Screening Potential Drugs for COVID-19 Based on Bound Nuclear Norm Regularization

The novel coronavirus pneumonia COVID-19 infected by SARS-CoV-2 has attracted worldwide attention. It is urgent to find effective therapeutic strategies for stopping COVID-19. In this study, a Bounded Nuclear Norm Regularization (BNNR) method is developed to predict anti-SARS-CoV-2 drug candidates. First, three virus-drug association datasets are compiled. Second, a heterogeneous virus-drug network is constructed. Third, complete genomic sequences and Gaussian association profiles are integrated to compute virus similarities; chemical structures and Gaussian association profiles are integrated to calculate drug similarities. Fourth, a BNNR model based on kernel similarity (VDA-GBNNR) is proposed to predict possible anti-SARS-CoV-2 drugs. VDA-GBNNR is compared with four existing advanced methods under fivefold cross-validation. The results show that VDA-GBNNR computes better AUCs of 0.8965, 0.8562, and 0.8803 on the three datasets, respectively. There are 6 anti-SARS-CoV-2 drugs overlapping in any two datasets, that is, remdesivir, favipiravir, ribavirin, mycophenolic acid, niclosamide, and mizoribine. Molecular dockings are conducted for the 6 small molecules and the junction of SARS-CoV-2 spike protein and human angiotensin-converting enzyme 2. In particular, niclosamide and mizoribine show higher binding energy of −8.06 and −7.06 kcal/mol with the junction, respectively. G496 and K353 may be potential key residues between anti-SARS-CoV-2 drugs and the interface junction. We hope that the predicted results can contribute to the treatment of COVID-19.

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Blocking Effect of Demethylzeylasteral on the Interaction between Human ACE2 Protein and SARS-CoV-2 RBD Protein Discovered Using SPR Technology

Molecules ◽

10.3390/molecules26010057 ◽

2020 ◽

Vol 26 (1) ◽

pp. 57

Author(s):

Zhi-Ling Zhu ◽

Xiao-Dan Qiu ◽

Shuo Wu ◽

Yi-Tong Liu ◽

Ting Zhao ◽

...

Keyword(s):

Therapeutic Strategy ◽

Blocking Effect ◽

Spike Protein ◽

Binding Affinities ◽

The Novel ◽

Converting Enzyme ◽

Primary Method ◽

Angiotensin Converting Enzyme 2 ◽

Novel Coronavirus ◽

Effective Drugs

The novel coronavirus disease (2019-nCoV) has been affecting global health since the end of 2019, and there is no sign that the epidemic is abating. Targeting the interaction between the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein and the human angiotensin-converting enzyme 2 (ACE2) receptor is a promising therapeutic strategy. In this study, surface plasmon resonance (SPR) was used as the primary method to screen a library of 960 compounds. A compound 02B05 (demethylzeylasteral, CAS number: 107316-88-1) that had high affinities for S-RBD and ACE2 was discovered, and binding affinities (KD, μM) of 02B05-ACE2 and 02B05-S-RBD were 1.736 and 1.039 μM, respectively. The results of a competition experiment showed that 02B05 could effectively block the binding of S-RBD to ACE2 protein. Furthermore, pseudovirus infection assay revealed that 02B05 could inhibit entry of SARS-CoV-2 pseudovirus into 293T cells to a certain extent at nontoxic concentration. The compoundobtained in this study serve as references for the design of drugs which have potential in the treatment of COVID-19 and can thus accelerate the process of developing effective drugs to treat SARS-CoV-2 infections.

