Main Protease Inhibitors Research Articles

Ligand-based and structure-based studies to develop predictive models for SARS-CoV-2 main protease inhibitors through the 3d-qsar.com portal

The main protease (Mpro) of SARS-Cov-2 is the essential enzyme for maturation of functional proteins implicated in viral replication and transcription. The peculiarity of its specific cleavage site joint with its high degree of conservation among all coronaviruses promote it as an attractive target to develop broad-spectrum inhibitors, with high selectivity and tolerable safety profile. Herein is reported a combination of three-dimensional quantitative structure–activity relationships (3-D QSAR) and comparative molecular binding energy (COMBINE) analysis to build robust and predictive ligand-based and structure-based statistical models, respectively. Models were trained on experimental binding poses of co-crystallized Mpro-inhibitors and validated on available literature data. By means of deep optimization both models’ goodness and robustness reached final statistical values of r2/q2 values of 0.97/0.79 and 0.93/0.79 for the 3-D QSAR and COMBINE approaches respectively, and an overall predictiveness values of 0.68 and 0.57 for the SDEPPRED and AAEP metrics after application to a test set of 60 compounds covered by the training set applicability domain. Despite the different nature (ligand-based and structure-based) of the employed methods, their outcome fully converged. Furthermore, joint ligand- and structure-based structure–activity relationships were found in good agreement with nirmatrelvir chemical features properties, a novel oral Mpro-inhibitor that has recently received U.S. FDA emergency use authorization (EUA) for the oral treatment of mild-to-moderate COVID-19 infected patients. The obtained results will guide future rational design and/or virtual screening campaigns with the aim of discovering new potential anti-coronavirus lead candidates, minimizing both time and financial resources. Moreover, as most of calculation were performed through the well-established web portal 3d-qsar.com the results confirm the portal as a useful tool for drug design.Graphical abstract

Small-Molecule Thioesters as SARS-CoV-2 Main Protease Inhibitors: Enzyme Inhibition, Structure-Activity Relationships, Antiviral Activity, and X-ray Structure Determination.

The main protease (Mpro, 3CLpro) of SARS-CoV-2 is an attractive target in coronaviruses because of its crucial involvement in viral replication and transcription. Here, we report on the design, synthesis, and structure–activity relationships of novel small-molecule thioesters as SARS-CoV-2 Mpro inhibitors. Compounds 3w and 3x exhibited excellent SARS-CoV-2 Mpro inhibition with kinac/Ki of 58,700 M–1 s–1 (Ki = 0.0141 μM) and 27,200 M–1 s–1 (Ki = 0.0332 μM), respectively. In Calu-3 and Vero76 cells, compounds 3h, 3i, 3l, 3r, 3v, 3w, and 3x displayed antiviral activity in the nanomolar range without host cell toxicity. Co-crystallization of 3w and 3af with SARS-CoV-2 Mpro was accomplished, and the X-ray structures showed covalent binding with the catalytic Cys145 residue of the protease. The potent SARS-CoV-2 Mpro inhibitors also inhibited the Mpro of other beta-coronaviruses, including SARS-CoV-1 and MERS-CoV, indicating that they might be useful to treat a broader range of coronaviral infections.

A computational biology approach for the identification of potential SARS-CoV-2 main protease inhibitors from natural essential oil compounds.

