scholarly journals Direct ACE2- Spike RBD Binding Disruption with Small Molecules: A Strategy for COVID-19 Treatment

2020 ◽  
Author(s):  
Sandra Smieszek ◽  
Bart Przychodzen ◽  
Vasilios Polymeropoulos ◽  
Christos Polymeropoulos ◽  
Mihael Polymeropoulos
Keyword(s):  
Small Molecules ◽  
Viral Entry ◽  
In Silico ◽  
Spike Protein ◽  
Interface Residue ◽  
Chemical Library ◽  
Susceptibility Data ◽  
Multiple Routes ◽  
Viral Nature

ACE2 is a key receptor for SARS-CoV-2 cell entry. Binding of SARS-Cov-2 to ACE2 involves the viral Spike protein. The molecular interaction between ACE2 and Spike has been resolved. Interfering with this interaction might be used in treating patients with COVID-19. Inhibition of this interaction can be attained via multiple routes: here we focus on identifying small molecules that would prevent the interaction. Specifically we focus on small molecules and peptides that have the capacity to effectively bind the ACE2: RBD contact domain to prevent and reduce SARS-CoV-2 entry into the cell. We aim to identify molecules that prevent the docking of viral spike protein (mediated by RBD) onto cells expressing ACE2, without inhibiting the activity of ACE2. We utilize the most recent ACE2-RBD crystallography resolved model (PDB-ID:6LZG). Based on animal susceptibility data we narrowed down our interest to the location of amino acid 34 (Histidine) located on ACE2. We performed an in silico screen of a chemical library of compounds with several thousand small molecules including FDA approved compounds. All compounds were tested for binding to the proximal binding site located close to histidine 34 on ACE2. We report a list of four potential small molecules that potentially have the capacity to bind target residue: AY-NH2, a selective PAR4 receptor agonist peptide (CAS number: 352017-71-1), NAD+ (CAS number: 53-84-9), Reproterol, a short-acting β2 adrenoreceptor agonist used in the treatment of asthma (CAS number: 54063-54-6), and Thymopentin, a synthetic immune-stimulant which enhances production of thymic T cells (CAS number: 69558-55-0). The focus is on a High Throughput Screen Assay (HTSA), or in silico screen, delineating small molecules that are selectively binding/masking the crucial interface residue on ACE2 at His34. Consequently, inhibiting SARS-CoV-2 binding to host ACE2 and viral entry is a potent strategy to reduce cellular entry of the virus. We suggest that this anti-viral nature of this interaction is a viable strategy for COVID19 whereas the small molecules including peptides warrant further in vitro screens.

scholarly journals Direct ACE2- Spike RBD Binding Disruption with Small Molecules: A Strategy for COVID-19 Treatment

2020 ◽  
Author(s):  
Sandra Smieszek ◽  
Bart Przychodzen ◽  
Vasilios Polymeropoulos ◽  
Christos Polymeropoulos ◽  
Mihael Polymeropoulos
Keyword(s):  
Small Molecules ◽  
Viral Entry ◽  
In Silico ◽  
Spike Protein ◽  
Interface Residue ◽  
Chemical Library ◽  
Susceptibility Data ◽  
Multiple Routes ◽  
Viral Nature

ACE2 is a key receptor for SARS-CoV-2 cell entry. Binding of SARS-Cov-2 to ACE2 involves the viral Spike protein. The molecular interaction between ACE2 and Spike has been resolved. Interfering with this interaction might be used in treating patients with COVID-19. Inhibition of this interaction can be attained via multiple routes: here we focus on identifying small molecules that would prevent the interaction. Specifically we focus on small molecules and peptides that have the capacity to effectively bind the ACE2: RBD contact domain to prevent and reduce SARS-CoV-2 entry into the cell. We aim to identify molecules that prevent the docking of viral spike protein (mediated by RBD) onto cells expressing ACE2, without inhibiting the activity of ACE2. We utilize the most recent ACE2-RBD crystallography resolved model (PDB-ID:6LZG). Based on animal susceptibility data we narrowed down our interest to the location of amino acid 34 (Histidine) located on ACE2. We performed an in silico screen of a chemical library of compounds with several thousand small molecules including FDA approved compounds. All compounds were tested for binding to the proximal binding site located close to histidine 34 on ACE2. We report a list of four potential small molecules that potentially have the capacity to bind target residue: AY-NH2, a selective PAR4 receptor agonist peptide (CAS number: 352017-71-1), NAD+ (CAS number: 53-84-9), Reproterol, a short-acting β2 adrenoreceptor agonist used in the treatment of asthma (CAS number: 54063-54-6), and Thymopentin, a synthetic immune-stimulant which enhances production of thymic T cells (CAS number: 69558-55-0). The focus is on a High Throughput Screen Assay (HTSA), or in silico screen, delineating small molecules that are selectively binding/masking the crucial interface residue on ACE2 at His34. Consequently, inhibiting SARS-CoV-2 binding to host ACE2 and viral entry is a potent strategy to reduce cellular entry of the virus. We suggest that this anti-viral nature of this interaction is a viable strategy for COVID19 whereas the small molecules including peptides warrant further in vitro screens.

