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Article ; Online: Current Therapeutic Strategies of Xeroderma Pigmentosum.

Hossain, Mozammel / Hasan, Ashraful / Shawan, Mohammad Mahfuz Ali Khan / Banik, Subrata / Jahan, Iffat

2022 Volume 66, Issue 6, Page(s) 660–667

Abstract: Xeroderma pigmentosum (XP) is an autosomal recessive genetic disease caused by a defect in the DNA repair system, exhibiting skin cancer on sun exposure. As it is an incurable disease, therapeutic strategies of this disease are critical. This review ... ...

Abstract	Xeroderma pigmentosum (XP) is an autosomal recessive genetic disease caused by a defect in the DNA repair system, exhibiting skin cancer on sun exposure. As it is an incurable disease, therapeutic strategies of this disease are critical. This review article takes an attempt to explore the current therapeutic advancements in XP. Different approaches including sun avoidance; surgical removal of cancerous lesions; laser and photodynamic therapy; use of retinoid, 5-fluorouracil, imiquimod, photolyase, and antioxidant; interferon therapy and gene therapy are chosen by doctors and patients to lessen the adverse effects of this disease. Among these options, sun avoidance, use of 5-fluorouracil and imiquimod, and interferon therapy are effective. However, some approaches including laser and photodynamic therapy, and the use of retinoids are effective against skin cancer having severe side effects. Furthermore, surgical removal of cancerous lesions and use of antioxidants are considered to be effective against this disease; however, efficacies of these are not experimentally determined. In addition, some approaches including oral vismodegib, immunotherapy, nicotinamide, acetohexamide, glimepiride-restricted diet are found to be effective to minimize the complications secondary to defects in the nucleotide excision repair (NER) system and also enhance the NER, which are under experimental level yet. Besides these, gene therapy, including the introduction of missing genes and genome edition, may be a promising approach to combat this disease, which is also not well established now. In the near future, these approaches may be effective tools to manage XP.
Language	English
Publishing date	2022-03-09
Publishing country	India
Document type	Journal Article ; Review
ZDB-ID	416069-1
ISSN	1998-3611 ; 0019-5154
ISSN (online)	1998-3611
ISSN	0019-5154
DOI	10.4103/ijd.ijd_329_21
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Article: Advances in Computational and Bioinformatics Tools and Databases for Designing and Developing a Multi-Epitope-Based Peptide Vaccine.

Shawan, Mohammad Mahfuz Ali Khan / Sharma, Ashish Ranjan / Halder, Sajal Kumar / Arian, Tawsif Al / Shuvo, Md Nazmussakib / Sarker, Satya Ranjan / Hasan, Md Ashraful

International journal of peptide research and therapeutics

2023 Volume 29, Issue 4, Page(s) 60

Abstract: A vaccine is defined as a biologic preparation that trains the immune system, boosts immunity, and protects against a deadly microbial infection. They have been used for centuries to combat a variety of contagious illnesses by means of subsiding the ... ...

Abstract	A vaccine is defined as a biologic preparation that trains the immune system, boosts immunity, and protects against a deadly microbial infection. They have been used for centuries to combat a variety of contagious illnesses by means of subsiding the disease burden as well as eradicating the disease. Since infectious disease pandemics are a recurring global threat, vaccination has emerged as one of the most promising tools to save millions of lives and reduce infection rates. The World Health Organization reports that immunization protects three million individuals annually. Currently, multi-epitope-based peptide vaccines are a unique concept in vaccine formulation. Epitope-based peptide vaccines utilize small fragments of proteins or peptides (parts of the pathogen), called epitopes, that trigger an adequate immune response against a particular pathogen. However, conventional vaccine designing and development techniques are too cumbersome, expensive, and time-consuming. With the recent advancement in bioinformatics, immunoinformatics, and vaccinomics discipline, vaccine science has entered a new era accompanying a modern, impressive, and more realistic paradigm in designing and developing next-generation strong immunogens.
Language	English
Publishing date	2023-05-23
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2192632-3
ISSN	1573-3904 ; 1573-3149
ISSN (online)	1573-3904
ISSN	1573-3149
DOI	10.1007/s10989-023-10535-0
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Article ; Online: Luteolin and abyssinone II as potential inhibitors of SARS-CoV-2: an in silico molecular modeling approach in battling the COVID-19 outbreak.