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ACE2 Nascence, trafficking, and SARS-CoV-2 pathogenesis: the saga continues

Human Genomics ◽

10.1186/s40246-021-00304-9 ◽

2021 ◽

Vol 15 (1) ◽

Author(s):

Sally Badawi ◽

Bassam R. Ali

Keyword(s):

Cell Surface ◽

Angiotensin Converting Enzyme ◽

The Novel ◽

Converting Enzyme ◽

Post Translational Modifications ◽

Angiotensin Converting Enzyme 2 ◽

Viral Attachment ◽

Novel Coronavirus ◽

Effective Medication ◽

Potential Use

AbstractWith the emergence of the novel coronavirus SARS-CoV-2 since December 2019, more than 65 million cases have been reported worldwide. This virus has shown high infectivity and severe symptoms in some cases, leading to over 1.5 million deaths globally. Despite the collaborative and concerted research efforts that have been made, no effective medication for COVID-19 (coronavirus disease-2019) is currently available. SARS-CoV-2 uses the angiotensin-converting enzyme 2 (ACE2) as an initial mediator for viral attachment and host cell invasion. ACE2 is widely distributed in the human tissues including the cell surface of lung cells which represent the primary site of the infection. Inhibiting or reducing cell surface availability of ACE2 represents a promising therapy for tackling COVID-19. In this context, most ACE2–based therapeutic strategies have aimed to tackle the virus through the use of angiotensin-converting enzyme (ACE) inhibitors or neutralizing the virus by exogenous administration of ACE2, which does not directly aim to reduce its membrane availability. However, through this review, we present a different perspective focusing on the subcellular localization and trafficking of ACE2. Membrane targeting of ACE2, and shedding and cellular trafficking pathways including the internalization are not well elucidated in literature. Therefore, we hereby present an overview of the fate of newly synthesized ACE2, its post translational modifications, and what is known of its trafficking pathways. In addition, we highlight the possibility that some of the identified ACE2 missense variants might affect its trafficking efficiency and localization and hence may explain some of the observed variable severity of SARS-CoV-2 infections. Moreover, an extensive understanding of these processes is necessarily required to evaluate the potential use of ACE2 as a credible therapeutic target.

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Quinoline and Quinazoline Alkaloids against COVID-19: An In Silico Multitarget Approach

Journal of Chemistry ◽

10.1155/2021/3613268 ◽

2021 ◽

Vol 2021 ◽

pp. 1-11

Author(s):

Esraa M. O. A. Ismail ◽

Shaza W. Shantier ◽

Mona S. Mohammed ◽

Hassan H. Musa ◽

Wadah Osman ◽

...

Keyword(s):

Antimalarial Activity ◽

The Novel ◽

Socioeconomic Impacts ◽

Health Crisis ◽

Natural Sources ◽

Angiotensin Converting Enzyme 2 ◽

Main Protease ◽

Recent Outbreak ◽

Novel Coronavirus ◽

Potential Inhibitors

The recent outbreak of the highly contagious coronavirus disease 2019 (COVID-19) caused by the novel coronavirus SARS-CoV-2 has created a global health crisis with socioeconomic impacts. Although, recently, vaccines have been approved for the prevention of COVID-19, there is still an urgent need for the discovery of more efficacious and safer drugs especially from natural sources. In this study, a number of quinoline and quinazoline alkaloids with antiviral and/or antimalarial activity were virtually screened against three potential targets for the development of drugs against COVID-19. Among seventy-one tested compounds, twenty-three were selected for molecular docking based on their pharmacokinetic and toxicity profiles. The results identified a number of potential inhibitors. Three of them, namely, norquinadoline A, deoxytryptoquivaline, and deoxynortryptoquivaline, showed strong binding to the three targets, SARS-CoV-2 main protease, spike glycoprotein, and human angiotensin-converting enzyme 2. These alkaloids therefore have promise for being further investigated as possible multitarget drugs against COVID-19.

