Molecular docking of monkeypox (mpox) virus proteinase with FDA approved lead molecules

S5092 inhibit ASFV infection by targeting the pS273R protease activity in vitro

African Swine Fever (ASF) is a highly infectious viral disease caused by African swine fever virus (ASFV). Currently, there is no effective vaccine, and it is urgent to discover antiviral agents to deal with the epidemic. ASFV pS273R is the only known cysteine protease that catalyzes the maturation of the polyprotein precursors pp220 and pp62 through proteolytic cleavage, a critical step in ASFV assembly. In this study, we performed a high-throughput screening of an FDA-approved drug library to identify several compounds that target the active site of the ASFV pS273R enzyme via molecular docking. We initially identified 778 molecules based on the "Drug-like Five Principles", with S5092 emerging as the most promising candidate. S5092 is a prodrug that can be metabolized into Fenbendazole (FBZ) and Oxfendazole (OFZ). In exogenous cleavage experiments, S5092, FBZ, and OFZ significantly inhibited the cleavage of the viral polyprotein pp220 and pp62, as well as the host antiviral protein gasdermin D (GSDMD) by pS273R, indicating that these compounds inhibit the enzymatic activity of pS273R. Importantly, S5092 and its metabolites reduced the level of ASFV infection, as evidenced by the detection of viral genomic copies and viral titer. Collectively, our findings indicate that S5092 suppresses ASFV infection by inhibiting the enzyme activity of pS273R, a multifunction protein, positioning it as a novel and specific drug candidate for the prevention and control of ASF.

From phytomedicine to conventional drug research, to look for new drug molecule against monkey pox virus; a molecular docking, virtual screening and ADME analysis

Globally, traditional and complementary therapies (such as homeopathy, phytotherapy and herbal medications) are becoming increasingly prevalent alongside modern medical care. The therapeutic substances used in homeopathy and other traditional complementary medicine disciplines are derived from these traditional applications. Numerous notable clinical and preclinical studies have shown their impact during COVID-19. This study aims to investigate the potential antiviral effects of medicinal alkaloids against the monkeypox virus in the current scenario. The structures of 47 known phytochemicals of commonly used medicines in CAM were obtained from PubChem in SDF format, minimized, and then docked against the 3D crystal structure of monkeypox virus methyltransferase VP39 (PDB: 8B07). The results were analyzed, and compounds with significant docking scores were further evaluated. The docking results showed that six compounds-Sarsaponin, Luteolin, Quercetin, Apigenin, and Ducimarine-had better docking scores than Tecovirimat, a standard drug used in managing monkeypox. Additionally, most compounds exhibited better docking scores than Cidofovir, another drug used against monkeypox. Interaction analysis revealed that hydrogen bonding, pi-pi T-shaped, and pi-alkyl interactions were responsible for the observed docking scores. Key amino acid residues involved in the interaction between the compounds and monkeypox virus methyltransferase VP39 included GLY 96, LEU 159, PHE 115, VAL 139, VAL 116, GLY 68, ARG 140, ILE 94, ASN 156, and ARG 156. Five phytochemicals-Luteolin, Quercetin, Apigenin, Sarsaponin, and Ducimarine-show strong potential as monkeypox virus methyltransferase inhibitors. Apigenin and Ducimarine are particularly promising due to their favorable profiles, including no PAINS alerts and good drug-like properties. Sarsaponin, while highly permeable, has high lipophilicity, which may limit its use. Luteolin and Quercetin also show potential but require further investigation due to PAINS alerts.

Insight into Protein Engineering: From In silico Modelling to In vitro Synthesis

Protein engineering alters the polypeptide chain to obtain a novel protein with improved functional properties. This field constantly evolves with advanced in silico tools and techniques to design novel proteins and peptides. Rational incorporating mutations, unnatural amino acids, and post-translational modifications increases the applications of engineered proteins and peptides. It aids in developing drugs with maximum efficacy and minimum side effects. Currently, the engineering of peptides is gaining attention due to their high stability, binding specificity, less immunogenic, and reduced toxicity properties. Engineered peptides are potent candidates for drug development due to their high specificity and low cost of production compared with other biologics, including proteins and antibodies. Therefore, understanding the current perception of designing and engineering peptides with the help of currently available in silico tools is crucial. This review extensively studies various in silico tools available for protein engineering in the prospect of designing peptides as therapeutics, followed by in vitro aspects. Moreover, a discussion on the chemical synthesis and purification of peptides, a case study, and challenges are also incorporated.

