Dual-Site Inhibitionof SARS-CoV‑2 RNA-DependentRNA Polymerase by Small Molecules Able to Block Viral ReplicationIdentified through a Computer-Aided Drug Discovery Approach

Integrating multi-omics and computer-aided drug discovery approaches can overcome the limitations of traditional methods and help develop highly effective, specific, and environmentally safe biofungicides to control crop diseases. Chickpea is a valuable legume crop in terms of nutrition, food security, economic sustainability, and environmental benefits. Fusarium wilt caused by the soil-borne fungus Fusarium oxysporum f.sp. ciceri is one of the most important diseases affecting chickpea. Several disease management methods, including crop rotation, soil fumigation with chemical fungicides, soil solarization, etc., are practiced to manage the disease. However, these methods have various limitations and cannot completely control the disease. Moreover, chemical fungicides indiscriminately kill even the beneficial soil microbes, pollute groundwater, and enter the food chain. Hence, modern approaches emphasizing innovative strategies and technologies need to be explored to manage the disease effectively. In this review, we propose integrating multi-omics (genomics, proteomics, metabolomics, etc.) and computer-aided drug discovery (CADD) approaches to develop biofungicides targeting vital pathogen proteins. Multi-omics approaches can delve deeper into the plant-pathogen interaction and reveal essential pathogen genes or proteins. These proteins could be targeted using CADD to identify phytochemical-based potential biofungicides, either using structure- or ligand-based drug design approaches. The potential biofungicides can be subjected to the prediction of carcinogenicity, hepatotoxicity, mutagenicity, etc., to identify biofungicides that are safe to use and are highly specific to the target pathogen. In vivo and in vitro validation studies can be followed to establish the efficacy and safety of the identified biofungicides for their practical application. This integrated approach can reduce the time and cost compared to the traditional methods and accelerate the discovery of highly effective biofungicides to protect crops from various diseases.

Natural plant sources are essential in the development of several anticancer drugs, such as vincristine, vinblastine, vinorelbine, docetaxel, paclitaxel, camptothecin, etoposide, and teniposide. However, various chemotherapies fail due to adverse reactions, drug resistance, and target specificity. Researchers are now focusing on developing drugs that use natural compounds to overcome these issues. These drugs can affect multiple targets, have reduced adverse effects, and are effective against several cancer types. Developing a new drug is a highly complex, expensive, and time-consuming process. Traditional drug discovery methods take up to 15 years for a new medicine to enter the market and cost more than one billion USD. However, recent Computer Aided Drug Discovery (CADD) advancements have changed this situation. This paper aims to comprehensively describe the different CADD approaches in identifying anticancer drugs from natural products. Data from various sources, including Science Direct, Elsevier, NCBI, and Web of Science, are used in this review. In-silico techniques and optimization algorithms can provide versatile solutions in drug discovery ventures. The structure-based drug design technique is widely used to understand chemical constituents' molecular-level interactions and identify hit leads. This review will discuss the concept of CADD, in-silico tools, virtual screening in drug discovery, and the concept of natural products as anticancer therapies. Representative examples of molecules identified will also be provided.

Background and Purpose: Tuberculosis (TB) remains a significant global health threat, with millions of new cases and high mortality rates reported each year and exacerbated by the emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains of Mycobacterium tuberculosis. Current treatment options face limitations in efficacy, particularly against dormant bacterial cells, and are further challenged by the rise of drug-resistant TB. The present study investigates the potential of drug repurposing—a strategy that identifies new therapeutic applications for existing drugs—to discover compounds with effective antitubercular activity. Methods: A computer-aided drug discovery approach was employed, targeting two essential M. tuberculosis proteins: catalase peroxidase (KatG) and enoyl-acyl transferase. Potential anti-tubercular agents were selected based on structural similarity to known anti-tubercular drugs (isoniazid and ethionamide) and virtual screening was conducted to assess the binding affinities of the candidate drugs, followed by pharmacophore modeling to analyze critical features for protein-ligand interactions. Results: Ten drugs demonstrated strong binding affinities for the target proteins, with micafungin, pafolacianine, piperacillin, bisacodyl, and flucloxacillin showing the most promising interactions. Pharmacophore analysis revealed essential structural features, including hydrogen bond acceptors and donors, that could enhance drug efficacy and bioavailability, suggesting that these compounds may have favorable pharmacokinetic properties for TB treatment. Conclusion: The findings indicate that drugs like micafungin and flucloxacillin could be viable candidates for further study in TB treatment, offering a potential pathway to address the urgent need for novel antitubercular therapies. This study underscores the utility of computational drug discovery in identifying promising agents for repurposing, potentially expediting the development of effective treatments for TB.

The heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) is a versatile RNA-binding protein playing a critical role in alternative pre-mRNA splicing regulation in cancer. Emerging data have implicated hnRNP A1 as a central player in a splicing regulatory circuit involving its direct transcriptional control by c-Myc oncoprotein and the production of the constitutively active ligand-independent alternative splice variant of androgen receptor, AR-V7, which promotes castration-resistant prostate cancer (CRPC). As there is an urgent need for effective CRPC drugs, targeting hnRNP A1 could, therefore, serve a dual purpose of preventing AR-V7 generation as well as reducing c-Myc transcriptional output. Herein, we report compound VPC-80051 as the first small molecule inhibitor of hnRNP A1 splicing activity discovered to date by using a computer-aided drug discovery approach. The inhibitor was developed to target the RNA-binding domain (RBD) of hnRNP A1. Further experimental evaluation demonstrated that VPC-80051 interacts directly with hnRNP A1 RBD and reduces AR-V7 messenger levels in 22Rv1 CRPC cell line. This study lays the groundwork for future structure-based development of more potent and selective small molecule inhibitors of hnRNP A1–RNA interactions aimed at altering the production of cancer-specific alternative splice isoforms.

The integration of computational techniques into drug development has led to a substantial increase in the knowledge of structural, chemical, and biological data. These techniques are useful for handling the big data generated by empirical and clinical studies. Over the last few years, computer-aided drug discovery methods such as virtual screening, pharmacophore modeling, quantitative structure-activity relationship analysis, and molecular docking have been employed by pharmaceutical companies and academic researchers for the development of pharmacologically active drugs. Toll-like receptors (TLRs) play a vital role in various inflammatory, autoimmune, and neurodegenerative disorders such as sepsis, rheumatoid arthritis, inflammatory bowel disease, Alzheimer’s disease, multiple sclerosis, cancer, and systemic lupus erythematosus. TLRs, particularly TLR4, have been identified as potential drug targets for the treatment of these diseases, and several relevant compounds are under preclinical and clinical evaluation. This review covers the reported computational studies and techniques that have provided insights into TLR4-targeting therapeutics. Furthermore, this article provides an overview of the computational methods that can benefit a broad audience in this field and help with the development of novel drugs for TLR-related disorders.

Despite the tremendous improvement in overall global health heralded by the adoption of the Millennium Declaration in the year 2000, tropical infections remain a major health problem in the developing world. Recent estimates indicate that the major tropical infectious diseases, namely, malaria, tuberculosis, trypanosomiasis, and leishmaniasis, account for more than 2.2 million deaths and a loss of approximately 85 million disability-adjusted life years annually. The crucial role of chemotherapy in curtailing the deleterious health and economic impacts of these infections has invigorated the search for new drugs against tropical infectious diseases. The research efforts have involved increased application of computational technologies in mainstream drug discovery programs at the hit identification, hit-to-lead, and lead optimization stages. This review highlights various computer-aided drug discovery approaches that have been utilized in efforts to identify novel antimalarial, antitubercular, antitrypanosomal, and antileishmanial agents. The focus is largely on developments over the past 5 years (2010-2014).