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has fomented a climate of fear worldwide due to its rapidly spreading nature, and high mortality rate. The World Health Organization declared it a global pandemic on 11 March 2020. Many endeavors have been made to find appropriate medications to restrain the SARS-CoV-2 infection from spreading but there is no specific antiviral therapy to date. However, a computer-aided drug design approach can be an alternative to identify probable drug candidates within a short time. SARS-CoV-2 main protease is a proven drug target, and it plays a pivotal role in viral replication and transcription. Methods: In this study, we identified a total of 114 essential oil compounds as a feasible anti-SARS-CoV-2 agent from several online reservoirs. These compounds were screened by incorporating absorption, distribution, metabolism, excretion, and toxicity (ADMET) profiling, molecular docking, and 50 ns of molecular dynamics simulation to identify potential drug candidates. The crystallized SARS-CoV-2 main protease structure was collected from the Research Collaboratory for Structural Bioinformatics Protein Data Bank database (Protein Data Bank ID 6LU7). Results: According to the results of the ADMET study, none of the compounds have any side effects that could reduce their druglikeness or pharmacokinetic properties. Among 114 compounds, we selected bisabololoxide B, eremanthin, and leptospermone as top drug candidates based on their higher binding affinity scores, and strong interaction with the Cys 145-His 41 catalytic dyad. Finally, the molecular dynamics simulation was implemented to evaluate the structural stability of the ligand-receptor complex. Molecular dynamics simulation disclosed that all the hits showed conformational stability compared to the positive control α-ketoamide. Conclusions: Our study showed that the top three hits might work as potential anti-SARS-CoV-2 agents, which can pave the way for discovering new drugs, but further in vivo trials will require for experimental validation.

A Computational Approach to Elucidate the Interactions of Chemicals From Artemisia annua Targeted Toward SARS-CoV-2 Main Protease Inhibition for COVID-19 Treatment.

The inhibitory potential of Artemisia annua, a well-known antimalarial herb, against several viruses, including the coronavirus, is increasingly gaining recognition. The plant extract has shown significant activity against both the Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and the novel SARS-CoV-2 that is currently ravaging the world. It is therefore necessary to evaluate individual chemicals of the plant for inhibitory potential against SARS-CoV-2 for the purpose of designing drugs for the treatment of COVID-19. In this study, we employed computational techniques comprising molecular docking, binding free energy calculations, pharmacophore modeling, induced-fit docking, molecular dynamics simulation, and ADMET predictions to identify potential inhibitors of the SARS-CoV-2 main protease (Mpro) from 168 bioactive compounds of Artemisia annua. Rhamnocitrin, isokaempferide, kaempferol, quercimeritrin, apigenin, penduletin, isoquercitrin, astragalin, luteolin-7-glucoside, and isorhamnetin were ranked the highest, with docking scores ranging from −7.84 to −7.15 kcal/mol compared with the −6.59 kcal/mol demonstrated by the standard ligand. Rhamnocitrin, Isokaempferide, and kaempferol, like the standard ligand, interacted with important active site amino acid residues like HIS 41, CYS 145, ASN 142, and GLU 166, among others. Rhamnocitrin demonstrated good stability in the active site of the protein as there were no significant conformational changes during the simulation process. These compounds also possess acceptable druglike properties and a good safety profile. Hence, they could be considered for experimental studies and further development of drugs against COVID-19.

A Study of Drug Repurposing to Identify SARS-CoV-2 Main Protease (3CLpro) Inhibitors.

The outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) wreaked havoc all over the world. Although vaccines for the disease have recently become available and started to be administered to the population in various countries, there is still a strong and urgent need for treatments to cure COVID-19. One of the safest and fastest strategies is represented by drug repurposing (DRPx). In this study, thirty compounds with known safety profiles were identified from a chemical library of Phase II-and-up compounds through a combination of SOM Biotech’s Artificial Intelligence (AI) technology, SOMAIPRO, and in silico docking calculations with third-party software. The selected compounds were then tested in vitro for inhibitory activity against SARS-CoV-2 main protease (3CLpro or Mpro). Of the thirty compounds, three (cynarine, eravacycline, and prexasertib) displayed strong inhibitory activity against SARS-CoV-2 3CLpro. VeroE6 cells infected with SARS-CoV-2 were used to find the cell protection capability of each candidate. Among the three compounds, only eravacycline showed potential antiviral activities with no significant cytotoxicity. A further study is planned for pre-clinical trials.