scholarly journals Screening of Common Herbal Medicines as Promising Direct Inhibitors of Sars-Cov-2 in Silico

2020 ◽  
pp. 53-67
Author(s):  
Zahraa Kamaz ◽  
Mohammad J. Al- Jassani ◽  
Umar Haruna
Keyword(s):  
Viral Entry ◽  
In Silico ◽  
Herbal Medicines ◽  
Spike Protein ◽  
Kinetic Properties ◽  
In Silico Docking ◽  
Human Lung Cells ◽  
Main Protease ◽  
Study Results

Background: Molecular docking has been used recently in pharma industry for drug designing, it’s a powerful tool to find ligand-substrate interactions at molecules level. Since urgent need to develop anti-viral drug that target new coronavirus main proteins, in silico docking has been used to achieve this purpose. Materials and Methods: Thirteen herbs are known for their antioxidants and antiviral properties have been selected to investigate their abilities in inhibiting SARS-COV2 spike protein and main protease Mpro. pdb files for RBD (Receptor Binding Domain) region of spike protein and for Mpro and mol2 files for all herbs understudy were uploaded for swiss dock online server, the docking results were analyzed using chimera software. Full fitness energy and hydrogens bonds interactions were considered for docking evaluation.  Pharma kinetic properties for compounds have good binding results were evaluated through AMES and ADMET tests. Results: All compounds showed negative full fitness energy that means they are able to complex with both SARS-COV2 spike protein and main protease, however some of the herbs form very powerful hydrogen bonding with the RBD site of the spike protein and the catalytic site of Mpro such as coumarylquinic acid, while stigmasterol has strong binding with the spike protein only. Both compounds appear to be safe drugs for human according to AMES test results. Conclusion: Coumarylquinic acid and stigmasterol have powerful binding in silico, further in vitro studies include using viral infected human lung cells and testing above compounds ability for inhibiting viral entry and replication should be proceed to confirm the study results.

scholarly journals Andrographis paniculata (Burm. F.) Wall. Ex Nees, Andrographolide, and Andrographolide Analogues as SARS-CoV-2 Antivirals? A Rapid Review

2021 ◽  
Vol 16 (5) ◽  
pp. 1934578X2110166
Author(s):  
Xin Yi Lim ◽  
Janice Sue Wen Chan ◽  
Terence Yew Chin Tan ◽  
Bee Ping Teh ◽  
Mohd Ridzuan Mohd Abd Razak ◽  
...  
Keyword(s):  
Inhibitory Activity ◽  
In Silico ◽  
Rna Binding ◽  
Symptomatic Relief ◽  
Andrographis Paniculata ◽  
Spike Protein ◽  
Rapid Review ◽  
In Silico Studies

Drug repurposing is commonly employed in the search for potential therapeutic agents. Andrographis paniculata, a medicinal plant commonly used for symptomatic relief of the common cold, and its phytoconstituent andrographolide, have been repeatedly identified as potential antivirals against SARS-CoV-2. In light of new evidence emerging since the onset of the COVID-19 pandemic, this rapid review was conducted to identify and evaluate the current SARS-CoV-2 antiviral evidence for A. paniculata, andrographolide, and andrographolide analogs. A systematic search and screen strategy of electronic databases and gray literature was undertaken to identify relevant primary articles. One target-based in vitro study reported the 3CLpro inhibitory activity of andrographolide as being no better than disulfiram. Another Vero cell-based study reported potential SARS-CoV-2 inhibitory activity for both andrographolide and A. paniculata extract. Eleven in silico studies predicted the binding of andrographolide and its analogs to several key antiviral targets of SARS-CoV-2 including the spike protein-ACE-2 receptor complex, spike protein, ACE-2 receptor, RdRp, 3CLpro, PLpro, and N-protein RNA-binding domain. In conclusion, in silico and in vitro studies collectively suggest multi-pathway targeting SARS-CoV-2 antiviral properties of andrographolide and its analogs, but in vivo data are needed to support these predictions.