Shawan, Mohammad Mahfuz Ali Khan / Halder, Sajal Kumar / Hasan, Md Ashraful

Bulletin of the National Research Centre

2021 Volume 45, Issue 1, Page(s) 27

Abstract: Background: At present, the entire world is in a war against COVID-19 pandemic which has gradually led us toward a more compromised "new normal" life. SARS-CoV-2, the pathogenic microorganism liable for the recent COVID-19 outbreak, is extremely ... ...

Abstract	Background: At present, the entire world is in a war against COVID-19 pandemic which has gradually led us toward a more compromised "new normal" life. SARS-CoV-2, the pathogenic microorganism liable for the recent COVID-19 outbreak, is extremely contagious in nature resulting in an unusual number of infections and death globally. The lack of clinically proven therapeutic intervention for COVID-19 has dragged the world's healthcare system into the biggest challenge. Therefore, development of an efficient treatment scheme is now in great demand. Screening of different biologically active plant-based natural compounds could be a useful strategy for combating this pandemic. In the present research, a collection of 43 flavonoids of 7 different classes with previously recorded antiviral activity was evaluated via computational and bioinformatics tools for their impeding capacity against SARS-CoV-2. In silico drug likeness, pharmacophore and Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) profile analysis of the finest ligands were carried out using DataWarrior, DruLiTo and admetSAR programs, respectively. Molecular docking was executed by AutoDock Vina, while molecular dynamics simulation of the target protein-ligand bound complexes was done using nanoscalable molecular dynamics and visual molecular dynamics software package. Finally, the molecular target analysis of the selected ligands within Results: Out of the forty-three flavonoids, luteolin and abyssinone II were found to develop successful docked complex within the binding sites of target proteins in terms of lowest binding free energy and inhibition constant. The root mean square deviation and root mean square fluctuation values of the docked complex displayed stable interaction and efficient binding between the ligands and target proteins. Both of the flavonoids were found to be safe for human use and possessed good drug likeness properties and target accuracy. Conclusions: Conclusively, the current study proposes that luteolin and abyssinone II might act as potential therapeutic candidates for SARS-CoV-2 infection. In vivo and in vitro experiments, however, should be taken under consideration to determine the efficiency and to demonstrate the mechanism of action.
Language	English
Publishing date	2021-01-20
Publishing country	Germany
Document type	Journal Article
ISSN	2522-8307
ISSN (online)	2522-8307
DOI	10.1186/s42269-020-00479-6
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Article ; Online: In Silico Identification and Analysis of Potentially Bioactive Antiviral Phytochemicals against SARS-CoV-2: A Molecular Docking and Dynamics Simulation Approach.

Halder, Sajal Kumar / Sultana, Ive / Shuvo, Md Nazmussakib / Shil, Aparna / Himel, Mahbubul Kabir / Hasan, Md Ashraful / Shawan, Mohammad Mahfuz Ali Khan

BioMed research international

2023 Volume 2023, Page(s) 5469258

Abstract: SARS-CoV-2, a deadly coronavirus sparked COVID-19 pandemic around the globe. With an increased mutation rate, this infectious agent is highly transmissible inducing an escalated rate of infections and death everywhere. Hence, the discovery of a viable ... ...

