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1.
Curr Med Chem ; 28(41): 8559-8594, 2021.
Article in English | MEDLINE | ID: covidwho-1690554

ABSTRACT

There is a new public health crisis threatening the world with the emergence and spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The disease was later named novel coronavirus disease or COVID-19. It was then declared a pandemic by the World Health Organization on March 11, 2020. The virus originated in bats and was transmitted to humans through unknown intermediary animals in Wuhan, Hubei province, China, in December 2019. As of February 5, 2021, 103 million laboratory-confirmed cases and nearly 2.3 million deaths were reported globally. The number of death tolls continues to rise, and a large number of countries have been forced to maintain social distance in public place and enforce lockdown. As per literature, coronavirus is transmitted human to human or human to animal via airborne droplets. Coronavirus enters the human cell through the membrane ACE-2 exopeptidase receptor. WHO, ECDC, and ICMR advised avoiding public places and close contact with infected persons and pet animals. To date, there is no evidence of any effective treatment for COVID-19. The main therapies being used to treat the disease are antiviral drugs, chloroquine/hydroxychloroquine, and respiratory therapy. Although several therapies have been proposed, quarantine is the only intervention that appears to be effective in decreasing the contagion rate. We conducted a literature review of publicly available information to summarize knowledge about the pathogen and the current epidemic. In the present literature review, the causative agent of the pandemic, epidemiology, pathogenesis, and diagnostic techniques are discussed. Further, currently used treatment, preventive strategies along with vaccine trials and computational tools are all described in detail.


Subject(s)
COVID-19 , SARS-CoV-2 , Animals , Communicable Disease Control , Humans , Hydroxychloroquine , Pandemics
2.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-305909

ABSTRACT

A new and more aggressive strain of coronavirus, known as SARS-CoV-2, which is highly contagious, has rapidly spread across the planet within a short period of time. Due to its high transmission rate and the significant time–space between infection and manifestation of symptoms, the WHO recently declared this a pandemic. Because of the exponentially growing number of new cases of both infections and deaths, development of new therapeutic options to help fight this pandemic is urgently needed. The target molecules of this study were the nitro derivatives of quinoline and quinoline N-oxide. Computational design at the DFT level, docking studies, and molecular dynamics methods as a well-reasoned strategy will aid in elucidating the fundamental physicochemical properties and molecular functions of a diversity of compounds, directly accelerating the process of discovering new drugs. In this study, we discovered isomers based on the nitro derivatives of quinoline and quinoline N-oxide, which are biologically active compounds and may be low-cost alternatives for the treatment of infections induced by SARS-CoV-2.

3.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-313324

ABSTRACT

Understanding the effects of metabolism on the rational design of novel and more effective drugs is still a considerable challenge. To the best of our knowledge, there are no entirely computational strategies that make it possible to predict these effects. From this perspective, the development of such methodologies could contribute to significantly reduce the side effects of medicines, leading to the emergence of more effective and safer drugs. Thereby, in this study, our strategy is based on simulating the electron ionization mass spectrometry (EI-MS) fragmentation of the drug molecules and combined with molecular docking and ADMET models in two different situations. In the first model, the drug is docked without considering the possible metabolic effects. In the second model, each of the intermediates from the EI-MS results is docked, and metabolism occurs before the drug accesses the biological target. As a proof of concept, in this work, we investigate the main antiviral drugs used in clinical research to treat COVID-19. As a result, our strategy made it possible to assess the biological activity and toxicity of all potential by-products. We believed that our findings provide new chemical insights that can benefit the rational development of novel drugs in the future.

4.
Sensors (Basel) ; 21(23)2021 Nov 24.
Article in English | MEDLINE | ID: covidwho-1542715

ABSTRACT

Selective, sensitive and affordable techniques to detect disease and underlying health issues have been developed recently. Biosensors as nanoanalytical tools have taken a front seat in this context. Nanotechnology-enabled progress in the health sector has aided in disease and pandemic management at a very early stage efficiently. This report reflects the state-of-the-art of nanobiosensor-based virus detection technology in terms of their detection methods, targets, limits of detection, range, sensitivity, assay time, etc. The article effectively summarizes the challenges with traditional technologies and newly emerging biosensors, including the nanotechnology-based detection kit for COVID-19; optically enhanced technology; and electrochemical, smart and wearable enabled nanobiosensors. The less explored but crucial piezoelectric nanobiosensor and the reverse transcription-loop mediated isothermal amplification (RT-LAMP)-based biosensor are also discussed here. The article could be of significance to researchers and doctors dedicated to developing potent, versatile biosensors for the rapid identification of COVID-19. This kind of report is needed for selecting suitable treatments and to avert epidemics.