Discovery of novel SARS-CoV-2 inhibitors targeting the main protease Mpro by virtual screenings and hit optimization

Two years after its emergence, SARS-CoV-2 still represents a serious and global threat to human health. Antiviral drug development usually takes a long time and, to increase the chances of success, chemical variability of hit compounds represents a valuable source for the discovery of new antivirals. In this work, we applied a platform of variably oriented virtual screening campaigns to seek for novel chemical scaffolds for SARS-CoV-2 main protease (Mpro) inhibitors. The study on the resulting 30 best hits led to the identification of a series of structurally unrelated Mpro inhibitors. Some of them exhibited antiviral activity in the low micromolar range against SARS-CoV-2 and other human coronaviruses (HCoVs) in different cell lines. Time-of-addition experiments demonstrated an antiviral effect during the viral replication cycle at a time frame consistent with the inhibition of SARS-CoV-2 Mpro activity. As a proof-of-concept, to validate the pharmaceutical potential of the selected hits against SARS-CoV-2, we rationally optimized one of the hit compounds and obtained two potent SARS-CoV-2 inhibitors with increased activity against Mpro both in vitro and in a cellular context, as well as against SARS-CoV-2 replication in infected cells. This study significantly contributes to the expansion of the chemical variability of SARS-CoV-2 Mpro inhibitors and provides new scaffolds to be exploited for pan-coronavirus antiviral drug development.

Computational Investigation on the Efficiency of Small Molecule Inhibitors Identified from Indian Spices against SARS-CoV-2 Mpro

Recently, small compounds from Indian spices (Carnosol, Arjunglucoside-I, and Rosmanol) have been identified as SARS-CoV-2 main protease (Mpro) inhibitors. The structural dynamics and characteristic features of binding of these small molecules to the SARS-CoV-2 Mpro are not well understood. Here, we have constructed the potential of mean force (PMF) for dissociating Mpro-small molecule inhibitor complexes from the umbrella sampling simulations using the weighted histogram analysis method. Mpro-small molecule inhibitor complexes exhibited relatively higher dissociation energy values than the alpha-ketoamide-Mpro complex (positive control) from the PMF calculations. We found that binding affinity between protein and ligand is higher in Mpro-Arjunglucoside-I complex [∆Gbind = -19.74 kcal mol-1 from MM-GBSA and ∆Gbind = -9.13 kcal mol-1 from MM-PBSA] than in other three SARS-CoV-2 small molecule complexes. The MM-GBSA/MM-PBSA calculations revealed that the small molecule inhibitors studied in this work have substantially higher binding affinity for Mpro. We found the residues present in SARS-CoV-2 Mpro's binding pocket contributed the most binding free energy to SARS-CoV-2 Mpro-small molecule interactions. Our findings emphasize the structural and binding features of the identified small molecule inhibitors with SARS-CoV-2 Mpro, which could be relevant in developing therapeutic candidates to combat SARS-CoV-2.

Identification of Novel Inhibitors of SARS-CoV-2 Mpro from NCI Database by a Drug Repurposing Approach

Background: The global spread of SARS-CoV-2 and the mortality it has caused have prompted research organizations to develop novel medications to fight against COVID-19. The main protease (Mpro) of SARS-CoV-2 is crucial to the virus’s replication and propagation in host cells. Therefore, it is a promising therapeutic target. Objectives: There are officially no certified specific drugs or available interventions for COVID-19 infection. Repurposing standard pharmaceutical drugs for COVID-19 is a promising strategy to identify potent therapeutic candidates quickly. Methods: The NCI (National Cancer Institute) database compounds, COVID-19 Mpro, and the reference ligand were prepared, and the docking, ADMET, and MMGBSA analyses were carried out using Maestro (Schrödinger Suite). Results: The study shows the results after screening NCI molecules (265,242) against COVID-19 Mpro. Compounds NCI19775, NCI226834, NCI115535, NCI270893, NCI89644, NCI332542, NCI617217, NCI43927, NCI67474, NCI250293, and NCI59266 fit in the active site of the COVID- 19 Mpro, showing a tighter interaction than the reference ligand X77. The docking score of these NCI compounds is also higher than X77. As a result, these compounds could be promising anti-COVID Mpro agents. NCI19775 (6,6-bis (benzylthio) hexane-1,2,3,4,5-pentaol)was shown to be a more potent inhibitor of COVID-19 main protease, and the outcomes also exhibit the potential for NCI compounds to interact with COVID Mpro. Conclusions: Our computational strategy identified promising and efficacious SARS-CoV-2 inhibitors that could be investigated further in clinical trials.