Abstract	SARS-CoV-2, a deadly coronavirus sparked COVID-19 pandemic around the globe. With an increased mutation rate, this infectious agent is highly transmissible inducing an escalated rate of infections and death everywhere. Hence, the discovery of a viable antiviral therapy option is urgent. Computational approaches have offered a revolutionary framework to identify novel antimicrobial treatment regimens and allow a quicker, cost-effective, and productive conversion into the health center by evaluating preliminary and safety investigations. The primary purpose of this research was to find plausible plant-derived antiviral small molecules to halt the viral entrance into individuals by clogging the adherence of Spike protein with human ACE2 receptor and to suppress their genome replication by obstructing the activity of Nsp3 (Nonstructural protein 3) and 3CLpro (main protease). An in-house library of 1163 phytochemicals were selected from the NPASS and PubChem databases for downstream analysis. Preliminary analysis with SwissADME and pkCSM revealed 149 finest small molecules from the large dataset. Virtual screening using the molecular docking scoring and the MM-GBSA data analysis revealed that three candidate ligands CHEMBL503 (Lovastatin), CHEMBL490355 (Sulfuretin), and CHEMBL4216332 (Grayanoside A) successfully formed docked complex within the active site of human ACE2 receptor, Nsp3, and 3CLpro, respectively. Dual method molecular dynamics (MD) simulation and post-MD MM-GBSA further confirmed efficient binding and stable interaction between the ligands and target proteins. Furthermore, biological activity spectra and molecular target analysis revealed that all three preselected phytochemicals were biologically active and safe for human use. Throughout the adopted methodology, all three therapeutic candidates significantly outperformed the control drugs (Molnupiravir and Paxlovid). Finally, our research implies that these SARS-CoV-2 protein antagonists might be viable therapeutic options. At the same time, enough wet lab evaluations would be needed to ensure the therapeutic potency of the recommended drug candidates for SARS-CoV-2.
MeSH term(s)	Humans ; SARS-CoV-2/metabolism ; Antiviral Agents/pharmacology ; Antiviral Agents/therapeutic use ; Antiviral Agents/chemistry ; Molecular Docking Simulation ; COVID-19 ; Pandemics ; Ligands ; Angiotensin-Converting Enzyme 2/metabolism ; Viral Nonstructural Proteins/chemistry ; Molecular Dynamics Simulation ; Phytochemicals/pharmacology ; Phytochemicals/therapeutic use
Chemical Substances	Antiviral Agents ; nirmatrelvir and ritonavir drug combination ; Ligands ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23) ; Viral Nonstructural Proteins ; Phytochemicals
Language	English
Publishing date	2023-05-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	2698540-8
ISSN	2314-6141 ; 2314-6133
ISSN (online)	2314-6141
ISSN	2314-6133
DOI	10.1155/2023/5469258
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Article ; Online: Progeny Transfer Effects of Chitosan-Coated Cobalt Ferrite Nanoparticles.

Shakil, Md Salman / Uddin, Md Forhad / Morshed, Md Reaz / Bhuiya, Md Simul / Alam, Morshed / Hossen, Md Sakib / Niloy, Mahruba Sultana / Khan Shawan, Mohammad Mahfuz Ali / Hoque, Sheikh Manjura / Hasan, Md Ashraful

ACS omega

2023 Volume 8, Issue 17, Page(s) 15152–15159

Abstract: Cobalt ferrite nanoparticles (CFNs) are promising materials for their enticing properties for different biomedical applications, including magnetic resonance imaging (MRI) contrast, drug carriers, biosensors, and many more. In our previous study, a ... ...

Abstract	Cobalt ferrite nanoparticles (CFNs) are promising materials for their enticing properties for different biomedical applications, including magnetic resonance imaging (MRI) contrast, drug carriers, biosensors, and many more. In our previous study, a chitosan-coated CFN (CCN) nanocomplex demonstrated potential as an MRI contrast dye by improving the biocompatibility of CFN. In this study, we report the progeny transfer effects of CCN following a single intravenous injection of CCN (20, 40, or 60 mg/kg) in pregnant albino Wistar rats. Biochemical and histological observation reveals that CCN is tolerated with respect to maternal organ functions (e.g., liver, kidney). Atomic absorption spectroscopy results showed that CCN or CCN-leached iron could cross the placental barrier and deposit in the fetus. Furthermore, this deposition accelerated lipid peroxidation in the placenta and fetus.
Language	English
Publishing date	2023-04-19
Publishing country	United States
Document type	Journal Article
ISSN	2470-1343
ISSN (online)	2470-1343
DOI	10.1021/acsomega.3c00148
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Article ; Online: Luteolin and abyssinone II as potential inhibitors of SARS-CoV-2