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Investigation of the genetic variation in ACE2 on the structural recognition by the novel coronavirus (SARS-CoV-2)

10.21203/rs.3.rs-29037/v2 ◽

2020 ◽

Author(s):

Xingyi Guo ◽

Zhishan Chen ◽

Yumin Xia ◽

Weiqiang Lin ◽

Hongzhi Li

Keyword(s):

Genetic Variation ◽

The Novel ◽

S Protein ◽

Angiotensin Converting Enzyme 2 ◽

Missense Variants ◽

Catalytic Metal ◽

Using Data ◽

Novel Coronavirus ◽

Insight Into

Abstract Background: The outbreak of coronavirus disease (COVID-19) was caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), through its surface spike glycoprotein (S-protein) recognition on the receptor Angiotensin-converting enzyme 2 (ACE2) in humans. However, it remains unclear how genetic variations in ACE2 may affect its function and structure, and consequently alter the recognition by SARS-CoV-2. Methods: We have systemically characterized missense variants in the gene ACE2 using data from the Genome Aggregation Database (gnomAD; N = 141,456). To investigate the putative deleterious role of missense variants, six existing functional prediction tools were applied to evaluate their impact. We further analyzed the structural flexibility of ACE2 and its protein-protein interface with the S-protein of SARS-CoV-2 using our developed Legion Interfaces Analysis (LiAn) program.Results: Here, we characterized a total of 12 ACE2 putative deleterious missense variants. Of those 12 variants, we further showed that p.His378Arg could directly weaken the binding of catalytic metal atom to decrease ACE2 activity and p.Ser19Pro could distort the most important helix to the S-protein. Another seven missense variants may affect secondary structures (i.e. p.Gly211Arg; p.Asp206Gly; p.Arg219Cys; p.Arg219His, p.Lys341Arg, p.Ile468Val, and p.Ser547Cys), whereas p.Ile468Val with AF = 0.01 is only present in Asian.Conclusions: We provide strong evidence of putative deleterious missense variants in ACE2 that are present in specific populations, which could disrupt the function and structure of ACE2. These findings provide novel insight into the genetic variation in ACE2 which may affect the SARS-CoV-2 recognition and infection, and COVID-19 susceptibility and treatment.

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Arterial Hypertension as a Risk Comorbidity Associated with COVID-19 Pathology

International Journal of Hypertension ◽

10.1155/2020/8019360 ◽

2020 ◽

Vol 2020 ◽

pp. 1-7

Author(s):

Alexander Kamyshnyi ◽

Inna Krynytska ◽

Victoriya Matskevych ◽

Mariya Marushchak ◽

Oleh Lushchak

Keyword(s):

Arterial Hypertension ◽

Pressure Control ◽

The Novel ◽

Global Public Health ◽

Angiotensin Converting Enzyme 2 ◽

Cardiovascular Comorbidities ◽

Public Health Challenge ◽

Novel Coronavirus ◽

Ace2 Gene

Coronavirus disease 2019 (COVID-19), caused by the novel coronavirus severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), is an ongoing global public health challenge. Current clinical data suggest that, in COVID-19 patients, arterial hypertension (AH) is one of the most common cardiovascular comorbidities; it can worsen outcomes and increase the risk of admission to intensive care unit (ICU). The exact mechanisms through which AH contributes to the poor prognosis in COVID-19 are not yet clear. The putative relationship between AH and COVID-19 may be linked to the role of angiotensin-converting enzyme 2 (ACE2), a key element of the AH pathophysiology. Another mechanism connecting AH and COVID-19 is the dysregulation of the immune system resulting in a cytokine storm, mediated by an imbalanced response of T helper cells subtypes. Therefore, it is essential to optimize blood pressure control in hypertensive patients and monitor them carefully for cardiovascular and other complications for the duration of COVID-19 infection. The question whether AH-linked ACE2 gene polymorphisms increase the risk and/or worsen the course of SARS-CoV-2 infection should also receive further consideration.

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Molecular interaction and inhibition of SARS-CoV-2 binding to the ACE2 receptor

Nature Communications ◽

10.1038/s41467-020-18319-6 ◽

2020 ◽

Vol 11 (1) ◽

Cited By ~ 7

Author(s):

Jinsung Yang ◽

Simon J. L. Petitjean ◽

Melanie Koehler ◽

Qingrong Zhang ◽

Andra C. Dumitru ◽

...