Subject(s)
Biosensing Techniques , COVID-19 , Humans , Nanotechnology , Nucleic Acid Amplification Techniques , Pandemics , SARS-CoV-2 , Sensitivity and Specificity
5.
Vaccines (Basel) ; 9(10)2021 Oct 04.
Article in English | MEDLINE | ID: covidwho-1463843

ABSTRACT

SARS-CoV-2 claimed numerous lives and put nations on high alert. The lack of antiviral medications and the small number of approved vaccines, as well as the recurrence of adverse effects, necessitates the development of novel treatment ways to combat COVID-19. In this context, using databases such as PubMed, Google Scholar, and Science Direct, we gathered information about nanotechnology's involvement in the prevention, diagnosis and virus-like particle vaccine development. This review revealed that various nanomaterials like gold, polymeric, graphene and poly amino ester with carboxyl group coated magnetic nanoparticles have been explored for the fast detection of SARS-CoV-2. Personal protective equipment fabricated with nanoparticles, such as gloves, masks, clothes, surfactants, and Ag, TiO2 based disinfectants played an essential role in halting COVID-19 transmission. Nanoparticles are used not only in vaccine delivery, such as lipid nanoparticles mediated transport of mRNA-based Pfizer and Moderna vaccines, but also in the development of vaccine as the virus-like particles elicit an immune response. There are now 18 virus-like particle vaccines in pre-clinical development, with one of them, developed by Novavax, reported being in phase 3 trials. Due to the probability of upcoming COVID-19 waves, and the rise of new diseases, the future relevance of virus-like particles is imperative. Furthermore, psychosocial variables linked to vaccine reluctance constitute a critical problem that must be addressed immediately to avert pandemic.

6.
Sci Rep ; 11(1): 19998, 2021 10 07.
Article in English | MEDLINE | ID: covidwho-1462031

ABSTRACT

Understanding the effects of metabolism on the rational design of novel and more effective drugs is still a considerable challenge. To the best of our knowledge, there are no entirely computational strategies that make it possible to predict these effects. From this perspective, the development of such methodologies could contribute to significantly reduce the side effects of medicines, leading to the emergence of more effective and safer drugs. Thereby, in this study, our strategy is based on simulating the electron ionization mass spectrometry (EI-MS) fragmentation of the drug molecules and combined with molecular docking and ADMET models in two different situations. In the first model, the drug is docked without considering the possible metabolic effects. In the second model, each of the intermediates from the EI-MS results is docked, and metabolism occurs before the drug accesses the biological target. As a proof of concept, in this work, we investigate the main antiviral drugs used in clinical research to treat COVID-19. As a result, our strategy made it possible to assess the biological activity and toxicity of all potential by-products. We believed that our findings provide new chemical insights that can benefit the rational development of novel drugs in the future.


Subject(s)
Antiviral Agents/metabolism , COVID-19/drug therapy , Drug Discovery , SARS-CoV-2/drug effects , Adenine/adverse effects , Adenine/analogs & derivatives , Adenine/metabolism , Adenine/pharmacology , Adenosine/adverse effects , Adenosine/analogs & derivatives , Adenosine/metabolism , Adenosine/pharmacology , Adenosine Monophosphate/adverse effects , Adenosine Monophosphate/analogs & derivatives , Adenosine Monophosphate/metabolism , Adenosine Monophosphate/pharmacology , Alanine/adverse effects , Alanine/analogs & derivatives , Alanine/metabolism , Alanine/pharmacology , Amides/adverse effects , Amides/metabolism , Amides/pharmacology , Antiviral Agents/adverse effects , Antiviral Agents/pharmacology , COVID-19/metabolism , Chloroquine/adverse effects , Chloroquine/analogs & derivatives , Chloroquine/metabolism , Chloroquine/pharmacology , Drug Design , Humans , Metabolic Networks and Pathways , Molecular Docking Simulation , Nitro Compounds/adverse effects , Nitro Compounds/metabolism , Nitro Compounds/pharmacology , Pyrazines/adverse effects , Pyrazines/metabolism , Pyrazines/pharmacology , Pyrrolidines/adverse effects , Pyrrolidines/metabolism , Pyrrolidines/pharmacology , Ribavirin/adverse effects , Ribavirin/metabolism , Ribavirin/pharmacology , SARS-CoV-2/metabolism , Thiazoles/adverse effects , Thiazoles/metabolism , Thiazoles/pharmacology
7.
Int J Mol Sci ; 22(7)2021 Mar 24.
Article in English | MEDLINE | ID: covidwho-1369767

