In silico anti-SARS-CoV-2 activities of five-membered heterocycle-substituted benzimidazoles

Identification of potential MMP-8 inhibitors through virtual screening of natural product databases

Matrix metalloproteinase-8 (MMP-8), a type II collagenase, is a key enzyme in the degradation of collagens and is implicated in various pathological processes, making it a promising target for drug discovery. Despite advancements in the development of MMP-8 inhibitors, concerns over potential adverse effects persist. This study aims to address these concerns by focusing on the development of novel compounds with improved safety profiles while maintaining efficacy. In this study, we employed a computational approach to screen potent and safe inhibitors of MMP-8 from the Natural Product Activity and Species Source Database (NPASS). Initially, we constructed a pharmacophore model based on the crystal structure of the MMP-8-FIN complex (PDB ID: 4EY6) utilizing the Pharmit tool. This model then guided the selection of 44 promising molecules from NPASS, setting the stage for further analysis and evaluation. We comprehensively evaluated their drug-likeness and toxicity profiles. Molecules 21, 4, and 44 were identified as potentially effective MMP-8 inhibitors through a robust pipeline that included ADMET profiling, molecular docking, and molecular dynamics simulations. Notably, molecule 21 stood out for its low toxicity, high binding stability, and favorable ADMET profile, while molecule 44 demonstrated excellent affinity. These compounds offer structural novelty compared to known MMP-8 inhibitors. These computational results can be combined with in vitro experiments in the future to validate their activity and safety. These findings provide an important reference for drug design of MMP-8 inhibitors.

In Vitro Screening of an In-House Library of Structurally Distinct Chemotypes Towards the Identification of Novel SARS-CoV-2 Inhibitors

Background/Objectives: Four years after the COVID-19 pandemic, a very limited number of drugs has been marketed; thus, the search for new medications still represents a compelling need. In our previous work on antiviral, antiparasitic, and antiproliferative agents, we described several compounds (1-13 and 16-20) structurally related to clofazimine, chloroquine, and benzimidazole derivatives. Thus, we deemed it worthwhile to test them against the replication of SARS-CoV-2, together with a few other compounds (14, 15 and 21-25), which showed some analogy to miscellaneous anti-coronavirus agents. Methods: Twenty-five structurally assorted compounds were evaluated in vitro for cytotoxicity against Vero E6 and for their ability to inhibit SARS-CoV-2 replication. Results: Several compounds (2, 3, 10, 11, 13-15, 18-20) demonstrated antiviral activity (IC50 range 1.5-28 µM) and six of them exhibited an interesting selectivity index in the range 4.5-20. The chloroquine analogs 10 and 11 were more potent than the reference chloroquine itself and doubled its SI value (20 versus 11). Also, the benzimidazole ring emerged as a valuable scaffold, originating several compounds (13-15 and 18-20) endowed with anti-SARS-CoV-2 activity. Despite the modest activity, the cytisine and the arylamino enone derivatives 23 and 25, respectively, also deserve further consideration as model compounds. Conclusions: The investigated chemotypes may represent valuable hit compounds, deserving further in-depth biological studies to define their mechanisms of action. The derived information will guide the subsequent chemical optimization towards the development of more efficient anti-SARS-CoV-2 agents.

AI Promoted Virtual Screening, Structure-Based Hit Optimization, and Synthesis of Novel COVID-19 S-RBD Domain Inhibitors

Coronavirus disease 2019 (COVID-19) is caused by a new, highly pathogenic severe-acute-respiratory syndrome coronavirus 2 (SARS-CoV-2) that infects human cells through its transmembrane spike (S) glycoprotein. The receptor-binding domain (RBD) of the S protein interacts with the angiotensin-converting enzyme II (ACE2) receptor of the host cells. Therefore, pharmacological targeting of this interaction might prevent infection or spread of the virus. Here, we performed a virtual screening to identify small molecules that block S-ACE2 interaction. Large compound libraries were filtered for drug-like properties, promiscuity and protein-protein interaction-targeting ability based on their ADME-Tox descriptors and also to exclude pan-assay interfering compounds. A properly designed AI-based virtual screening pipeline was applied to the remaining compounds, comprising approximately 10% of the starting data sets, searching for molecules that could bind to the RBD of the S protein. All molecules were sorted according to their screening score, grouped based on their structure and postfiltered for possible interaction patterns with the ACE2 receptor, yielding 31 hits. These hit molecules were further tested for their inhibitory effect on Spike RBD/ACE2 (19-615) interaction. Six compounds inhibited the S-ACE2 interaction in a dose-dependent manner while two of them also prevented infection of human cells from a pseudotyped virus whose entry is mediated by the S protein of SARS-CoV-2. Of the two compounds, the benzimidazole derivative CKP-22 protected Vero E6 cells from infection with SARS-CoV-2, as well. Subsequent, hit-to-lead optimization of CKP-22 was effected through the synthesis of 29 new derivatives of which compound CKP-25 suppressed the Spike RBD/ACE2 (19-615) interaction, reduced the cytopathic effect of SARS-CoV-2 in Vero E6 cells (IC50 = 3.5 μM) and reduced the viral load in cell culture supernatants. Early in vitro ADME-Tox studies showed that CKP-25 does not possess biodegradation or liver metabolism issues, while isozyme-specific CYP450 experiments revealed that CKP-25 was a weak inhibitor of the CYP450 system. Moreover, CKP-25 does not elicit mutagenic effect on Escherichia coli WP2 uvrA strain. Thus, CKP-25 is considered a lead compound against COVID-19 infection.