scholarly journals Focus Your Screening Library: Rapid Identification of Novel PDE2 Inhibitors with in silico Driven Library Prioritization and MicroScale Thermophoresis

2020 ◽  
Author(s):  
Florian Kaiser ◽  
Maximilian G. Plach ◽  
Thomas Schubert ◽  
V. Joachim Haupt
Keyword(s):  
In Silico ◽  
High Throughput Screening ◽  
Rapid Identification ◽  
Chemical Diversity ◽  
Chemical Library ◽  
Binding Behavior ◽  
Microscale Thermophoresis ◽  
Excellent Starting Point ◽  
Starting Point

Accelerated development of lead structures is of high interest to the pharmaceutical industry in order to decrease development times and costs. We showcase how an intelligent combination of AI-based drug screening with state-of-the-art biophysics drives the rapid identification of novel inhibitor structures with high chemical diversity for cGMP-dependent 3’,5’-cyclic phosphodiesterase (PDE2). The starting point was an off-the-shelve chemical library of two million drug-like compounds. In a single in silico reduction step, we short-listed 125 compounds – the focused library – as potential binders to PDE2 and tested their binding behavior in vitro using MicroScale Thermophoresis (MST). Of this focused library, seven compounds indicated binding to PDE2, translating to a hit rate of 6%. Three of these compounds have affinities in the lower micromolar range. The compound with the highest affinity showed a KD of 10 µM and is thus an excellent starting point for further medicinal chemistry optimization. The results show how innovative and structure-driven in silico approaches and biophysics can be used to accelerate drug discovery and to obtain new molecular scaffolds at a fraction of the costs and time – compared with standard high-throughput screening.

scholarly journals Aberrant glycosylation of anti-SARS-CoV-2 IgG is a pro-thrombotic stimulus for platelets

2021 ◽  
Author(s):  
Alexander P Bye ◽  
Willianne Hoepel ◽  
Joanne L Mitchell ◽  
Sophie Jegouic ◽  
Silvia Loureiro ◽  
...  
Keyword(s):  
Immune Response ◽  
Small Molecules ◽  
Tyrosine Kinases ◽  
Spike Protein ◽  
Respiratory Problems ◽  
Aberrant Glycosylation ◽  
Von Willebrand ◽  
Willebrand Factor ◽  
P2y12 Antagonist

A subset of patients with COVID-19 become critically ill, suffering from severe respiratory problems and also increased rates of thrombosis. The causes of thrombosis in severely ill COVID-19 patients are still emerging, but the coincidence of critical illness with the timing of the onset of adaptive immunity could implicate an excessive immune response. We hypothesised that platelets might be susceptible to activation by anti-SARS-CoV-2 antibodies and contribute to thrombosis. We found that immune complexes containing recombinant SARS-CoV-2 spike protein and anti-spike IgG enhanced platelet-mediated thrombosis on von Willebrand Factor in vitro, but only when the glycosylation state of the Fc domain was modified to correspond with the aberrant glycosylation previously identified in patients with severe COVID-19. Furthermore, we found that activation was dependent on FcγRIIA and we provide in vitro evidence that this pathogenic platelet activation can be counteracted by therapeutic small molecules R406 (fostamatinib) and ibrutinib that inhibit tyrosine kinases syk and btk respectively or by the P2Y12 antagonist cangrelor.

scholarly journals Current Perspectives in the Discovery of Newer Medications Against the Outbreak of COVID-19

2021 ◽  
Vol 8 ◽  
Author(s):  
M. Ramesh ◽  
Krishnan Anand ◽  
Mohd Shahbaaz ◽  
Magda H. Abdellattif
Keyword(s):  
Small Molecules ◽  
Viral Entry ◽  
Respiratory Illness ◽  
Disease Outbreak ◽  
Spike Protein ◽  
Severe Illness ◽  
Human Lungs ◽  
Synthetic Approaches ◽  
Severe Respiratory Illness