Mohammad Mahfuz Ali Khan Shawan / Sajal Kumar Halder / Md. Ashraful Hasan

Bulletin of the National Research Centre, Vol 45, Iss 1, Pp 1-

an in silico molecular modeling approach in battling the COVID-19 outbreak

2021 Volume 21

Abstract: Abstract Background At present, the entire world is in a war against COVID-19 pandemic which has gradually led us toward a more compromised “new normal” life. SARS-CoV-2, the pathogenic microorganism liable for the recent COVID-19 outbreak, is extremely ... ...

Abstract	Abstract Background At present, the entire world is in a war against COVID-19 pandemic which has gradually led us toward a more compromised “new normal” life. SARS-CoV-2, the pathogenic microorganism liable for the recent COVID-19 outbreak, is extremely contagious in nature resulting in an unusual number of infections and death globally. The lack of clinically proven therapeutic intervention for COVID-19 has dragged the world’s healthcare system into the biggest challenge. Therefore, development of an efficient treatment scheme is now in great demand. Screening of different biologically active plant-based natural compounds could be a useful strategy for combating this pandemic. In the present research, a collection of 43 flavonoids of 7 different classes with previously recorded antiviral activity was evaluated via computational and bioinformatics tools for their impeding capacity against SARS-CoV-2. In silico drug likeness, pharmacophore and Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) profile analysis of the finest ligands were carried out using DataWarrior, DruLiTo and admetSAR programs, respectively. Molecular docking was executed by AutoDock Vina, while molecular dynamics simulation of the target protein–ligand bound complexes was done using nanoscalable molecular dynamics and visual molecular dynamics software package. Finally, the molecular target analysis of the selected ligands within Homo sapiens was conducted with SwissTargetPredcition web server. Results Out of the forty-three flavonoids, luteolin and abyssinone II were found to develop successful docked complex within the binding sites of target proteins in terms of lowest binding free energy and inhibition constant. The root mean square deviation and root mean square fluctuation values of the docked complex displayed stable interaction and efficient binding between the ligands and target proteins. Both of the flavonoids were found to be safe for human use and possessed good drug likeness properties and target accuracy. ...
Keywords	Abyssinone II ; COVID-19 pandemic ; Flavonoids ; Luteolin ; Molecular docking ; Molecular dynamics simulation ; Science ; Q
Subject code	540
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	SpringerOpen
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Investigation of Antimicrobial Activity and Biocompatibility of Biogenic Silver Nanoparticles Synthesized using

Mahmud, Kazi Mustafa / Hossain, Md Monir / Polash, Shakil Ahmed / Takikawa, Masato / Shakil, Md Salman / Uddin, Md Forhad / Alam, Morshed / Ali Khan Shawan, Mohammad Mahfuz / Saha, Tanushree / Takeoka, Shinji / Hasan, Md Ashraful / Sarker, Satya Ranjan

ACS omega

2022 Volume 7, Issue 31, Page(s) 27216–27229

Abstract: Nanotherapeutics has emerged as the most sought after approach to tackle the menace of drug-resistant pathogenic bacteria. Among others, biogenic silver nanoparticles (bAgNPs) synthesized using medicinal plant extracts demonstrate promising antibacterial ...

Abstract	Nanotherapeutics has emerged as the most sought after approach to tackle the menace of drug-resistant pathogenic bacteria. Among others, biogenic silver nanoparticles (bAgNPs) synthesized using medicinal plant extracts demonstrate promising antibacterial propensity with excellent biocompatibility. Herein, bAgNPs were synthesized through the green chemistry approach using
Language	English
Publishing date	2022-07-25
Publishing country	United States
Document type	Journal Article
ISSN	2470-1343
ISSN (online)	2470-1343
DOI	10.1021/acsomega.2c01922
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Article: Structure to function analysis with antigenic characterization of a hypothetical protein,HPAG1_0576 from Helicobacter pylori HPAG1.