Keyword(s):

Binding Pocket ◽

Living Cells ◽

Host Cells ◽

The Novel ◽

Angiotensin Converting Enzyme 2 ◽

Force Microscopy ◽

Binding Interface ◽

Atomic Force ◽

Viral Glycoproteins ◽

Novel Coronavirus

Abstract Study of the interactions established between the viral glycoproteins and their host receptors is of critical importance for a better understanding of virus entry into cells. The novel coronavirus SARS-CoV-2 entry into host cells is mediated by its spike glycoprotein (S-glycoprotein), and the angiotensin-converting enzyme 2 (ACE2) has been identified as a cellular receptor. Here, we use atomic force microscopy to investigate the mechanisms by which the S-glycoprotein binds to the ACE2 receptor. We demonstrate, both on model surfaces and on living cells, that the receptor binding domain (RBD) serves as the binding interface within the S-glycoprotein with the ACE2 receptor and extract the kinetic and thermodynamic properties of this binding pocket. Altogether, these results provide a picture of the established interaction on living cells. Finally, we test several binding inhibitor peptides targeting the virus early attachment stages, offering new perspectives in the treatment of the SARS-CoV-2 infection.

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Fluid and Electrolyte Disturbances in COVID-19 and Their Complications

BioMed Research International ◽

10.1155/2021/6667047 ◽

2021 ◽

Vol 2021 ◽

pp. 1-5

Author(s):

Mohammad Pourfridoni ◽

Seyede Mahsa Abbasnia ◽

Fateme Shafaei ◽

Javad Razaviyan ◽

Reza Heidari-Soureshjani

Keyword(s):

Kidney Injury ◽

Respiratory Illness ◽

The Novel ◽

Acute Respiratory Illness ◽

Gi Tract ◽

Angiotensin Converting Enzyme 2 ◽

Intensive Care Patients ◽

Electrolyte Disturbances ◽

Novel Coronavirus ◽

Tract Damage

The novel coronavirus disease 2019 (COVID-19) is the cause of an acute respiratory illness which has spread around the world. The virus infects the host by binding to the angiotensin-converting enzyme 2 (ACE2) receptors. Due to the presence of ACE2 receptors in the kidneys and gastrointestinal (GI) tract, kidneys and GI tract damage arising from the virus can be seen in patients and can cause acute conditions such as acute kidney injury (AKI) and digestive problems for the patient. One of the complications of kidneys and GI involvement in COVID-19 is fluid and electrolyte disturbances. The most common ones of these disorders are hyponatremia, hypernatremia, hypokalemia, hypocalcemia, hypochloremia, hypervolemia, and hypovolemia, which if left untreated, cause many problems for patients and even increase mortality. Fluid and electrolyte disturbances are more common in hospitalized and intensive care patients. Children are also at greater risk for fluid and electrolyte disturbances complications. Therefore, clinicians should pay special attention to the fluid and electrolyte status of patients. Changes in fluid and electrolyte levels can be a good indicator of disease progression.

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Are we there yet? Analyzing scientific research related to COVID-19 drug repurposing

10.21203/rs.3.rs-80893/v1 ◽

2020 ◽

Author(s):

Namu Park ◽

Hyeyoung Ryu ◽

Ying Ding ◽

Qi Yu ◽

Yi Bu ◽

...

Keyword(s):