A rapid and increasing spread of COVID-19 pandemic disease has been perceived worldwide in 2020. The current COVID-19 disease outbreak is due to the spread of SARS-CoV-2. SARS-CoV-2 is a new strain of coronavirus that has spike protein on the envelope. The spike protein of the virus binds with the ACE-2 receptor of the human lungs surface for entering into the host. Therefore, the blocking of viral entry into the host by targeting the spike protein has been suggested to be a valid strategy to treat COVID-19. The patients of COVID-19 were found to be asymptomatic, cold, mild to severe respiratory illness, and leading to death. The severe illness has been noted mainly in old age people, cardiovascular disease patients, and respiratory disease patients. However, the long-term health effects due to COVID-19 are not yet known. Recently, the vaccines were authorized to protect from COVID-19. However, the researchers have put an effort to discover suitable targets and newer medications in the form of small molecules or peptides, based on in-silico methods and synthetic approaches. This manuscript describes the current perspectives of the causative agent, diagnostic procedure, therapeutic targets, treatment, clinical trials, and development of potential clinical candidates of COVID-19. The study will be useful to identify the potential newer medications for the treatment of COVID-19.

scholarly journals In-vivo Protection from SARS-CoV-2 infection by ATN-161 in k18-hACE2 transgenic mice

2021 ◽  
Author(s):  
Amruta Narayanappa ◽  
Elizabeth B Engler-Chiurazzi ◽  
Isabel C Murray-Brown ◽  
Timothy E Gressett ◽  
Ifechukwude J Biose ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Viral Entry ◽  
Therapeutic Potential ◽  
Host Cells ◽  
Spike Protein ◽  
Cell Infection ◽  
Integrin Alpha5beta1 ◽  
Chemokine Ligand

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an infectious disease that has spread worldwide. Current treatments are limited in both availability and efficacy, such that improving our understanding of the factors that facilitate infection is urgently needed to more effectively treat infected individuals and to curb the pandemic. We and others have previously demonstrated the significance of interactions between the SARS-CoV-2 spike protein, integrin alpha5beta1 and human ACE2 to facilitate viral entry into host cells in vitro. We previously found that inhibition of integrin alpha5beta1 by the clinically validated small peptide ATN-161 inhibits these spike protein interactions and cell infection in vitro. In continuation with our previous findings, here we have further evaluated the therapeutic potential of ATN-161 on SARS-CoV-2 infection in k18-hACE2 transgenic (SARS-CoV-2 susceptible) mice in vivo. We discovered that treatment with single- or repeated intravenous doses of ATN-161 (1 mg/kg) within 48 hours after intranasal inoculation with SARS-CoV-2 lead to a reduction of lung viral load, viral immunofluorescence and improved lung histology in a majority of mice 72 hours post-infection. Furthermore, ATN-161 reduced SARS-CoV-2-induced increased expression of lung integrin alpha 5 and alpha v (an alpha 5-related integrin that has also been implicated in SARS-CoV-2 interactions) as well as the C-X-C motif chemokine ligand 10 (Cxcl10), further supporting the potential involvement of these integrins, and the anti-inflammatory potential of ATN-161, respectively, in SARS-CoV-2 infection. To the best of our knowledge, this is the first study demonstrating the potential therapeutic efficacy of targeting integrin alpha5beta1 in SARS-CoV-2 infection in vivo and supports the development of ATN-161 as a novel SARS-CoV-2 therapy.

scholarly journals Conformational Perturbation of SARS-CoV-2 Spike Protein Using N-Acetyl Cysteine, a Molecular Scissor: A Probable Strategy to Combat COVID-19

2020 ◽  
Author(s):  
Utsab Debnath ◽  
Varun Dewaker ◽  
Yenamandra S. Prabhakar ◽  
Parthasarathi Bhattacharyya ◽  
Amit Mandal
Keyword(s):  
Disulfide Bond ◽  
In Silico ◽  
Ex Vivo ◽  
Virus Disease ◽  
Spike Protein ◽  
Early 21St Century ◽  
Acetyl Cysteine ◽  
Structural Architecture