Ashrafi, Hanan / Siraji, Muntequa Ishtiaq / Showva, Nazmir Nur / Hossain, Md Mozamme / Hossan, Tareq / Hasan, Md Ashraful / Shohael, Abdullah Mohammad / Shawan, Mohammad Mahfuz Ali Khan

Bioinformation

2019 Volume 15, Issue 7, Page(s) 456–466

Abstract: Helicobacter pylori, a unique gastric pathogen causing chronic inflammation in the gastric mucosa with a possibility to develop gastric cancer has one-third of its proteins still uncharacterized. In this study, a hypothetical protein (HP) namely ... ...

Abstract	Helicobacter pylori, a unique gastric pathogen causing chronic inflammation in the gastric mucosa with a possibility to develop gastric cancer has one-third of its proteins still uncharacterized. In this study, a hypothetical protein (HP) namely HPAG1_0576 from H. pylori HPAG1 was chosen for detailed computational analysis of its structural, functional and epitopic properties. The primary, secondary and 3D structure/model of the selected HP was constructed. Then refinement and structure validation were done, which indicated a good quality of the newly constructed model. ProFunc and STRING suggested that HPAG1_0576 shares 98% identity with a carcinogenic factor, TNF-α inducing protein (Tip-α ) of H. pylori. IEDB immunoinformatics tool predicted VLMLQACTCPNTSQRNS from position 19-35 as most potential B-cell linear epitope and SFLKSKQL from position 5-12 as most potent conformational epitope. Alternatively, FALVRARGF and FLCGLGVLM were predicted as most immunogenic CD8+ and CD4+ T-cell epitopes respectively. At the same time findings of IFN epitope tool suggests that, HPAG1_0576 had a great potential to evoke interferon-gamma (IFN-γ) mediated immune response. However, this experiment is a primary approach for in silico vaccine designing from a HP, findings of this study will provide significant insights in further investigations and will assist in identifying new drug targets/vaccine candidates.
Language	English
Publishing date	2019-07-31
Publishing country	Singapore
Document type	Journal Article
ZDB-ID	2203786-X
ISSN	0973-2063
ISSN	0973-2063
DOI	10.6026/97320630015456
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Article ; Online: Designing an effective therapeutic siRNA to silence RdRp gene of SARS-CoV-2.

Shawan, Mohammad Mahfuz Ali Khan / Sharma, Ashish Ranjan / Bhattacharya, Manojit / Mallik, Bidyut / Akhter, Farhana / Shakil, Md Salman / Hossain, Md Mozammel / Banik, Subrata / Lee, Sang-Soo / Hasan, Md Ashraful / Chakraborty, Chiranjib

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases

2021 Volume 93, Page(s) 104951

Abstract: The devastating outbreak of COVID-19 has spread all over the world and has become a global health concern. There is no specific therapeutics to encounter the COVID-19. Small interfering RNA (siRNA)-based therapy is an efficient strategy to control human ... ...

