Potential clinical drugs as covalent inhibitors of the priming proteases of the spike protein of SARS-CoV-2

Covalent inhibitors: An ambitious approach for the discovery of newer oncotherapeutics

Covalent inhibitors have been used to treat several diseases for over a century. However, strategic approaches for the rational design of covalent drugs have taken a definitive shape in recent times. Since the first appearance of covalent inhibitors in the late 18th century, the field has grown tremendously and around 30% of marketed drugs are covalent inhibitors especially, for oncology indications. However, the off-target toxicity and safety concerns can be significant issues related to the covalent drugs. Covalent kinase inhibitor (CKI) targeted oncotherapeutics has advanced dramatically over the last two decades since the discovery of afatinib (Gilotrif®), an EGFR inhibitor. Since then, US FDA has approved 10 CKIs for diverse cancer targets. The present review broadly summarizes the ongoing development in the discovery of newer CKIs from 2016 till the end of 2022. We believe that these efforts will assist the modern medicinal chemist actively working in the field of CKI discovery for varied indications.

Targeting epidermal growth factor receptor signalling pathway: A promising therapeutic option for COVID-19

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is continuously producing new variants, necessitating effective therapeutics. Patients are not only confronted by the immediate symptoms of infection but also by the long-term health issues linked to long COVID-19. Activation of epidermal growth factor receptor (EGFR) signalling during SARS-CoV-2 infection promotes virus propagation, mucus hyperproduction, and pulmonary fibrosis, and suppresses the host's antiviral response. Over the long term, EGFR activation in COVID-19, particularly in COVID-19-induced pulmonary fibrosis, may be linked to the development of lung cancer. In this review, we have summarised the significance of EGFR signalling in the context of SARS-CoV-2 infection. We also discussed the targeting of EGFR signalling as a promising strategy for COVID-19 treatment and highlighted erlotinib as a superior option among EGFR inhibitors. Erlotinib effectively blocks EGFR and AAK1, thereby preventing SARS-CoV-2 replication, reducing mucus hyperproduction, TNF-α expression, and enhancing the host's antiviral response. Nevertheless, to evaluate the antiviral efficacy of erlotinib, relevant clinical trials involving an appropriate patient population should be designed.

Recent status of sesaminol and its glucosides: Synthesis, metabolism, and biological activities

Sesamum indicum is a major and important oilseed crop that is believed to promote human health in many countries, especially in China. Sesame seeds contain two types of lignans: lipid-soluble lignans and water-soluble glucosylated lignans. The major glucosylated lignans are sesaminol glucosides (SGs). So far, four sesaminol isomers and four SGs are identified. During the naturally occurring process of SGs production, sesaminol is generated first from two molecules of E-coniferyl alcohol, and then the sugar is added to the sesaminol one by one, leading to production of SGs. Sesaminol can be prepared from SGs, from sesamolin, and through artificial synthesis. SGs are metabolized in the liver and intestine and are then transported to other tissues. They exhibit several biological activities, most of which are based on their antioxidant and anti-inflammatory activities. In this paper, we present an overview of the current status of research on sesaminol and SGs. We have also discussed their synthesis, preparation, metabolism, and biological activities. It has been suggested that sesaminol and SGs are important biological substances with strong antioxidant properties in vitro and in vivo and are widely used in the food industry, medicine, and cosmetic products. The recovery and utilization of SGs from sesame seed cake after oil processing will generate massive economic benefits.

Cathepsins and SARS-CoV-2 infection: From pathogenic factors to potential therapeutic targets

Coronavirus disease-19 (COVID-19) is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection. The COVID-19 pandemic began in March 2020 and has wrought havoc on health and economic systems worldwide. Efficacious treatment for COVID-19 is lacking: Only preventive measures as well as symptomatic and supportive care are available. Preclinical and clinical studies have indicated that lysosomal cathepsins might contribute to the pathogenesis and disease outcome of COVID-19. Here, we discuss cutting-edge evidence on the pathological roles of cathepsins in SARS-CoV-2 infection, host immune dysregulations, and the possible underlying mechanisms. Cathepsins are attractive drug targets because of their defined substrate-binding pockets, which can be exploited as binding sites for pharmaceutical enzyme inhibitors. Accordingly, the potential modulatory strategies of cathepsin activity are discussed. These insights could shed light on the development of cathepsin-based interventions for COVID-19.