Repositioning of anti-infective compounds against monkeypox virus core cysteine proteinase: a molecular dynamics study

Monkeypox virus (MPXV) core cysteine proteinase (CCP) is one of the major drug targets used to examine the inhibitory action of chemical moieties. In this study, an in silico technique was applied to screen 1395 anti-infective compounds to find out the potential molecules against the MPXV-CCP. The top five hits were selected after screening and processed for exhaustive docking based on the docked score of ≤ -9.5 kcal/mol. Later, the top three hits based on the exhaustive-docking score and interaction profile were selected to perform MD simulations. The overall RMSD suggested that two compounds, SC75741 and ammonium glycyrrhizinate, showed a highly stable complex with a standard deviation of 0.18 and 0.23 nm, respectively. Later, the MM/GBSA binding free energies of complexes showed significant binding strength with ΔGTOTAL from -21.59 to -15 kcal/mol. This report reported the potential inhibitory activity of SC75741 and ammonium glycyrrhizinate against MPXV-CCP by competitively inhibiting the binding of the native substrate.

Computational drug repurposing for viral infectious diseases: a case study on monkeypox

The traditional method of drug reuse or repurposing has significantly contributed to the identification of new antiviral compounds and therapeutic targets, enabling rapid response to developing infectious illnesses. This article presents an overview of how modern computational methods are used in drug repurposing for the treatment of viral infectious diseases. These methods utilize data sets that include reviewed information on the host's response to pathogens and drugs, as well as various connections such as gene expression patterns and protein-protein interaction networks. We assess the potential benefits and limitations of these methods by examining monkeypox as a specific example, but the knowledge acquired can be applied to other comparable disease scenarios.

Computational Analysis of a Marine-Derived Drug From Rhizophora mucronata Against the Capsid Protein of Rubella Virus

Background Rubella, commonly known as German measles, is caused by a single-stranded RNA genome. Vaccination is currently the most effective method for preventing rubella and its complications. Molecular docking, a computer-based technique used in drug discovery and development, is used to investigate the interactions between potential drug candidates and their target proteins. It predicts the binding interactions between small molecules (ligands) and the target protein. In this study, we examined a marine-derived drug from Rhizophora mucronata for its potential antiviral properties against the rubella capsid virus. Our objective was to identify the active inhibitory sites of the capsid virus. Materials and methods Protein and ligand molecules were retrieved from Protein Data Bank (PDB) and PubChem databases. The Lamarckian genetic algorithm was used to calculate molecular docking using Autodock Tools 1.5.7. The docking parameters used for each docked molecule were determined from 100 separate docking experiments with a maximum of 2.5×10-6 energy and a mutation rate of 2.0 and mass over ratio of 0.8. The results were recorded as docking parameter files (DPF). PyMOL was used to view and investigate the interactions between ligand fragments and rubella capsid protein. Results This approach plays a crucial role in the development of structure-based drugs. The results of the molecular docking suggest that Rhizophorin has the potential to bind with the rubella capsid protein. The strong binding affinity of -6.05 kcal/mol between the ligand and the protein further supports the potential of Rhizophorin as a therapeutic agent. The formation of hydrogen bonds between the ligand and amino acid residues Glu79, Arg82, and Thr118 indicates the significance of electrostatic interactions in the binding process. Furthermore, the hydrophobic interactions between the ligand and residues Ala81, Val84, Leu87, and Ile119 suggest the role of non-polar interactions in stabilizing the complex. The identified amino acid residues involved in these binding interactions could serve as potential targets for drug development. In future studies, experimental validation of the predicted interactions could provide further insights into the potential of Rhizophorin as an antiviral agent. Conclusion According to the findings of this study, the in silico investigation successfully identified a target for inhibiting the rubella virus (RuV) capsid receptor molecule. Future investigations on these compounds will require in vitro and in vivo studies using models that are more relevant to the medicinal potential of the capsid protein molecule.