Withasomniferol C, a new potential SARS-CoV-2 main protease inhibitor from the Withania somnifera plant proposed by in silico approaches.

Exploring potent herbal medicine candidates is a promising strategy for combating a pandemic in the present global health crisis. In Ayurveda (a traditional medicine system in India), Withania somnifera (WS) is one of the most important herbs and it has been used for millennia as Rasayana (a type of juice) for its wide-ranging health benefits. WS phytocompounds display a broad spectrum of biological activities (such as antioxidant, anticancer and antimicrobial) modulate detoxifying enzymes, and enhance immunity. Inspired by the numerous biological actions of WS phytocompounds, the present investigation explored the potential of the WS phytocompounds against the SARS-CoV-2 main protease (3CLpro). We selected 11 specific withanolide compounds, such as withaphysalin, withasomniferol, and withafastuosin, through manual literature curation against 3CLpro. A molecular similarity analysis showed their similarity with compounds that have an established inhibitory activity against the SARS-CoV-2. In silico molecular docking and molecular dynamics simulations elucidated withasomniferol C (WS11) as a potential candidate against SARS-CoV-2 3CLpro. Additionally, the present work also presents a new method of validating docking poses using the AlteQ method.

Accurate Mass Identification of an Interfering Water Adduct and Strategies in Development and Validation of an LC-MS/MS Method for Quantification of MPI8, a Potent SARS-CoV-2 Main Protease Inhibitor, in Rat Plasma in Pharmacokinetic Studies.

MPI8, a peptidyl aldehyde, is a potent antiviral agent against coronavirus. Due to unique tri-peptide bonds and the formyl functional group, the bioassay of MPI8 in plasma was challenged by a strong interference from water MPI8. Using QTOF LC-MS/MS, we identified MPI8•H2O as the major interference form that co-existed with MPI8 in aqueous and biological media. To avoid the resolution of MPI8 and MPI8•H2O observed on reverse phase columns, we found that a Kinetex hydrophilic interaction liquid chromatography (HILIC) column provided co-elution of both MPI8 and MPI8•H2O with a good single chromatographic peak and column retention of MPI8 which is suitable for quantification. Thus, a sensitive, specific, and reproducible LC-MS/MS method for the quantification of MPI8 in rat plasma was developed and validated using a triple QUAD LC-MS/MS. The chromatographic separation was achieved on a Kinetex HILIC column with a flow rate of 0.4 mL/min under gradient elution. The calibration curves were linear (r2 > 0.99) over MPI8 concentrations from 0.5–500 ng/mL. The accuracy and precision are within acceptable guidance levels. The mean matrix effect and recovery were 139% and 73%, respectively. No significant degradation of MPI8 occurred under the experimental conditions. The method was successfully applied to a pharmacokinetic study of MPI8 after administration of MPI8 sulfonate in rats.

Progress and Challenges in Targeting the SARS-CoV-2 Papain-like Protease.

SARS-CoV-2 is the causative agent of the COVID-19 pandemic. The approval of vaccines and small-molecule antivirals is vital in combating the pandemic. The viral polymerase inhibitors remdesivir and molnupiravir and the viral main protease inhibitor nirmatrelvir/ritonavir have been approved by the U.S. FDA. However, the emergence of variants of concern/interest calls for additional antivirals with novel mechanisms of action. The SARS-CoV-2 papain-like protease (PLpro) mediates the cleavage of viral polyprotein and modulates the host’s innate immune response upon viral infection, rendering it a promising antiviral drug target. This Perspective highlights major achievements in structure-based design and high-throughput screening of SARS-CoV-2 PLpro inhibitors since the beginning of the pandemic. Encouraging progress includes the design of non-covalent PLpro inhibitors with favorable pharmacokinetic properties and the first-in-class covalent PLpro inhibitors. In addition, we offer our opinion on the knowledge gaps that need to be filled to advance PLpro inhibitors to the clinic.