SCARdock: A Web Server and Manually Curated Resource for Discovering Covalent Ligands

BACKGROUND

Covalent drugs have been intentionally discarded historically due to the concern of off-target side effects, but the past decade has seen a fast resurgence of the discovery of covalent drugs. Compared to noncovalent ligands, covalent ligands might have better biochemical efficiency, lower patient burden, less dosing frequency, less drug resistance, and improved target specificity.

RESULTS

Previously, we proposed the steric-clashes alleviating receptor (SCAR) strategy for screening and repurposing covalent inhibitors. To help the discovery of covalent ligands targeting protein targets, we have developed a web server dedicated to providing the SCARdock protocol to general users. Along with this server, we presented three high-quality data sets for the discovery of covalent ligands: a manually curated data set containing 954 high-quality complex structures of covalent ligands and proteins, a manually curated data set of 68 experimentally confirmed covalent warheads targeting 11 different residues, and a prefiltered, classified, and ready-to-use data set of 690,018 entries of purchasable virtual compounds containing these experimentally verified warheads.

CONCLUSIONS

The SCARdock server and the accompanied data sets would be of great value to the discovery of covalent ligands and are available freely at http://www.liugroup.site/scardock/ or https://scardock.com.

Advanced approaches of developing targeted covalent drugs

In recent years, the development of targeted covalent inhibitors has gained popularity around the world. Specific groups (electrophilic warheads) form irreversible bonds with the side chain of nucleophilic amino acid residues, thus changing the function of biological targets such as proteins. Since the first targeted covalent inhibitor was disclosed in the 1990s, great efforts have been made to develop covalent ligands from known reversible leads or drugs by addition of tolerated electrophilic warheads. However, high reactivity and "off-target" toxicity remain challenging issues. This review covers the concept of targeted covalent inhibition to diseases, discusses traditional and interdisciplinary strategies of cysteine-focused covalent drug discovery, and exhibits newly disclosed electrophilic warheads majorly targeting the cysteine residue. Successful applications to address the challenges of designing effective covalent drugs are also introduced.

Recent computational drug repositioning strategies against SARS-CoV-2

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We performed a comprehensive review of computational drug repositioning methods applied to COVID-19 based on differing data types including sequence data, expression data, structure data and interaction data.

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We found that graph theory and neural network were the most used strategies for drug repositioning in the case of COVID-19.

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Integrating different levels of data may improve the success rate for drug repositioning.

Since COVID-19 emerged in 2019, significant levels of suffering and disruption have been caused on a global scale. Although vaccines have become widely used, the virus has shown its potential for evading immunities or acquiring other novel characteristics. Whether current drug treatments are still effective for people infected with Omicron remains unclear. Due to the long development cycles and high expense requirements of de novo drug development, many researchers have turned to consider drug repositioning in the search to find effective treatments for COVID-19. Here, we review such drug repositioning and combination efforts towards providing better handling. For potential drugs under consideration, aspects of both structure and function require attention, with specific categories of sequence, expression, structure, and interaction, the key parameters for investigation. For different data types, we show the corresponding differing drug repositioning methods that have been exploited. As incorporating drug combinations can increase therapeutic efficacy and reduce toxicity, we also review computational strategies to reveal drug combination potential. Taken together, we found that graph theory and neural network were the most used strategy with high potential towards drug repositioning for COVID-19. Integrating different levels of data may further improve the success rate of drug repositioning.

