immunotherapy ; Oximes ; Viral Nonstructural Proteins ; Antibodies, Viral
Chemical Substances	Ligands ; Tetanus Toxin ; Peptides ; Oximes ; Viral Nonstructural Proteins ; Antibodies, Viral
Language	English
Publishing date	2024-01-20
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.2024.129562
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Zs.B 2374: Show issues

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Article ; Online: Structure-based virtual screening approach reveals natural multi-target compounds for the development of antimalarial drugs to combat drug resistance.

Naik, Biswajit / Gupta, Nidhi / Godara, Priya / Srivastava, Varshita / Kumar, Prateek / Giri, Rajanish / Prajapati, Vijay Kumar / Pandey, Kailash C / Prusty, Dhaneswar

Journal of biomolecular structure & dynamics

2023 , Page(s) 1–25

Abstract: Compared to the previous year, there has been an increase of nearly 2 million malaria cases in 2021. The emergence of drug-resistant strains ... ...

Abstract	Compared to the previous year, there has been an increase of nearly 2 million malaria cases in 2021. The emergence of drug-resistant strains of
Language	English
Publishing date	2023-08-01
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2240415
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Zs.A 2093: Show issues

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Article: Reverse Y stenting in the management of vertebrobasilar junction fenestrated aneurysm: A novel technique.

Nayak, Manoj Kumar / Sahoo, Biswajit / Mahajan, Anshu / Naik, Suprava / Deep Bag, Nerbadyswari / Mishra, Biswamohan / Dash, Chinmaya

Journal of neurosciences in rural practice

2023 Volume 15, Issue 1, Page(s) 126–129

Abstract: Fenestrated aneurysm at vertebrobasilar junction (VBJ) is very rare and can occur due to non-fusion of longitudinal neural axis forming basilar artery in the early stage of embryonic life. Due to defects in tunica media and weakness in its wall, these ... ...

Abstract	Fenestrated aneurysm at vertebrobasilar junction (VBJ) is very rare and can occur due to non-fusion of longitudinal neural axis forming basilar artery in the early stage of embryonic life. Due to defects in tunica media and weakness in its wall, these fenestrations are more likely to develop an aneurysm. Various treatment strategies are required for the management of these types of aneurysms including simple coiling, stent-assisted coiling, balloon remodeling technique, and more recently kissing flow diverters. Herein, we report the case of ruptured fenestrated VBJ aneurysm which was managed successfully with novel reverse Y stenting with coiling.
Language	English
Publishing date	2023-10-31
Publishing country	United States
Document type	Journal Article
ZDB-ID	2601242-X
ISSN	0976-3155 ; 0976-3147
ISSN (online)	0976-3155
ISSN	0976-3147
DOI	10.25259/JNRP_423_2023
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Article: Identification of antiviral peptide inhibitors for receptor binding domain of SARS-CoV-2 omicron and its sub-variants: an in-silico approach.

Singh, Swati / Banavath, Hemanth Naick / Godara, Priya / Naik, Biswajit / Srivastava, Varshita / Prusty, Dhaneswar

3 Biotech

2022 Volume 12, Issue 9, Page(s) 198

Abstract: Omicron, a variant of concern (VOC) of SARS-CoV-2, emerged in South Africa in November 2021. Omicron has been continuously acquiring a series of new mutations, especially in the spike (S) protein that led to high infectivity and transmissibility. ... ...

