Update on the target structures of SARS-CoV-2: A systematic review

Prajapat, Manisha; Sarma, Phulen; Shekhar, Nishant; Prakash, Ajay; Avti, Pramod K.; Bhattacharyya, Anusuya; Kaur, Hardeep; Kumar, Subodh; Bansal, Seema; Sharma, Amit; Medhi, Bikash

doi:10.4103/ijp.ijp_338_20

Cited by 49 publications

(29 citation statements)

References 38 publications

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“…Human ACE2 (hACE2) is a receptor, which highly expresses on intestinal cells and lung cells. It has a comparable affinity to SARS-CoV SB and SARS-CoV-2 SB, which both use the C-terminal domain to interact with hACE2 [61]. The structure of SARS-COV-2-CTD is similar to that of SARS-COV, and the sequence consistency is up to 73.9%.…”

Section: Membrane Fusion and Virus Invasionmentioning

confidence: 93%

“…The structure of SARS-COV-2-CTD is similar to that of SARS-COV, and the sequence consistency is up to 73.9%. There are many similar binding sites between SARS-COV-2 and SARS-COV in their binding to hACE2, indicating that CoV has evolved to bind to hACE2 in the "hotspot" region [61]. However, SARS-COV-2 S protein binds to hACE2 more closely than SARS-COV with more chemical bonds and a larger buried surface area [61,62].…”

Section: Membrane Fusion and Virus Invasionmentioning

confidence: 99%

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Update on treatment and preventive interventions against COVID-19: an overview of potential pharmacological agents and vaccines

Xiao

Guo

et al. 2020

Mol Biomed

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The outbreak of coronavirus disease 2019 (COVID-19) triggered by the new member of the coronaviridae family, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has created an unprecedented challenge for global health. In addition to mild to moderate clinical manifestations such as fever, cough, and fatigue, severe cases often developed lethal complications including acute respiratory distress syndrome (ARDS) and acute lung injury. Given the alarming rate of infection and increasing trend of mortality, the development of underlying therapeutic and preventive treatment, as well as the verification of its effectiveness, are the top priorities. Current research mainly referred to and evaluated the application of the empirical treatment based on two precedents, severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), including antiviral drugs targeting different stages of virus replication, immunotherapy modulating the overactivated inflammation response, and other therapies such as herbal medicine and mesenchymal stem cells. Besides, the ongoing development of inventing prophylactic interventions such as various vaccines by companies and institutions worldwide is crucial to decline morbidity and mortality. This review mainly focused on promising candidates for the treatment of COVID-19 and collected recently updated evidence relevant to its feasibility in clinical practice in the near future.

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Section: Membrane Fusion and Virus Invasionmentioning

confidence: 93%

Section: Membrane Fusion and Virus Invasionmentioning

confidence: 99%

Update on treatment and preventive interventions against COVID-19: an overview of potential pharmacological agents and vaccines

Xiao

Guo

et al. 2020

Mol Biomed

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“…Different studies have identified various structural targets of SARS-CoV-2. Most of the studies targeted spike (S) protein; the other targets include RNA-dependent RNA polymerase, main protease/M Pro/3CL pro and nonstructural protein 15 Endoribonuclease [ 19 ]. The target protein structures of SARS-CoV‑2 are essential for drug designing against the virus.…”

Section: Metal Nanoparticles Affect Sars-cov-2 Targetsmentioning

confidence: 99%

Ayurvedic metal nanoparticles could be novel antiviral agents against SARS-CoV-2

Sarkar

Mukhopadhyay

2021

Int Nano Lett

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“…Various drug development strategies have been targeted towards inhibition of the RdRP of the SARS-CoV-2 to minimize the viral replication. [15][16][17][18] One of the major efforts has been put in identifying nucleotide analogues which would help in pre-mature termination of the RNA by interfering the RNA replication process. 19,20 Nucleotide analogues are resultant of the modifications in the natural nucleotides namely, Adenosine-5'-triphosphate (ATP), Guanosine-5'-triphosphate (GTP), Cytidine-5'-triphosphate (CTP), Thymidine-5'-triphospate (TTP) and Uridine-5'-triphosphate (UTP).…”

Section: Introductionmentioning

confidence: 99%

Exploring the Conformational Dynamics of RNA Dependent RNA Polymerase of SARS-CoV-2 in the Presence of Various Nucleotide Analogues

Koulgi¹,

Jani²,

N³

et al. 2020

Preprint

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<p>RNA dependent RNA polymerase (RdRP) from positive stranded RNA viruses has always been a hot target for designing of new drugs as it is responsible for viral replication. The major class of drugs that are targeted against RdRP are nucleotide analogues. An extensive docking and molecular dynamics study describing the role of natural nucleotides (NTPs) and its analogues in imparting an inhibitory effect on the RdRP has been presented here. RdRP simulations in its apo, NTP-bound and analogue-bound form have been performed for a cumulative time of 1.9 μs. The conformational flexibility of the RdRP molecule was explored using Principal Component Analysis (PCA) and Markov State Modeling (MSM) Analysis. PCA inferred the presence of correlated motions along the conserved motifs of the RdRP. The ligand binding motif F and template binding motif G showed motions that are negatively correlated with one another. LYS 551, ARG 553 and ARG 555 which are a part of the motif F appear to form strong interactions with the ligand molecules. ARG 836, a primer binding residue was observed to strongly bind to the nucleotide analogues. The MSM analysis helped to observe different conformational states explored by the RdRP. The ensemble docking of the ligands on the Markov states suggested the involvement of the above residues in ligand interactions. The Markov states obtained clearly demarcated the open and closed conformations. The closed states were observed to have more favorable docking of the ligands. MSM analysis predicted a probable inhibitory mechanism involving the closing of the template entry site by reduction in the distance between the flanking finger and thumb subdomain. </p>

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Update on the target structures of SARS-CoV-2: A systematic review

Cited by 49 publications

References 38 publications

Update on treatment and preventive interventions against COVID-19: an overview of potential pharmacological agents and vaccines

Update on treatment and preventive interventions against COVID-19: an overview of potential pharmacological agents and vaccines

Ayurvedic metal nanoparticles could be novel antiviral agents against SARS-CoV-2

Exploring the Conformational Dynamics of RNA Dependent RNA Polymerase of SARS-CoV-2 in the Presence of Various Nucleotide Analogues

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