Setomimycin as a potential molecule for COVID‑19 target: in silico approach and in vitro validation

Abstract

COVID-19 pandemic caused by the SARS-CoV-2 virus has led to a worldwide crisis. In view of emerging variants time to time, there is a pressing need of effective COVID-19 therapeutics. Setomimycin, a rare tetrahydroanthracene antibiotic, remained unexplored for its therapeutic uses. Herein, we report our investigations on the potential of setomimycin as COVID-19 therapeutic. Pure setomimycin was isolated from Streptomyces sp. strain RA-WS2 from NW Himalayan region followed by establishing in silico as well as in vitro anti-SARS-CoV-2 property of the compound against SARS-CoV-2 main protease (M^pro). It was found that the compound targets M^pro enzyme with an IC₅₀ value of 12.02 ± 0.046 μM. The molecular docking study revealed that the compound targets Glu166 residue of M^pro enzyme, hence preventing dimerization of SARS-CoV-2 M^pro monomer. Additionally, the compound also exhibited anti-inflammatory and anti-oxidant property, suggesting that setomimycin may be a viable option for application against COVID-19 infections.

Graphical abstract

Antiviral activities of 4H-chromen-4-one scaffold-containing flavonoids against SARS-CoV-2 using computational and in vitro approaches

The widespread outbreak of the novel coronavirus called severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused the main health challenge worldwide. This pandemic has attracted the attention of the research communities in various fields, prompting efforts to discover rapid drug molecules for the treatment of the life-threatening COVID-19 disease. This study is aimed at investigating 4H-chromen-4-one scaffold-containing flavonoids that combat the SARS-CoV-2 virus using computational and in vitro approaches. Virtual screening studies of the molecule's library for 4H-chromen-4-one scaffold were performed with the recently reported coronavirus main protease (M^pro, also called 3CL^pro) because it plays an essential role in the maturation and processing of the viral polyprotein. Based on the virtual screening, the top hit molecules such as isoginkgetin and afzelin molecules were selected for further estimating in vitro antiviral efficacies against SARS-CoV-2 in Vero cells. Additionally, these molecules were also docked with RNA-dependent RNA Polymerase (RdRp) to reveal the ligands-protein molecular interaction. In the in vitro study, isoginkgetin showed remarkable inhibition potency against the SARS-CoV-2 virus, with an IC₅₀ value of 22.81 μM, compared to remdesivir, chloroquine, and lopinavir with IC₅₀ values of 7.18, 11.63, and 11.49 μM, respectively. Furthermore, the complex stability of isoginkgetin with an active binding pocket of the SARS-CoV-2 M^pro and RdRp supports its inhibitory potency against the SARS-CoV-2. Thus, isoginkgetin is a potent leading drug candidate and needs to be used in in vivo trials for the treatment of SARS-CoV-2 infected patients.

Computer-Aided Drug Design of Anti-inflammatory Agents Targeting Microsomal Prostaglandin E2 Synthase-1 (mPGES-1)

Inflammation is a natural process in response to external stimuli associated with organism protection. However, this reaction could be exaggerated, leading to severe damages related to physiopathological processes, such as rheumatoid arthritis, cancer, diabetes, allergies, infections, among others. Inflammation is mainly characterized by pain, increased temperature, flushing, and edema, which can be controlled using anti-inflammatory drugs. In this context, prostaglandin E2 (PGE2) inhibition has been targeted for designing new compounds with anti-inflammatory properties. It is a bioactive lipid overproduced during an inflammatory process, in which its increased production is carried out mainly by COX-1, COX-2, and microsomal prostaglandin E2 synthase-1 (mPGES-1). Recently, studies have demonstrated that mPGES-1 inhibition is a safe strategy to develop anti-inflammatory agents, which could protect against pain, acute inflammation, arthritis, autoimmune diseases, and different types of cancers. To decrease production costs and increase the probability of discovering active substances, computer-aided drug design (CADD) approaches have been increasingly used for designing new inhibitors. Thus, this review will cover all aspects involving high-throughput virtual screening, molecular docking, dynamics, fragment-based drug design, quantitative structure-activity relationship in seeking new promising mPGES-1 inhibitors.