### Cardiac Myosin Binding Protein C is an Ultra-early and Cardiac-specific Biomarker of Myocardial Necrosis Diederik W Kuster1, Adriana Cardenas-Ospina2, Lawson Miller2, Christian Troidl3, Holger M Nef3, Christoph Liebetrau3, Mollmann Helge3, Karen S Pieper4, Kenneth W Mahaffey4, Neal S Kleiman5, Bruno D Stuyvers2, Ali J Marian6, Sakthivel Sadayappan1; 1Loyola Univ Chicago, Maywood, IL, 2Memorial Univ, St John’s, Canada, 3Kerckhoff Heart and Thorax Cntr, Bad Neuheim, Germany, 4Duke Univ Med Cntr, Durham, NC, 5The Methodist DeBakey Heart and Vascular Cntr, Houston, TX, 6Univ of Texas Health Sciences, Houston, TX Rationale: We recently demonstrated that proteolytic cleavage fragments of cardiac myosin binding protein-C (cMyBP-C) can be detected in the serum after myocardial infarction (MI) in a rat model and in patients with MI. The findings implied that serum cMyBP-C might be useful as cardiac-specific biomarker for MI. The release kinetics of cMyBP-C in the circulation post-MI remains to be elucidated. Objective: Determine the release kinetics of cMyBP-C as an ultra-early and cardiac-specific biomarker of myocardial necrosis. Method and Results: To determine the exact timing of cMyBP-C release in the bloodstream post-acute MI, left anterior descending (LAD) coronary artery was ligated in adult swine (n=6). ECG showed significant ST elevation. Infarct size represented 12.4 ± 1.9% of total ventricular mass. Blood samples were collected before and at predetermined time points between 30 min and 14 days after LAD ligation. Plasma cMyBP-C level was quantified using a highly sensitive and rapid sandwich enzyme-linked immunosorbent assay. Compared with baseline, cMyBP-C levels were increased in post-MI serum within 45 min (0.64 ± 0.52 ng/ml) after LAD ligation and declined after 16 hrs to the baseline level (0.01 ± 0.00 ng/ml). In contrast, cardiac troponin I (cTnI) level peaked after …

The Notch pathway is a cell-cell communication system where membrane-bound ligands interact with the extracellular region of Notch receptors to induce intracellular, downstream effects on gene expression. Aberrant Notch signaling promotes tumorigenesis, and the Notch pathway has tremendous potential for novel targeting strategies in cancer treatment. While γ-secretase inhibitors as Notch-inhibiting agents are already promising in clinical trials, they are highly non-specific with adverse side-effects. One of the underlying challenges is that two of the four known human Notch paralogs, NOTCH1 and 2, share very high structural similarity but play opposing roles in some tumorigenesis pathways. This perspective explores the feasibility of developing Notch-specific small molecule inhibitors targeting the anti-NOTCH2 antibody-binding epitopes or the "S2-Leu-plug-binding site" using a computer-aided drug discovery approach.

The discovery of some promising putative binders of KRAS G12D receptor using computer-aided drug discovery approach

Tilapia Lake Virus (TiLV) is a disease that affects tilapia fish, causing a high rate of sudden death at any stage in their life cycle. Unfortunately, there are currently no effective antiviral drugs or vaccines to prevent or control the progression of this disease. Researchers have discovered that the CRM1 protein plays a critical function in the development and spreading of animal viruses. By inhibiting CRM1, the virus's spread in commercial fish farms can be suppressed. With this in mind, this study intended to identify potential antiviral drugs from two different tropical mangrove plants from tropical regions: Heritiera fomes and Ceriops candolleana. To identify promising compounds that target the CRM1 protein, a computer-aided drug discovery approach is employed containing molecular docking, ADME (absorption, distribution, metabolism and excretion) analysis, toxicity assessment as well as molecular dynamics (MD) simulation. To estimate binding affinities of all phytochemicals, molecular docking is used and the top three candidate compounds with the highest docking scores were selected, which are CID107876 (-8.3 Kcal/mol), CID12795736 (-8.2 Kcal/mol), and CID12303662 (-7.9 Kcal/mol). We also evaluated the ADME and toxicity properties of these compounds. Finally, MD simulation was conducted to analyze the stability of the protein-ligand complex structures and confirm the suitability of these compounds. The computational study demonstrated that the phytochemicals found in H. fomes and C. candolleana could potentially serve as important inhibitors of TiLV, offering practical utility. However, further in vivo investigations are necessary to investigate and potentially confirm the effectiveness of these compounds as antiviral drugs against the virus TiLV.