Abstract	Omicron, a variant of concern (VOC) of SARS-CoV-2, emerged in South Africa in November 2021. Omicron has been continuously acquiring a series of new mutations, especially in the spike (S) protein that led to high infectivity and transmissibility. Peptides targeting the receptor-binding domain (RBD) of the spike protein by which omicron and its variants attach to the host receptor, angiotensin-converting enzyme (ACE2) can block the viral infection at the first step. This study aims to identify antiviral peptides from the Antiviral peptide database (AVPdb) and HIV-inhibitory peptide database (HIPdb) against the RBD of omicron by using a molecular docking approach. The lead RBD binder peptides obtained through molecular docking were screened for allergenicity and physicochemical criteria (isoelectric point (pI) and net charge) required for peptide-based drugs. The binding affinity of the best five peptide inhibitors with the RBD of omicron was validated further by molecular dynamics (MD) simulation. Our result introduces five antiviral peptides, including AVP1056, AVP1059, AVP1225, AVP1801, and HIP755, that may effectively hinder omicron-host interactions. It is worth mentioning that all the three major sub-variants of omicron, BA.1 (B.1.1.529.1), BA.2 (B.1.1.529.2), and BA.3 (B.1.1.529.3), exhibits conserved ACE-2 interacting residues. Hence, the screened antiviral peptides with similar affinity can also interrupt the RBD-mediated invasion of different major sub-variants of omicron. Altogether, these peptides can be considered in the peptide-based therapeutics development for omicron treatment after further experimentation. Supplementary information: The online version contains supplementary material available at 10.1007/s13205-022-03258-4.
Language	English
Publishing date	2022-08-01
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2600522-0
ISSN	2190-5738 ; 2190-572X
ISSN (online)	2190-5738
ISSN	2190-572X
DOI	10.1007/s13205-022-03258-4
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Article: Identification of antiviral peptide inhibitors for receptor binding domain of SARS-CoV-2 omicron and its sub-variants: an in-silico approach

Singh, Swati / Banavath, Hemanth Naick / Godara, Priya / Naik, Biswajit / Srivastava, Varshita / Prusty, Dhaneswar

3 Biotech. 2022 Sept., v. 12, no. 9

2022

Abstract	Omicron, a variant of concern (VOC) of SARS-CoV-2, emerged in South Africa in November 2021. Omicron has been continuously acquiring a series of new mutations, especially in the spike (S) protein that led to high infectivity and transmissibility. Peptides targeting the receptor-binding domain (RBD) of the spike protein by which omicron and its variants attach to the host receptor, angiotensin-converting enzyme (ACE2) can block the viral infection at the first step. This study aims to identify antiviral peptides from the Antiviral peptide database (AVPdb) and HIV-inhibitory peptide database (HIPdb) against the RBD of omicron by using a molecular docking approach. The lead RBD binder peptides obtained through molecular docking were screened for allergenicity and physicochemical criteria (isoelectric point (pI) and net charge) required for peptide-based drugs. The binding affinity of the best five peptide inhibitors with the RBD of omicron was validated further by molecular dynamics (MD) simulation. Our result introduces five antiviral peptides, including AVP1056, AVP1059, AVP1225, AVP1801, and HIP755, that may effectively hinder omicron-host interactions. It is worth mentioning that all the three major sub-variants of omicron, BA.1 (B.1.1.529.1), BA.2 (B.1.1.529.2), and BA.3 (B.1.1.529.3), exhibits conserved ACE-2 interacting residues. Hence, the screened antiviral peptides with similar affinity can also interrupt the RBD-mediated invasion of different major sub-variants of omicron. Altogether, these peptides can be considered in the peptide-based therapeutics development for omicron treatment after further experimentation.
Keywords	Severe acute respiratory syndrome coronavirus 2 ; allergenicity ; computer simulation ; databases ; isoelectric point ; lead ; molecular dynamics ; pathogenicity ; peptides ; peptidyl-dipeptidase A ; therapeutics ; South Africa
Language	English
Dates of publication	2022-09
Size	p. 198.
Publishing place	Springer International Publishing
Document type	Article
ZDB-ID	2600522-0
ISSN	2190-5738 ; 2190-572X
ISSN (online)	2190-5738
ISSN	2190-572X
DOI	10.1007/s13205-022-03258-4
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Rational designing of peptide-ligand conjugates-based immunotherapy for the treatment of complicated malaria.

Godara, Priya / Naik, Biswajit / Meghwal, Rajshree / Ojha, Rupal / Srivastava, Varshita / Prajapati, Vijay Kumar / Prusty, Dhaneswar

Life sciences

2022 Volume 311, Issue Pt A, Page(s) 121121

Abstract: Aims: Malaria deaths occur primarily due to complicated malaria associated with the sequestration of Plasmodium falciparum-infected erythrocyte (PfIE) in the capillary microvasculature. This study aims to design peptide ligand conjugates (PLCs) for ... ...