Therapeutically effective covalent spike protein inhibitors in treatment of SARS-CoV-2

COVID-19 [coronavirus disease 2019] has resulted in over 204,644,849 confirmed cases and over 4,323,139 deaths throughout the world as of 12 August 2021, a total of 4,428,168,759 vaccine doses have been administered. The lack of potentially effective drugs against the virus is making the situation worse and dangerous. Numerous forces are working on finding an effective treatment against the virus but it is believed that a de novo drug would take several months even if huge financial support is provided. The only solution left with is drug repurposing that would not only provide effective therapy with the already used clinical drugs, but also save time and cost of the de novo drug discovery. The initiation of the COVID-19 infection starts with the attachment of spike glycoprotein of SARS-CoV-2 to the host receptor. Hence, the inhibition of the binding of the virus to the host membrane and the entry of the viral particle into the host cell are one of the main therapeutic targets. This paper not only summarizes the structure and the mechanism of spike protein, but the main focus is on the potential covalent spike protein inhibitors.

Docking-generated multiple ligand poses for bootstrapping bioactivity classifying Machine Learning: Repurposing covalent inhibitors for COVID-19-related TMPRSS2 as case study

In the present work we introduce the use of multiple docked poses for bootstrapping machine learning-based QSAR modelling. Ligand-receptor contact fingerprints are implemented as descriptor variables. We implemented this method for the discovery of potential inhibitors of the serine protease enzyme TMPRSS2 involved the infectivity of coronaviruses. Several machine learners were scanned, however, Xgboost, support vector machines (SVM) and random forests (RF) were the best with testing set accuracies reaching 90%. Three potential hits were identified upon using the method to scan known untested FDA approved drugs against TMPRSS2. Subsequent molecular dynamics simulation and covalent docking supported the results of the new computational approach.

Molecular Modeling Targeting Transmembrane Serine Protease 2 (TMPRSS2) as an Alternative Drug Target Against Coronaviruses

Since November 2019, the new Coronavirus disease (COVID-19) caused by the etiological agent SARS-CoV-2 has been responsible for several cases worldwide, becoming pandemic in March 2020. Pharmaceutical industries and academics have joined their efforts to discover new therapies to control the disease, since there are no specific drugs to combat this emerging virus. Thus, several targets have been explored, among them the transmembrane protease serine 2 (TMPRSS2) has gained greater interest in the scientific community. In this context, this review will describe the importance of TMPRSS2 protease and the significant advances in virtual screening focused on discovering new inhibitors. In this review, it was observed that molecular modeling methods could be powerful tools in identifying new molecules against SARS-CoV-2. Thus, this review could be used to guide researchers worldwide to explore the biological and clinical potential of compounds that could be promising drug candidates against SARS-CoV-2, acting by inhibition of TMPRSS2 protein.

Use of molecular docking computational tools in drug discovery

Molecular docking has become an important component of the drug discovery process. Since first being developed in the 1980s, advancements in the power of computer hardware and the increasing number of and ease of access to small molecule and protein structures have contributed to the development of improved methods, making docking more popular in both industrial and academic settings. Over the years, the modalities by which docking is used to assist the different tasks of drug discovery have changed. Although initially developed and used as a standalone method, docking is now mostly employed in combination with other computational approaches within integrated workflows. Despite its invaluable contribution to the drug discovery process, molecular docking is still far from perfect. In this chapter we will provide an introduction to molecular docking and to the different docking procedures with a focus on several considerations and protocols, including protonation states, active site waters and consensus, that can greatly improve the docking results.

Identifying and repurposing antiviral drugs against severe acute respiratory syndrome coronavirus 2 with in silico and in vitro approaches

Coronavirus infectious diseases 2019 (COVID-19), a global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been a serious public health threat worldwide. So far, there are no drugs and vaccines whose efficacy has been well-proven. After the outbreak, there has been a massive search for anti-SARS-CoV-2 medications, focusing on approved drugs because repurposing approved drugs will take less time to reach clinical usage than new drugs. This article summarizes the studies using in silico and in vitro approaches to identify therapeutic candidates among approved drugs that target the SARS-CoV-2 life cycle.