A new semisynthetic derivative of the natural alkaloid, theobromine, has been designed as a lead antiangiogenic compound targeting the EGFR protein. The designed compound is an (m-tolyl)acetamide theobromine derivative, (T-1-MTA). Molecular Docking studies have shown a great potential for T-1-MTA to bind to EGFR. MD studies (100 ns) verified the proposed binding. By MM-GBSA analysis, the exact binding with optimal energy of T-1-MTA was also identified. Then, DFT calculations were performed to identify the stability, reactivity, electrostatic potential, and total electron density of T-1-MTA. Furthermore, ADMET analysis indicated the T-1-MTA's general likeness and safety. Accordingly, T-1-MTA has been synthesized to be examined in vitro. Intriguingly, T-1-MTA inhibited the EGFR protein with an IC50 value of 22.89 nM and demonstrated cytotoxic activities against the two cancer cell lines, A549, and HCT-116, with IC50 values of 22.49, and 24.97 μM, respectively. Interestingly, T-1-MTA's IC50 against the normal cell lines, WI-38, was very high (55.14 μM) indicating high selectivity degrees of 2.4 and 2.2, respectively. Furthermore, the flow cytometry analysis of A549 treated with T-1-MTA showed significantly increased ratios of early apoptosis (from 0.07% to 21.24%) as well as late apoptosis (from 0.73% to 37.97%).

Resistance to androgen-receptor (AR) directed therapies is, among other factors, associated with Myc transcription factors that are involved in development and progression of many cancers. Overexpression of N-Myc protein in prostate cancer (PCa) leads to its transformation to advanced neuroendocrine prostate cancer (NEPC) that currently has no approved treatments. N-Myc has a short half-life but acts as an NEPC stimulator when it is stabilized by forming a protective complex with Aurora A kinase (AURKA). Therefore, dual-inhibition of N-Myc and AURKA would be an attractive therapeutic avenue for NEPC. Following our computer-aided drug discovery approach, compounds exhibiting potent N-Myc specific inhibition and strong anti-proliferative activity against several N-Myc driven cell lines, were identified. Thereafter, we have developed dual inhibitors of N-Myc and AURKA through structure-based drug design approach by merging our novel N-Myc specific chemical scaffolds with fragments of known AURKA inhibitors. Favorable binding modes of the designed compounds to both N-Myc and AURKA target sites have been predicted by docking. A promising lead compound, 70812, demonstrated low-micromolar potency against both N-Myc and AURKA in vitro assays and effectively suppressed NEPC cell growth.