Invalidation of dieckol and 1,2,3,4,6-pentagalloylglucose (PGG) as SARS-CoV-2 main protease inhibitors and the discovery of PGG as a papain-like protease inhibitor.

The COVID-19 pandemic spurred a broad interest in antiviral drug discovery. The SARS-CoV-2 main protease (Mpro) and papain-like protease (PLpro) are attractive antiviral drug targets given their vital roles in viral replication and modulation of host immune response. Structurally disparate compounds were reported as Mpro and PLpro inhibitors from either drug repurposing or rational design. Two polyphenols dieckol and 1,2,3,4,6-pentagalloylglucose (PGG) were recently reported as SARS-CoV-2 Mpro inhibitors. With our continuous interest in studying the mechanism of inhibition and resistance of Mpro inhibitors, we report herein our independent validation/invalidation of these two natural products. Our FRET-based enzymatic assay showed that neither dieckol nor PGG inhibited SARS-CoV-2 Mpro (IC50 > 20 µM), which is in contrary to previous reports. Serendipitously, PGG was found to inhibit the SARS-CoV-2 PLpro with an IC50 of 3.90 µM. The binding of PGG to PLpro was further confirmed in the thermal shift assay. However, PGG was cytotoxic in 293T-ACE2 cells (CC50 = 7.7 µM), so its intracellular PLpro inhibitory activity could not be quantified by the cell-based Flip-GFP PLpro assay. In addition, we also invalidated ebselen, disulfiram, carmofur, PX12, and tideglusib as SARS-CoV-2 PLpro inhibitors using the Flip-GFP assay. Overall, our results call for stringent hit validation, and the serendipitous discovery of PGG as a putative PLpro inhibitor might worth further pursuing. Graphical abstract

Design, synthesis and docking study of Vortioxetine derivatives as a SARS-CoV-2 main protease inhibitor.

PurposeVortioxetine an anti-depressant FDA-drug recently reported showing better in vitro efficacy against SARS-CoV-2.MethodsIn this study, we have synthesized ten new derivatives having alkenes, alkynes, benzyl, aryl, and mixed carbamate at the N-terminal of vortioxetine. Then the binding energy and interactions with the crucial amino acid residues in the binding pocket of main protease (Mpro) of SARS-CoV-2, of reported and ten newly synthesized vortioxetine derivatives (total thirty-one) in comparison with remdesivir are analyzed and presented in this paper.ResultsBased on the docking scores predicted by ADV and AD, most vortioxetine derivatives showed better binding efficiency towards Mpro of SARS-CoV-2 in comparison with remdesivir (an EUA approved drug against SARS-CoV-2 Mpro) and vortioxetine.ConclusionThis study shows that some vortioxetine derivatives can be developed into promising drugs for COVID-19 treatment.Supplementary InformationThe online version contains supplementary material available at 10.1007/s40199-022-00441-z.

Identifying SARS-CoV-2 main protease inhibitors by applying the computer screening of a large database of molecules

ABSTRACT The outbreak of coronavirus disease 2019 (COVID-19) at the end of 2019 affected global health. Its infection agent was called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Wearing a mask, maintaining social distance, and vaccination are effective ways to prevent infection of SARS-CoV-2, but none of them help infected people. Targeting the enzymes of SARS-CoV-2 is an effective way to stop the replication of the virus in infected people and treat COVID-19 patients. SARS-CoV-2 main protease is a therapeutic target which the inhibition of its enzymatic activity prevents from the replication of SARS-CoV-2. A large database of molecules has been searched to identify new inhibitors for SARS-CoV-2 main protease enzyme. At the first step, ligand screening based on similarity search was used to select similar compounds to known SARS-CoV-2 main protease inhibitors. Then molecules with better predicted pharmacokinetic properties were selected. Structure-based virtual screening based on the application of molecular docking and molecular dynamics simulation methods was used to select more effective inhibitors among selected molecules in previous step. Finally two compounds were considered as SARS-CoV-2 main protease inhibitors.