A Comprehensive Update of Anti-COVID-19 Activity of Heterocyclic Compounds

The Coronavirus disease 2019 (COVID-19) pandemic is one of the most considerable health problems across the world. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the major causative agent of COVID-19. The severe symptoms of this deadly disease include shortness of breath, fever, cough, loss of smell, and a broad spectrum of other health issues such as diarrhea, pneumonia, bronchitis, septic shock, and multiple organ failure. Currently, there are no medications available for coronavirus patients, except symptom-relieving drugs. Therefore, SARS-CoV-2 requires the development of effective drugs and specific treatments. Heterocycles are important constituents of more than 85% of the physiologically active pharmaceutical drugs on the market now. Several FDA-approved drugs have been reported including molnupiravir, remdesivir, ritonavir, oseltamivir, favipiravir, chloroquine, and hydroxychloroquine for the cure of COVID-19. In this study, we discuss potent anti-SARS-CoV-2 heterocyclic compounds that have been synthesized over the past few years. These compounds included; indole, piperidine, pyrazine, pyrimidine, pyrrole, piperazine, quinazoline, oxazole, quinoline, isoxazole, thiazole, quinoxaline, pyrazole, azafluorene, imidazole, thiadiazole, triazole, coumarin, chromene, and benzodioxole. Both in vitro and in silico studies were performed to determine the potential of these heterocyclic compounds in the fight against various SARS-CoV-2 proteins.

Recent Advances in Nitrogen-Containing Heterocyclic Scaffolds as Antiviral Agents

This study aims to provide a thorough analysis of nitrogen-containing heterocycles, focusing on their therapeutic implications for the development of targeted and effective antiviral drugs. To better understand how nitrogen-containing heterocycles can be used to create antiviral drugs, this review adopts a systematic literature review strategy to compile and analyze pertinent research studies. It combines information from various fields to understand better the compounds' mode of action and their therapeutic potential. This review paper summarizes data from multiple sources to highlight the promising potential of heterocycles containing nitrogen as promising possibilities for future antiviral treatments. The capacity to engage selectively and modulate critical pathways bodes well for their use in developing new viral therapies. In conclusion, nitrogen-containing heterocycles are shown to be of utmost importance in the field of medicinal chemistry, as emphasized by the review paper. It emphasizes the central importance of chemical insights and pharmacological potential in developing novel and effective antiviral medicines by bringing them together.

Benzimidazole compound abrogates SARS-COV-2 receptor-binding domain (RBD)/ACE2 interaction In vitro

The development of clinically actionable pharmaceuticals against coronavirus disease (COVID-19); an infectious disease caused by the SARS-CoV-2 virus is very important for ending the pandemic. Coronavirus spike glycoprotein (GP)-Receptor Binding Domain (RBD) and its interaction with host receptor angiotensin converting enzyme 2 (ACE2) is one of the most structurally understood but therapeutically untapped aspect of COVID-19 pathogenesis. Binding interface based on previous x-ray structure of RBD/ACE2 were virtually screened to identify fragments with high-binding score from 12,000 chemical building blocks. The hit compound was subjected to fingerprint-based similarity search to identify compounds within the FDA-approved drug library containing the same core scaffold. Identified compounds were then re-docked into of RBD/ACE2. The best ranked compound was validated for RBD/ACE2 inhibition using commercial kit. Molecular dynamics simulation was conducted to provide further insight into the mechanism of inhibition. From the original 12000 chemical building blocks, benzimidazole (BAZ) scaffold was identified. Fingerprint-based similarity search of the FDA-approved drug library for BAZ-containing compounds identified 12 drugs with the benzimidazole-like substructure. When these compounds were re-docked into GP/ACE2 interface, the consensus docking identified bazedoxifene as the hit. In vitro RBD/ACE2 inhibition kinetics showed micromolar IC50 value (1.237 μM) in the presence of bazedoxifene. Molecular dynamics simulation of RBD/ACE2 in the presence BAZ resulted in loss of contact and specific hydrogen-bond interaction required for RBD/ACE2 stability. Taken together, these findings identified benzimidazole scaffold as a building block for developing novel RBD/ACE2 complex inhibitor and provided mechanistic basis for the use of bazedoxifene as a repurposable drug for the treatment of COVID-19 acting at RBD/ACE2 interface.

One pot bioprocessing in lignocellulosic biorefinery: A review

Practically, high-yield conversion of biomass into value-added products at low cost is a primary goal for any lignocellulosic refinery. In the industrial context, the limitation in the practical adaptation of the conventional techniques practically involves multiple reactors for the conversion of biomass to bioproducts. Therefore, the present manuscript critically reviewed the advancements in one-pot reaction systems with a major focus on the scientific production of value-added products from lignocellulosic biomass. In view of that, the novelty of one-pot reactions is shown during the fractionation of biomass into their individual constituents. The importance of the direct conversion of cellulose and lignin into a range of valuable products including organic acids and platform chemicals are separately discussed. Finally, the article is concluded with the opportunities, existing troubles, and possible solutions to overcome the challenges in lignocellulosic biorefinery. This article will assist the readers to identify the economic-friendly-one-pot conversion of lignocellulosic biomass.