ABSTRACT

According to Darwin's theory, endless evolution leads to a revolution. One such example is the Clustered Regularly Interspaced Palindromic Repeats (CRISPR)-Cas system, an adaptive immunity system in most archaea and many bacteria. Gene editing technology possesses a crucial potential to dramatically impact miscellaneous areas of life, and CRISPR-Cas represents the most suitable strategy. The system has ignited a revolution in the field of genetic engineering. The ease, precision, affordability of this system is akin to a Midas touch for researchers editing genomes. Undoubtedly, the applications of this system are endless. The CRISPR-Cas system is extensively employed in the treatment of infectious and genetic diseases, in metabolic disorders, in curing cancer, in developing sustainable methods for fuel production and chemicals, in improving the quality and quantity of food crops, and thus in catering to global food demands. Future applications of CRISPR-Cas will provide benefits for everyone and will save countless lives. The technology is evolving rapidly; therefore, an overview of continuous improvement is important. In this review, we aim to elucidate the current state of the CRISPR-Cas revolution in a tailor-made format from its discovery to exciting breakthroughs at the application level and further upcoming trends related to opportunities and challenges including ethical concerns.


Subject(s)
CRISPR-Cas Systems , Gene Editing/methods , Genetic Engineering/methods , Animals , Archaea/metabolism , Bacteria/metabolism , Clustered Regularly Interspaced Short Palindromic Repeats , Crops, Agricultural/genetics , Genetic Engineering/history , Genome , History, 20th Century , History, 21st Century , Humans , Livestock
8.
Curr Med Chem ; 28(41): 8559-8594, 2021.
Article in English | MEDLINE | ID: covidwho-1217013

ABSTRACT

There is a new public health crisis threatening the world with the emergence and spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The disease was later named novel coronavirus disease or COVID-19. It was then declared a pandemic by the World Health Organization on March 11, 2020. The virus originated in bats and was transmitted to humans through unknown intermediary animals in Wuhan, Hubei province, China, in December 2019. As of February 5, 2021, 103 million laboratory-confirmed cases and nearly 2.3 million deaths were reported globally. The number of death tolls continues to rise, and a large number of countries have been forced to maintain social distance in public place and enforce lockdown. As per literature, coronavirus is transmitted human to human or human to animal via airborne droplets. Coronavirus enters the human cell through the membrane ACE-2 exopeptidase receptor. WHO, ECDC, and ICMR advised avoiding public places and close contact with infected persons and pet animals. To date, there is no evidence of any effective treatment for COVID-19. The main therapies being used to treat the disease are antiviral drugs, chloroquine/hydroxychloroquine, and respiratory therapy. Although several therapies have been proposed, quarantine is the only intervention that appears to be effective in decreasing the contagion rate. We conducted a literature review of publicly available information to summarize knowledge about the pathogen and the current epidemic. In the present literature review, the causative agent of the pandemic, epidemiology, pathogenesis, and diagnostic techniques are discussed. Further, currently used treatment, preventive strategies along with vaccine trials and computational tools are all described in detail.


Subject(s)
COVID-19 , SARS-CoV-2 , Animals , Communicable Disease Control , Humans , Hydroxychloroquine , Pandemics
9.
Sci Rep ; 11(1): 6397, 2021 03 18.
Article in English | MEDLINE | ID: covidwho-1142453

ABSTRACT

A new and more aggressive strain of coronavirus, known as SARS-CoV-2, which is highly contagious, has rapidly spread across the planet within a short period of time. Due to its high transmission rate and the significant time-space between infection and manifestation of symptoms, the WHO recently declared this a pandemic. Because of the exponentially growing number of new cases of both infections and deaths, development of new therapeutic options to help fight this pandemic is urgently needed. The target molecules of this study were the nitro derivatives of quinoline and quinoline N-oxide. Computational design at the DFT level, docking studies, and molecular dynamics methods as a well-reasoned strategy will aid in elucidating the fundamental physicochemical properties and molecular functions of a diversity of compounds, directly accelerating the process of discovering new drugs. In this study, we discovered isomers based on the nitro derivatives of quinoline and quinoline N-oxide, which are biologically active compounds and may be low-cost alternatives for the treatment of infections induced by SARS-CoV-2.