Repurposing of Drugs and HTS to Combat SARS-CoV-2 Main Protease Utilizing Structure-Based Molecular Docking

Background: COVID-19, first reported in China, from the new strain of severe acute respiratory syndrome coronaviruses (SARS-CoV-2), poses a great threat to the world by claiming uncountable lives. SARS-CoV-2 is a highly infectious virus that has been spreading rapidly throughout the world. In the absence of any specific medicine to cure COVID-19, there is an urgent need to develop novel therapeutics, including drug repositioning along with diagnostics and vaccines to combat the COVID-19. Many antivirals, antimalarials, antiparasitic, antibacterials, immunosuppressive anti-inflammatory, and immunoregulatory agents are being clinically investigated for the treatment of COVID-19. Objectives: The earlier developed one parameter regression model correlating the dock scores with in vitro anti-SARS-CoV-2 main protease activity well predicted the six drugs viz remdesivir, chloroquine, favipiravir, ribavirin, penciclovir, and nitazoxanide as potential anti-COVID agents. To further validate our earlier model, the biological activity of nine more recently published SARS-CoV-2 main protease inhibitors has been predicted using our previously reported model. Methods: In the present study, this regression model has been used to screen the existing antiviral, antiparasitic, antitubercular, and anti pneumonia chemotherapeutics utilizing dock score analyses to explore the potential including mechanism of action of these compounds in combating SARS-CoV-2 main protease. Results: The high correlation (R=0.91) explaining 82.3% variance between the experimental versus predicted activities for the nine compounds is observed. It proves the robustness of our developed model. Therefore, this robust model has been further improved, taking a total number of 15 compounds to formulate another model with an R-value of 0.887 and the explained variance of 78.6%. These models have been used for high throughput screening (HTS) of the 21 diverse compounds belonging to antiviral, antiparasitic, antitubercular, and anti pneumonia chemotherapeutics as potential repurpose agents to combat SARS-CoV-2 main protease. The models screened that the drugs bedaquiline and lefamulin have higher binding affinities (dock scores of -8.989 and -9.153 Kcal/mol respectively) than the reference compound N-[2-(5-fluoranyl-1~H-indol-3-yl)ethyl]ethanamide (dock score of -7.998 Kcal/Mol), as well as higher predicted activities with pEC50 of 0.783 and 0.937 μM and the 0.611 and 0.724 μM respectively. The clinically used repurposed drugs dexamethasone and cefixime have been predicted with pEC50 values of -0.463 and -0.622 μM and -0.311 and -0.428 μM respectively for optimal inhibition. The drugs such as doxycycline, cefpodoxime, ciprofloxacin, sparfloxacin, moxifloxacin, and TBAJ-876 showed moderate binding affinity corresponding to the moderate predicted activity (-1.540 to -1.109 μM). Conclusion: In the present study, validation of our previously developed dock score-based one parametric regression model has been carried out by predicting 9 more SARS-CoV-2 main protease inhibitors. Another model has been formulated to explore the model's robustness. These models have been taken as a barometer for the screening of more potent compounds. The HTS revealed that the drugs such as bedaquiline and lefamulin are highly predicted active compounds, whereas dexamethasone and cefixime have optimal inhibition towards SARS-CoV-2 main protease. The drugs such as doxycycline, cefpodoxime, ciprofloxacin, sparfloxacin, moxifloxacin, and TBAJ-876 have moderately active compounds towards the target inhibition.