Scientific Research ◽

Drug Repurposing ◽

Drug Candidate ◽

The Novel ◽

Inverse Document Frequency ◽

Term Frequency ◽

Drug Candidates ◽

Document Frequency ◽

Explicit Consent ◽

Novel Coronavirus

Abstract Drug repurposing may be a pivotal means of fulfilling urgent needs for treatment of the novel coronavirus disease 2019 (COVID-19), but current studies on drug repurposing for COVID-19 seem to show a lack of consensus in their drug candidate focus. Using bibliometric methods in a non-expert perspective, in a review of 34 published articles on the COVID-19 and drug-repurposing, we investigated obvious and less obvious points of consensus on drug candidates. To establish these two types of consensus, we first implemented document clustering. Within a set of five clustered papers, we established an obvious consensus, relying solely on the occurrence of entities by using term frequency and inverse document frequency and a comparison of mentioned drugs, finding that remdesivir and chloroquine were discussed with a certain degree of agreement. For the less obvious consensus, we created a drug entity co-occurrence network to establish low-high centrality combinations to probe the crucial drugs found in article clustering that are not plainly apparent through the mere counting of the occurrence of drug entities occurrences. Lopinavir emerged as having possibly potent effects in spite of underuse, while the mainstream of studies focus more on drugs such as chloroquine that enjoy explicit consent. Using an entitymetrics perspective, we expect that our research will support investigations of drug repurposing, expediting the process of establishing treatment for COVID-19.

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ACE-2-derived Biomimetic Peptides for the Inhibition of Spike Protein of SARS-CoV-2

10.26434/chemrxiv.12335933.v1 ◽

2020 ◽

Author(s):

Saroj Kumar Panda ◽

Parth Sarthi Sen Gupta ◽

Satyaranjan Biswal ◽

Abhik Kumar Ray ◽

Malay Kumar Rana

Keyword(s):

Principal Component ◽

Host Cells ◽

Spike Protein ◽

Peptide Inhibitor ◽

The Novel ◽

Receptor Binding Domain ◽

Converting Enzyme ◽

Inhibition Assay ◽

Angiotensin Converting Enzyme 2 ◽

Novel Coronavirus

<p>SARS-CoV-2, a novel coronavirus causing overwhelming death and infection worldwide, has emerged as a pandemic. Compared to its predecessor SARS-CoV, SARS-CoV-2 is more infective for being highly contagious and exhibiting tighter binding with host angiotensin-converting enzyme 2 (hACE-2). The entry of the virus into host cells is mediated by the interaction of its spike protein with hACE-2. Thus, a peptide that has a resemblance to hACE-2 but can overpower the spike protein-hACE-2 interaction will be a potential therapeutic to contain this virus. The non-interacting residues in the receptor-binding domain of hACE-2 have been mutated to generate a library of 136 new peptides. Out of this library, docking and virtual screening discover seven peptides that can exert a stronger interaction with the spike protein than hACE-2. A peptide derived from simultaneous mutation of all the non-interacting residues of hACE-2 yields two-fold stronger interaction than hACE-2 and thus turns out here to be the best peptide-inhibitor of the novel coronavirus. The binding of the spike protein and the best peptide-inhibitor with hACE-2 is explored further by molecular dynamics, free energy, and principal component analysis to demonstrate its efficacy. Further, the inhibition assay study with the best peptide inhibitor is in progress. </p>

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Dilated Cardiomyopathy Risk in Patients with Coronavirus Disease 2019: How to Identify and Characterise it Early?

European Cardiology Review ◽

10.15420/ecr.2020.17 ◽

2020 ◽

Vol 15 ◽

Cited By ~ 1

Author(s):

Maki Komiyama ◽

Koji Hasegawa ◽

Akira Matsumori

Keyword(s):

Dilated Cardiomyopathy ◽

Poor Prognosis ◽

Myocardial Injury ◽

The Novel ◽

Elevated Blood ◽

Converting Enzyme ◽

Angiotensin Converting Enzyme 2 ◽

Direct Binding ◽

Novel Coronavirus ◽

Lines Of Evidence

Multiple lines of evidence have shown that elevated blood troponin is strongly associated with poor prognosis in patients with the novel coronavirus disease 2019 (COVID-19). Possible mechanisms of myocardial injury in COVID-19 include ischaemia due to circulatory and respiratory failure, epicardial or intramyocardial small coronary artery thrombotic obstruction due to increased coagulability, and myocarditis caused by systemic inflammation or direct binding of the virus to its receptor, angiotensin-converting enzyme-2 (ACE2), which is abundantly expressed in the heart. It is postulated that persistent immune activation upon viral infection increases the risk of developing dilated cardiomyopathy in COVID-19 patients.

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