Coronavirus disease-19 (COVID-19) pandemic caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has infected approximately 26 million people and caused more than 6 million deaths globally. Spike (S)-protein on the outer surface of the virus uses human trans-membrane serine protease-2 (TMPRSS2) to gain entry into the cell. Recent reports indicate that human dipeptidyl peptidase-4 inhibitors (DPP4 or CD26) could also be utilized to check the S-protein mediated viral entry into COVID-19 patients. RNA dependent RNA polymerase (RdRp) is another key virulence protein of SARS-CoV-2 life cycle. The study aimed to identify the potential anti-SARS-CoV-2 inhibitors present in Withania somnifera (Solanaceae) using computer aided drug discovery approach. Molecular docking results showed that flavone glycoside, sugar alcohol, and flavonoid present in W. somnifera showed − 11.69, − 11.61, − 10.1, − 7.71 kcal/mole binding potential against S-protein, CD26, RdRp, and TMPRSS2 proteins. The major standard inhibitors of the targeted proteins (Sitagliptin, VE607, Camostat mesylate, and Remdesivir) showed the − 7.181, − 6.6, − 5.146, and − 7.56 kcal/mole binding potential. Furthermore, the lead phytochemicals and standard inhibitors bound and non-bound RdRp and TMPRSS2 proteins were subjected to molecular dynamics (MD) simulation to study the complex stability and change in protein conformation. The result showed energetically favorable and stable complex formation in terms of RMSD, RMSF, SASA, Rg, and hydrogen bond formation. Drug likeness and physiochemical properties of the test compounds exhibited satisfactory results. Taken together, the present study suggests the presence of potential anti-SARS-CoV-2 phytochemicals in W. somnifera that requires further validation in in vitro and in vivo studies.Graphical Supplementary informationThe online version contains supplementary material available at 10.1007/s42535-022-00404-4.

Hendra virus (HeV) belongs to the paramyxoviridae family of viruses which is associated with the respiratory distress, neurological illness, and potential fatality of the affected individuals. So far, no competitive approved therapeutic substance is available for HeV. For that reason, the current research work was conducted to propose some novel compounds, by adopting a Computer Aided Drug Discovery approach, which could be used to combat HeV. The G attachment Glycoprotein (Ggp) of HeV was selected to achieve the primary objective of this study, as this protein makes the entry of HeV possible in the host cells. Briefly, a library of 6000 antiviral compounds was screened for potential drug-like properties, followed by the molecular docking of short-listed compounds with the Protein Data Bank (PDB) structure of Ggp. Docked complexes of top two hits, having maximum binding affinities with the active sites of Ggp, were further considered for molecular dynamic simulations of 200 ns to elucidate the results of molecular docking analysis. MD simulations and Molecular Mechanics Energies combined with the Generalized Born and Surface Area (MMGBSA) or Poisson–Boltzmann and Surface Area (MMPBSA) revealed that both docked complexes are stable in nature. Furthermore, the same methodology was used between lead compounds and HeV Ggp in complex with its functional receptor in human, Ephrin-B2. Surprisingly, no major differences were found in the results, which demonstrates that our identified compounds can also perform their action even when the Ggp is attached to the Ephrin-B2 ligand. Therefore, in light of all of these results, we strongly suggest that compounds (S)-5-(benzylcarbamoyl)-1-(2-(4-methyl-2-phenylpiperazin-1-yl)-2-oxoethyl)-6-oxo-3,6-dihydropyridin-1-ium-3-ide and 5-(cyclohexylcarbamoyl)-1-(2-((2-(3-fluorophenyl)-2-methylpropyl)amino)-2-oxoethyl)-6-oxo-3,6-dihydropyridin-1-ium-3-ide could be considered as potential therapeutic agents against HeV; however, further in vitro and in vivo experiments are required to validate this study.

In the current study, amphiphilic peptides were designed and screened against Jack bean urease by using computer aided drug discovery approach. The result showed that out of thirty-eight amphiphilic peptides 1, 3, 12, 18, 30, and 33 exhibit stronger binding affinity with the active site of the enzyme through chelation of charged amino acids with the nickel ions i.e., Ni+2 841 and Ni+2 842 as well as hydrophobic contacts of the nonpolar tail with the nonpolar residues in the active site. The selected amphiphilic peptides were synthesized by solid-phase peptide synthesis strategy, characterized by fast atomic bombardment mass spectroscopy (FAB-MS) and nuclear magnetic resonance spectroscopy (1H and 13C-NMR) and in vitro urease inhibitory activity of amphiphilic peptides was studied. Amphiphilic peptides 12 and 33 showed excellent urease inhibitory activity, (p < 0.001) with IC50 values 20.5 ± 0.01, and 28.1 ± 0.03 µM respectively, which was considerably better than thiourea used as positive control.