In Silico Identification of Piperazine Linked Thiohydantoin Derivatives as Novel Androgen Antagonist in Prostate Cancer Treatment

Bhati, Shipra; Kaushik, Vikas; Singh, Joginder

doi:10.1007/s10989-018-9734-5

Cited by 23 publications

(20 citation statements)

References 42 publications

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“…To investigate nonbonded atom-atom interactions associated with the ERRAT web-server (http://services.mbi.ucla.edu/ERRAT /) was also used to predict high-resolution crystallography structures. A Ramachandran plot was retrieved via RAMPAGE web-server (http://mordred.bioc.cam.ac.uk/~rapper/rampage.php) and describe the quality of the modeled structure by displaying the percentage of residues in disallowed and allowed regions [41].…”

Section: Resultsmentioning

confidence: 99%

Learning from COVID-19 Pandemic: In Silico Vaccine and Cloning Design Against Nipah Virus by Studying and Analyzing the Whole Nipah Virus Proteome.

Habib

2021

Preprint

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Nipah virus (NiV) is a zoonotic paramyxovirus of the Henipavirus genus first identified in Malaysia in 1998. Henipavirus have bat reservoir hosts and have been isolated from fruit bats found across Oceania, Asia, and Africa. Bat-to-human transmission is thought to be the primary mode of human NiV infection, although multiple intermediate hosts are described. Human infections with NiV were originally described as a syndrome of fever and rapid neurological decline following contact with swine. More recent outbreaks describe a syndrome with prominent respiratory symptoms and human-to-human transmission. Nearly annual outbreaks have been described since 1998 with case fatality rates reaching greater than 90%. To prevent the spreading of the Nipah virus and turning it into a new pandemic, we must be armed with a ready-made vaccine to save the time consuming that vaccine takes until production. Here we in this paper, we analyzed the whole Nipah virus proteome to find out the most antigenic, non-allergic, and immune inducing epitopes to construct different vaccines that undergone deep investigation to reveal the most appropriate vaccine to immunize humanity from this probably pandemic.

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Section: Resultsmentioning

confidence: 99%

Learning from COVID-19 Pandemic: In Silico Vaccine and Cloning Design Against Nipah Virus by Studying and Analyzing the Whole Nipah Virus Proteome.

Habib

2021

Preprint

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“…TLR3 (PDB ID: 1ZIW) was downloaded from Protein Databank (PDB) ( https://www.rcsb.org ). Online servers ClusPro 2.0 ( https://cluspro.bu.edu/login.php ), HADDOCK server ( https://haddock.science.uu.nl/ ), PatchDock server ( https://bioinfo3d.cs.tau.ac.il/PatchDock/php.php ), and FireDock server ( http://bioinfo3d.cs.tau.ac.il/FireDock/php.php ) were used for molecular docking and docking refinement, respectively 60 . Again, the docking was performed for the third time using the HawkDock server ( http://cadd.zju.edu.cn/hawkdock/ ), and subsequently, the Molecular Mechanics/Generalized Born Surface Area (MM-GBSA) score was also measured using the same server that predicts the result in the affinity score and the lowest prediction score is considered the better score 61 .…”

Section: Methodsmentioning

confidence: 99%

In silico analysis of epitope-based vaccine candidate against tuberculosis using reverse vaccinology

Bibi

Ullah

Zhu

et al. 2021

Sci Rep

124

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Tuberculosis (TB) kills more individuals in the world than any other disease, and a threat made direr by the coverage of drug-resistant strains of Mycobacterium tuberculosis (Mtb). Bacillus Calmette–Guérin (BCG) is the single TB vaccine licensed for use in human beings and effectively protects infants and children against severe military and meningeal TB. We applied advanced computational techniques to develop a universal TB vaccine. In the current study, we select the very conserved, experimentally confirmed Mtb antigens, including Rv2608, Rv2684, Rv3804c (Ag85A), and Rv0125 (Mtb32A) to design a novel multi-epitope subunit vaccine. By using the Immune Epitopes Database (IEDB), we predicted different B-cell and T-cell epitopes. An adjuvant (Griselimycin) was also added to vaccine construct to improve its immunogenicity. Bioinformatics tools were used to predict, refined, and validate the 3D structure and then docked with toll-like-receptor (TLR-3) using different servers. The constructed vaccine was used for further processing based on allergenicity, antigenicity, solubility, different physiochemical properties, and molecular docking scores. The in silico immune simulation results showed significant response for immune cells. For successful expression of the vaccine in E. coli, in-silico cloning and codon optimization were performed. This research also sets out a good signal for the design of a peptide-based tuberculosis vaccine. In conclusion, our findings show that the known multi-epitope vaccine may activate humoral and cellular immune responses and maybe a possible tuberculosis vaccine candidate. Therefore, more experimental validations should be exposed to it.

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“…designed and synthesized potential SARS-CoV-2 main protease inhibitors are possessing γ-lactam and fluoro substituted ring systems [10] . In continuation of our work of designing potential therapeutics by virtual screening [ 28 , 29 ], the present investigation includes rational design and exploitation of the pharmacological potential of flavonoid based therapeutics as anti-SARS-CoV-2 for the treatment of COVID-19. A series of quercetin based derivatives were rationally designed by incorporating gamma lactam ring, and various fluoro substituted heterocyclic ring systems.…”

Section: Introductionmentioning

confidence: 99%

Rational design of flavonoid based potential inhibitors targeting SARS-CoV 3CL protease for the treatment of COVID-19

Bhati

Kaushik

Singh

2021

Journal of Molecular Structure

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The current outbreak of Coronavirus Disease 2019 (COVID-19) pandemic has reported thousands of deaths worldwide due to the rapid transmission rate and the lack of antiviral drugs and vaccinations. There is an urgent need to develop potential antiviral drug candidates for the prevention of COVID-19 infection. In the present study, a series of potential inhibitors targeting SARS-CoV 3CL protease were rationally designed by incorporating gamma lactam ring, and various fluoro substituted heterocyclic ring systems to the flavonoid scaffold. The prediction of drug-likeness, oral bioavailability, toxicity, synthetic accessibility, and ADMET properties was made by computational means. Quercetin was used as standard. The binding affinity of the ligands towards the 3CL protease target was examined using docking simulations. The designed ligands possess favourable pharmacokinetic and pharmacodynamic properties. Ligand L4, L8, and L14 appeared to be the lead compounds in the series and can be considered for further in-vivo and in-vitro validation.

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In Silico Identification of Piperazine Linked Thiohydantoin Derivatives as Novel Androgen Antagonist in Prostate Cancer Treatment

Cited by 23 publications

References 42 publications

Learning from COVID-19 Pandemic: In Silico Vaccine and Cloning Design Against Nipah Virus by Studying and Analyzing the Whole Nipah Virus Proteome.

Learning from COVID-19 Pandemic: In Silico Vaccine and Cloning Design Against Nipah Virus by Studying and Analyzing the Whole Nipah Virus Proteome.

In silico analysis of epitope-based vaccine candidate against tuberculosis using reverse vaccinology

Rational design of flavonoid based potential inhibitors targeting SARS-CoV 3CL protease for the treatment of COVID-19

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