The infection caused by Severe Acute Respiratory Syndrome–CoronaVirus-2 (SARS-CoV-2) resulted in a pandemic across the globe with a huge death toll. The symptoms from SARS-CoV2 appear somewhat similar to the SARS-CoV-1 infection that appeared in early 21st century but the infectivity is far higher for the SARS-CoV-2. The virus attaches itself to exposed human epithelial cells through the spike protein. Recently discovered crystal structure of the complex of spike protein of SARS-CoV-2 with human angiotensin-converting enzyme 2 (ACE2) receptor indicated that the virus binds with the host cell very strongly. We hypothesized that the perturbation of the functionally active conformation of spike protein through the reduction of a solvent accessible disulfide bond (Cys391-Cys525) that provides its structural architecture, may 2 be a feasible strategy to disintegrate the spike protein from ACE2 receptor and thereby prevent the infection. Using in silico platform we showed that N-acetyl cysteine (NAC), a drug used as antioxidant and mucolytic agent, binds in the close proximity of above disulfide bond. The reduction of the disulfide bond via thiol/disulfide exchange, followed by covalent conjugation of NAC perturbed the stereo specific orientations of interacting key residues of spike protein. This resulted in threefold weakening in the binding affinity of spike protein with ACE2 receptor. This opens avenues for exploring the effect of NAC in vitro, ex vivo and in vivo and on successful observation of the similar effect as in silico, the intervention of NAC may be translated in the pharmacoprevention and treatment of Corona virus disease 2019.

scholarly journals An Overview of Biological and Computational Methods for Designing Mechanism-Informed Anti-biofilm Agents

2021 ◽  
Vol 12 ◽  
Author(s):  
Andy Y. An ◽  
Ka-Yee Grace Choi ◽  
Arjun S. Baghela ◽  
Robert E. W. Hancock
Keyword(s):  
Antibiotic Resistance ◽  
Small Molecules ◽  
In Silico ◽  
Biofilm Formation ◽  
Stringent Response ◽  
Antibiotic Resistant ◽  
Biologically Relevant ◽  
Biofilm Model

Bacterial biofilms are complex and highly antibiotic-resistant aggregates of microbes that form on surfaces in the environment and body including medical devices. They are key contributors to the growing antibiotic resistance crisis and account for two-thirds of all infections. Thus, there is a critical need to develop anti-biofilm specific therapeutics. Here we discuss mechanisms of biofilm formation, current anti-biofilm agents, and strategies for developing, discovering, and testing new anti-biofilm agents. Biofilm formation involves many factors and is broadly regulated by the stringent response, quorum sensing, and c-di-GMP signaling, processes that have been targeted by anti-biofilm agents. Developing new anti-biofilm agents requires a comprehensive systems-level understanding of these mechanisms, as well as the discovery of new mechanisms. This can be accomplished through omics approaches such as transcriptomics, metabolomics, and proteomics, which can also be integrated to better understand biofilm biology. Guided by mechanistic understanding, in silico techniques such as virtual screening and machine learning can discover small molecules that can inhibit key biofilm regulators. To increase the likelihood that these candidate agents selected from in silico approaches are efficacious in humans, they must be tested in biologically relevant biofilm models. We discuss the benefits and drawbacks of in vitro and in vivo biofilm models and highlight organoids as a new biofilm model. This review offers a comprehensive guide of current and future biological and computational approaches of anti-biofilm therapeutic discovery for investigators to utilize to combat the antibiotic resistance crisis.

Aryloxy Triester Phosphoramidates as Phosphoserine Biocleavable Masking Motifs

2019 ◽  
Author(s):  
Ageo Miccoli ◽  
Binar A. Dhiani ◽  
Peter J. Thornton ◽  
Olivia A. Lambourne ◽  
Edward James ◽  
...  
Keyword(s):  
Small Molecules ◽  
Protein Interactions ◽  
In Silico ◽  
Parent Compound ◽  
Cellular Protein ◽  
Carboxypeptidase Y ◽  
Protein Protein Interactions ◽  
Enzymatic Assays ◽  
Specific Targeting

Many cellular protein-protein interactions (PPIs) are mediated by phosphoserine. The specific targeting of these PPIs by phosphoserine-containing small molecules has been scarce due to the dephosphorylation of phosphoserine and its charged nature at physiological pH, which hinders its uptake into cells. To address these issues, we herein report the masking of the phosphate group of phosphoserine with biocleavable aryloxy triester phosphoramidate groups. A combination of <i>in vitro</i> enzymatic assays and <i>in silico</i> studies, using carboxypeptidase Y and Hint-1 respectively, showed that the phosphate masking groups are metabolized to release phosphoserine. To probe the applicability of this phosphoserine masking approach, it was applied to a phosphoserine-containing inhibitor of 14-3-3 dimerization, and this generated molecules with improved pharmacological activity in cells compared to their unmasked phosphoserine-containing parent compound. Collectively, the data showcases the masking of phosphoserine with biocleavable aryloxy triester phosphoramidate masking groups as an efficient intracellular delivery system for phosphoserine-containing molecules.

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