Abstract	The devastating outbreak of COVID-19 has spread all over the world and has become a global health concern. There is no specific therapeutics to encounter the COVID-19. Small interfering RNA (siRNA)-based therapy is an efficient strategy to control human viral infections employing post-transcriptional gene silencing (PTGS) through neutralizing target complementary mRNA. RNA-dependent RNA polymerase (RdRp) encoded by the viral RdRp gene as a part of the replication-transcription complex can be adopted as an acceptable target for controlling SARS-CoV-2 mediated infection. Therefore, in the current study, accessible siRNA designing tools, including significant algorithms and parameters, were rationally used to design the candidate siRNAs against SARS-COV-2 encoded RdRp. The designed siRNA molecules possessed adequate nucleotide-based and other features for potent gene silencing. The targets of the designed siRNAs revealed no significant matches within the whole human genome, ruling out any possibilities for off-target silencing by the siRNAs. Characterization with different potential parameters of efficacy allowed selecting the finest siRNA among all the designed siRNA molecules. Further, validation assessment and target site accessibility prediction also rationalized the suitability of this siRNA molecule. Molecular docking study between the selected siRNA molecule and component of RNA interference (RNAi) pathway gave an excellent outcome. Molecular dynamics of two complexes: siRNA and argonaute complex, guide RNA, and target protein complex, have shown structural stability of these proteins. Therefore, the designed siRNA molecule might act as an effective therapeutic agent against the SARS-CoV-2 at the genome level and can prevent further outbreaks of COVID-19 in humans.
MeSH term(s)	Argonaute Proteins/chemistry ; Argonaute Proteins/genetics ; Argonaute Proteins/metabolism ; Base Composition ; Coronavirus RNA-Dependent RNA Polymerase/genetics ; Coronavirus RNA-Dependent RNA Polymerase/metabolism ; Gene Silencing ; Genome, Human ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; RNA, Small Interfering/chemistry ; RNA, Small Interfering/genetics ; SARS-CoV-2/genetics ; Sequence Alignment
Chemical Substances	Argonaute Proteins ; RNA, Messenger ; RNA, Small Interfering ; Coronavirus RNA-Dependent RNA Polymerase (EC 2.7.7.48)
Language	English
Publishing date	2021-06-02
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2037068-4
ISSN	1567-7257 ; 1567-1348
ISSN (online)	1567-7257
ISSN	1567-1348
DOI	10.1016/j.meegid.2021.104951
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Article: Designing an effective therapeutic siRNA to silence RdRp gene of SARS-CoV-2

Shawan, Mohammad Mahfuz Ali Khan / Sharma, Ashish Ranjan / Bhattacharya, Manojit / Mallik, Bidyut / Akhter, Farhana / Shakil, Md. Salman / Hossain, Md. Mozammel / Banik, Subrata / Lee, Sang-Soo / Hasan, Md. Ashraful / Chakraborty, Chiranjib

Infection, genetics, and evolution. 2021 Sept., v. 93

2021

Abstract	The devastating outbreak of COVID-19 has spread all over the world and has become a global health concern. There is no specific therapeutics to encounter the COVID-19. Small interfering RNA (siRNA)-based therapy is an efficient strategy to control human viral infections employing post-transcriptional gene silencing (PTGS) through neutralizing target complementary mRNA. RNA-dependent RNA polymerase (RdRp) encoded by the viral RdRp gene as a part of the replication-transcription complex can be adopted as an acceptable target for controlling SARS-CoV-2 mediated infection. Therefore, in the current study, accessible siRNA designing tools, including significant algorithms and parameters, were rationally used to design the candidate siRNAs against SARS-COV-2 encoded RdRp. The designed siRNA molecules possessed adequate nucleotide-based and other features for potent gene silencing. The targets of the designed siRNAs revealed no significant matches within the whole human genome, ruling out any possibilities for off-target silencing by the siRNAs. Characterization with different potential parameters of efficacy allowed selecting the finest siRNA among all the designed siRNA molecules. Further, validation assessment and target site accessibility prediction also rationalized the suitability of this siRNA molecule. Molecular docking study between the selected siRNA molecule and component of RNA interference (RNAi) pathway gave an excellent outcome. Molecular dynamics of two complexes: siRNA and argonaute complex, guide RNA, and target protein complex, have shown structural stability of these proteins. Therefore, the designed siRNA molecule might act as an effective therapeutic agent against the SARS-CoV-2 at the genome level and can prevent further outbreaks of COVID-19 in humans.
Keywords	COVID-19 infection ; RNA interference ; RNA-directed RNA polymerase ; Severe acute respiratory syndrome coronavirus 2 ; evolution ; genes ; humans ; infection ; molecular dynamics ; prediction ; therapeutics
Language	English
Dates of publication	2021-09
Publishing place	Elsevier B.V.
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	2037068-4
ISSN	1567-1348
ISSN	1567-1348
DOI	10.1016/j.meegid.2021.104951
Database	NAL-Catalogue (AGRICOLA)

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