Subject(s)
Quinolines/chemistry , SARS-CoV-2/chemistry , COVID-19/drug therapy , Computer Simulation , Density Functional Theory , Drug Evaluation, Preclinical , Molecular Docking Simulation , Molecular Dynamics Simulation , Quinolines/therapeutic use
10.
Pharmaceuticals (Basel) ; 14(3)2021 Mar 05.
Article in English | MEDLINE | ID: covidwho-1129761

ABSTRACT

Since December 2019, SARS-CoV-2 (COVID-19) has been a worldwide pandemic with enormous consequences for human health and the world economy. Remdesivir is the only drug in the world that has been approved for the treating of COVID-19. This drug, as well as vaccination, still has uncertain effectiveness. Drug repurposing could be a promising strategy how to find an appropriate molecule: rapamycin could be one of them. The authors performed a systematic literature review of available studies on the research describing rapamycin in association with COVID-19 infection. Only peer-reviewed English-written articles from the world's acknowledged databases Web of Science, PubMed, Springer and Scopus were involved. Five articles were eventually included in the final analysis. The findings indicate that rapamycin seems to be a suitable candidate for drug repurposing. In addition, it may represent a better candidate for COVID-19 therapy than commonly tested antivirals. It is also likely that its efficiency will not be reduced by the high rate of viral RNA mutation.

11.
J Biomol Struct Dyn ; : 1-14, 2021 Jan 08.
Article in English | MEDLINE | ID: covidwho-1015104

ABSTRACT

The acute respiratory syndrome caused by the SARS-CoV-2, known as COVID-19, has been ruthlessly tormenting the world population for more than six months. However, so far no effective drug or vaccine against this plague have emerged yet, despite the huge effort in course by researchers and pharmaceutical companies worldwide. Willing to contribute with this fight to defeat COVID-19, we performed a virtual screening study on a library containing Food and Drug Administration (FDA) approved drugs, in a search for molecules capable of hitting three main molecular targets of SARS-CoV-2 currently available in the Protein Data Bank (PDB). Our results were refined with further molecular dynamics (MD) simulations and MM-PBSA calculations and pointed to 7 multi-target hits which we propose here for experimental evaluation and repurposing as potential drugs against COVID-19. Additional rounds of docking, MD simulations and MM-PBSA calculations with remdesivir suggested that this compound can also work as a multi-target drug against SARS-CoV-2.Communicated by Ramaswamy H. Sarma.

12.
Vaccines (Basel) ; 8(3)2020 Jul 28.
Article in English | MEDLINE | ID: covidwho-680834

ABSTRACT

The present study aimed to work out a peptide-based multi-epitope vaccine against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We predicted different B-cell and T-cell epitopes by using the Immune Epitopes Database (IEDB). Homology modeling of the construct was done using SWISS-MODEL and then docked with different toll-like-receptors (TLR4, TLR7, and TLR8) using PatchDock, HADDOCK, and FireDock, respectively. From the overlapped epitopes, we designed five vaccine constructs C1-C5. Based on antigenicity, allergenicity, solubility, different physiochemical properties, and molecular docking scores, we selected the vaccine construct 1 (C1) for further processing. Docking of C1 with TLR4, TLR7, and TLR8 showed striking interactions with global binding energy of -43.48, -65.88, and -60.24 Kcal/mol, respectively. The docked complex was further simulated, which revealed that both molecules remain stable with minimum RMSF. Activation of TLRs induces downstream pathways to produce pro-inflammatory cytokines against viruses and immune system simulation shows enhanced antibody production after the booster dose. In conclusion, C1 was the best vaccine candidate among all designed constructs to elicit an immune response SARS-CoV-2 and combat the coronavirus disease (COVID-19).

13.
Lett. Drug. Des. Discov. ; 4(17): 364-365, 2020.
Article in English | WHO COVID, ELSEVIER | ID: covidwho-87195
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