Abstract	Aims: Malaria deaths occur primarily due to complicated malaria associated with the sequestration of Plasmodium falciparum-infected erythrocyte (PfIE) in the capillary microvasculature. This study aims to design peptide ligand conjugates (PLCs) for treating complicated malaria using various in silico techniques. The PLC includes a natural ligand for the Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1): expressed explicitly on the surface of PfIE, and a highly immunogenic peptide derived from the commonly used peptide vaccines in malaria-endemic countries. The ligand is predicted to prevent the sequestration of PfIE, and the peptide is predicted to eliminate PfIE from circulation by the pre-existing vaccine-induced immunity. Main methods: The epitope identification from the vaccines and the analysis of physicochemical properties, antigenicity, allergenicity, and toxicity were performed using SVMTriP, ProtParam, VaxiJen, AllerTop, and ToxinPred servers, respectively. The high throughput virtual screening (HTVS) and drug-like properties analysis of natural compound ligands were carried out by Schrodinger-2021 software. The molecular dynamics simulations were performed through the WebGro server. Key findings: HTVS revealed three bioactive natural ligands for PfEMP1 from (NPASS) database. Three super immunogenic peptides were identified from malaria-endemic countries' commonly used peptide vaccines. Finally, Nine PLCs were designed with different combinations of peptides and ligands with the suitable non-cleavable triazole linker. Significance: Antimalarials have been losing efficacy in a time when malaria deaths in 2020 significantly increased than in 2019. In this scenario, further research on the designed PLCs may offer some innovative immune therapeutics for complicated malaria with minimum possibilities of drug resistance.
MeSH term(s)	Humans ; Malaria, Falciparum/drug therapy ; Malaria, Falciparum/prevention & control ; Ligands ; Malaria Vaccines/therapeutic use ; Plasmodium falciparum ; Malaria/drug therapy ; Erythrocytes ; Peptides/therapeutic use ; Immunotherapy
Chemical Substances	Ligands ; Malaria Vaccines ; Peptides
Language	English
Publishing date	2022-10-23
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	3378-9
ISSN	1879-0631 ; 0024-3205
ISSN (online)	1879-0631
ISSN	0024-3205
DOI	10.1016/j.lfs.2022.121121
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Uc I Zs.368: Show issues

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Article ; Online: Structure-based virtual screening against multiple Plasmodium falciparum kinases reveals antimalarial compounds.

Godara, Priya / Reddy, K Sony / Sahu, Welka / Naik, Biswajit / Srivastava, Varshita / Das, Rusham / Mahor, Ajay / Kumar, Prateek / Giri, Rajanish / Anirudh, Jivanage / Tak, Harshita / Banavath, Hemanth Naick / Bhatt, Tarun Kumar / Goyal, Amit Kumar / Prusty, Dhaneswar

Molecular diversity

2023

Abstract: The continuous emergence of resistance against most frontline antimalarial drugs has led to countless deaths in malaria-endemic countries, counting 619,000 deaths in 2021, with mutation in drug targets being the sole cause. As mutation is correlated ... ...

Abstract	The continuous emergence of resistance against most frontline antimalarial drugs has led to countless deaths in malaria-endemic countries, counting 619,000 deaths in 2021, with mutation in drug targets being the sole cause. As mutation is correlated frequently with fitness cost, the likelihood of mutation emergence in multiple targets at a time is extremely low. Hence, multitargeting compounds may seem promising to address drug resistance issues with additional benefits like increased efficacy, improved safety profile, and the requirement of fewer pills compared to traditional single and combinational drugs. In this study, we attempted to use the High Throughput Virtual Screening approach to predict multitarget inhibitors against six chemically validated Plasmodium falciparum (Pf) kinases (PfPKG, PfMAP2, PfCDPK4, PfTMK, PfPK5, PfPI4K), resulting in 21 multitargeting hits. The molecular dynamic simulation of the top six complexes (Myricetin-MAP2, Quercetin-CDPK4, Myricetin-TMK, Quercetin-PKG, Salidroside-PK5, and Salidroside-PI4K) showed stable interactions. Moreover, hierarchical clustering reveals the structural divergence of the compounds from the existing antimalarials, indicating less chance of cross-resistance. Additionally, the top three hits were validated through parasite growth inhibition assays, with quercetin and myricetin exhibiting an IC
Language	English
Publishing date	2023-12-21
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1376507-3
ISSN	1573-501X ; 1381-1991
ISSN (online)	1573-501X
ISSN	1381-1991
DOI	10.1007/s11030-023-10770-z
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