Repurposing SARS‐CoV‐2 Main Protease Inhibitors for HIV‐1 Protease Inhibition

Severe acute respiratory syndrome (SARS‐CoV‐2) led to the COVID‐19 global pandemic, with over 178 million people infected since the start of the pandemic. SARS‐CoV‐2 is a retrovirus that utilizes a main protease (Mpro). Mpro is a catalytic cys/his protease. Several treatments were proposed to stop the pandemic including repurposing drugs to inhibit the Mpro. Another retrovirus that uses a protease is human immunodeficiency virus (HIV‐1); which has been a global epidemic for 40 years and is a devastating disease that attacks the immune system. HIV‐1 has infected 77.5 million people since the start of the epidemic in 1981 and is still prevalent today. HIV‐1 retrovirus utilizes the host cell to transcribe viral RNA and translate gag‐pol protein. HIV‐1 protease is a dual aspartyl protease used to cleave this gag‐pol protein, thereby activating the protein, allowing for viral replication and infection of other cells. The focus of this research is to investigate whether these two proteases have a similar enough mechanism that SARS‐CoV‐2 Mpro inhibitors will also inhibit HIV‐1 protease. Four repurposed SARS‐CoV‐2 inhibitors: carmofur, leupeptin, rosuvastatin, and withanone were chosen to be repurposed for HIV‐1 protease due to their affordability and affinity for SARS‐CoV‐2 Mpro. Initially, computational analysis was utilized to acquire binding information of the repurposed SARS‐CoV‐2 inhibitors on HIV‐1 protease. POCASA (Pocket Cavity Search Algorithm) was used to identify the main binding pockets of HIV‐1 protease. Swissdock identified the center of the HIV‐1 protease homodimer being the most prevalent binding pocket. Analysis of this pocket showed thermodynamically favorable binding to leupeptin, carmofur, rosuvastatin, and withanone. Since computational analysis showed promising prevalence for the inhibitors, the next step was to test these experimentally; therefore HIV‐1 protease was purified from E. Coli cells. The pure HIV‐1 protease was used in a fluorescent binding assay to derive binding affinity of the inhibitors. Preliminary experimental binding results show carmofur binding (Kd= 1 ± 0.63 mM), and rosuvastatin binding (Kd= 0.025 ± 0.007 mM); leupeptin did not show binding. The next steps are to evaluate binding for withanone as well as activity inhibition of HIV‐1 protease using these repurposed SARS‐CoV‐2 Mpro inhibitors to further investigate whether these two proteases have a similar enough mechanism that SARS‐CoV‐2 Mpro inhibitors will also inhibit HIV‐1 protease.

IN-SILICO MOLECULAR DOCKING OF DICHLOLOROFLAVAN FROM ZINGIER OFFICINALE AND ALLICIN FROM ALLIUM SATIVUM AGAINST MPRO A DRUG TARGET OF SARS COV-2

From decades, viral diseases including emerging and chronic viral infections are increasing worldwide health concern. Corona virus, SARS COV-2, is a new strain identified in 2019 caused Covid-19, in Wuhan, China has caused more than 5,304,772 infections and ~342,029 deaths worldwide over 203 countries, and the numbers are increasing exponentially from time to time. Since no specific treatment and diagnosis are available for COVID-19, discovery of new antiviral agents have become the most urgent need than in past, especially from natural sources. Hence, our present study is aimed to investigate bioactive molecules from Zingiber officinale (ginger) and Allium sativum (garlic) as potential SARS COV-2 main protease inhibitors, using a molecular docking by Auto dock 4.2, with the Lamarckian Genetic Algorithm, to analyze the probability of docking. SARS COV-2 main protease was docked with five selected compounds (zingerone, gingerol, paradol, dichloro flavin (ginger), and allicin (garlic), and were analyzed by Auto dock 4.2, PyMol version 1.7.4.5. Chloroquine and hydroxy chloroquine were used as standards for comparison. The binding energies obtained from the docking of Covid-19 main protease with biological ligand; zingerone, gingerol, paradol, dichloro flavin, and allicin were -5.31, -4.73, -5.51, -6.05, -3.74 kcal/mol, while, standard drugs such as hydroxy chloroquine and chloroquine possess binding energies of -4.88 and -5.25 kcal/mol respectively. It indicates that, zingerone, paradol and dichloloroflavan show more binding energy than chloroquine and hydroxy chloroquine, whereas, gingerol and allicin exhibited lesser binding energy. Comparing these five molecules, dichloroflavan and paradol from ginger shows highest affinity and binding sites for target protein.

In silico bioprospecting of taraxerol as a main protease inhibitor of SARS-CoV-2 to develop therapy against COVID-19.

COVID-19 was caused by a novel coronavirus known as SARS-CoV-2. The COVID-19 disease outbreak has been avowed as a global pandemic by the World Health Organization at the end of March 2020. It leads to the global economic crash, resulting in the starvation of a large population belonging to economically backward countries. Hence, the development of an alternative medicine along with the vaccine is of the utmost importance for the management of COVID-19. Therefore, screening of several herbal leads was performed to explore their potential against SARS-CoV-2. Furthermore, viral main protease was selected as a key enzyme for performing the study. Various computational approaches, including molecular docking simulation, were used in the current study to find potential inhibitors of viral main protease from a library of 150 herbal leads. Toxicity and ADME prediction of selected molecules were also analysed by Osiris molecular property explorer software. Molecular dynamic simulation of the top 10 docked herbal leads was analysed for stability using 100 ns. Taraxerol (−10.17 kcal/mol), diosgenin (10.12 kcal/mol), amyrin (−9.56 kcal/mol), and asiaticoside (−9.54 kcal/mol) were among the top four herbal leads with the highest binding affinity with the main protease enzyme. Thus, taraxerol was found to be an effective drug candidate against the main protease enzyme for the management of COVID-19. Furthermore, its clinical effect and safety profile need to be established through an in vivo model.Supplementary informationThe online version contains supplementary material available at 10.1007/s11224-022-01943-x.

Design of D-Amino Acids SARS-CoV-2 Main Protease Inhibitors Using the Cationic Peptide from Rattlesnake Venom as a Scaffold

The C30 endopeptidase (3C-like protease; 3CLpro) is essential for the life cycle of SARS-CoV-2 (severe acute respiratory syndrome-coronavirus-2) since it plays a pivotal role in viral replication and transcription and, hence, is a promising drug target. Molecules isolated from animals, insects, plants, or microorganisms can serve as a scaffold for the design of novel biopharmaceutical products. Crotamine, a small cationic peptide from the venom of the rattlesnake Crotalus durissus terrificus, has been the focus of many studies since it exhibits activities such as analgesic, in vitro antibacterial, and hemolytic activities. The crotamine derivative L-peptides (L-CDP) that inhibit the 3CL protease in the low µM range were examined since they are susceptible to proteolytic degradation; we explored the utility of their D-enantiomers form. Comparative uptake inhibition analysis showed D-CDP as a promising prototype for a D-peptide-based drug. We also found that the D-peptides can impair SARS-CoV-2 replication in vivo, probably targeting the viral protease 3CLpro.

Synthesis and comparative spectroscopic studies, HOMO–LUMO analysis and molecular docking studies of 3,3′-(1,4-phenylene)bis[2-(6-chloropyridin-3-yl)prop‑2-enenitrile] based on DFT

A novel organic molecule, named as 3,3′-(1,4-phenylene)bis[2-(6-chloropyridin-3-yl)prop‑2-enenitrile](Pyr-CN)2B), having two pyridyl rings and cyano groups was designed and synthesized. Molecular structure, vibrational wavenumbers, electronic and Molecular Electrostatic Potential (MEP) properties of (Pyr-CN)2B molecule were investigated theoretically using Density Functional Theory (DFT). Experimental and theoretical results obtained from FT-IR, Raman and UV–Vis studies were compared to better explain the properties of the molecule. Chemical reactivity and high electron density due to the heteroatoms in its molecule structure, (Pyr-CN)2B molecule can be proposed as a candidate for many applications based on its chemical and electronic properties. In this scope, the effect of this functional molecule against coronavirus had been investigated by molecular docking studies. These studies had been performed to determine the interactions of the title molecule with the target macromolecule SARS-CoV-2 main protease (Mpro) inhibitor (PDB ID: 7C7P) where minimum binding energy was calculated as -7.30 kcal/mol.