Molecular Docking of Seaweed-Derived Drug Fucoxanthin Against the Monkeypox Virus

Background The monkeypox virus (MPXV) is classified as a zoonotic virus of the Poxviridae family, resulting from the MPXV strain of the Orthopoxvirus genus. Seaweeds, or marine macroalgae, are abundant reservoirs of bioactive compounds that demonstrate diverse biological properties, such as antiviral actions. In the field of computational analysis, in silico analysis refers to the use of computer-based methods to study and assess biological systems and processes. To forecast the binding affinity and interaction between the discovered chemical and the target proteins of the MPXV, a molecular docking analysis was conducted. Aim The research aims to conduct an in silico examination of a protein-ligand interaction of a drug produced from seaweed that targets the MPXV.  Methodology Protein Data Bank (PDB) and PubChem databases provided MPXV methyltransferase and fucoxanthin ligand compounds. AutoDockTools 1.5.7 calculated the molecular docking using the Lamarckian genetic algorithm. Autogrid created a grid box around target 8B07 active site hotspot residues. Each docked molecule's docking parameters were obtained from 100 docking experiments with a maximum of 2.5 × 106 energy evaluations, a 0.02 mutation rate, and a 0.8 crossover rate. The population comprised 250 randomly selected volunteers. PyMOL was utilized to observe ligand fragment interactions. Results The binding energy of the ligand fucoxanthin was -5.46 kcal/mol. Fucoxanthin interacts with receptor molecules via hydrogen bonding at the amino acid level: Chain A: PHE188 and TYR189; and Chain B: LYS33, GLN37, GLY38, GLY96, ARG97, PHE115, PRO202, and SER203. The higher the negative docking score, the stronger the binding affinity between the receptor and ligand molecules, indicating that bioactive substances are more effective. Conclusion The findings of this study indicate that fucoxanthin, a pharmaceutical derivative generated from seaweed, had antiviral activity against the MPXV. This conclusion was reached based on protein-ligand interactions.

Breaking Barriers: Current Advances and Future Directions in Mpox Therapy

BACKGROUND

Mpox, a newly discovered zoonotic infection, can be transmitted from animal to human and between humans. Serological and genomic studies are used to identify the virus.

OBJECTIVE

Currently, there are no proven effective treatments for Mpox. Also, the safety and efficacy of intravenous vaccinia immune globulin, oral Tecovirimat (an inhibitor of intracellular viral release), and oral Brincidofovir (a DNA polymerase inhibitor) against the Mpox virus are uncertain, highlighting the need for more effective and safe treatments. As a result, drug repurposing has emerged as a promising strategy to identify previously licensed drugs that can be repurposed to treat Mpox.

RESULTS

Various approaches have been employed to identify previously approved drugs that can target specific Mpox virus proteins, including thymidylate kinase, D9 decapping enzyme, E8 protein, Topoisomerase1, p37, envelope proteins (D13, A26, and H3), F13 protein, virus's main cysteine proteases, and DNA polymerase.

CONCLUSION

In this summary, we provide an overview of potential drugs that could be used to treat Mpox and discuss the underlying biological processes of their actions.

Molecular Modeling Insights into Metal-Organic Frameworks (MOFs) as a Potential Matrix for Immobilization of Lipase: An In Silico Study

CRL is a highly versatile enzyme that finds extensive utility in numerous industries, which is attributed to its selectivity and catalytic efficiency, which have been impeded by the impracticality of its implementation, leading to a loss of native catalytic activity and non-reusability. Enzyme immobilization is a necessary step for enabling its reuse, and it provides methods for regulating the biocatalyst's functional efficacy in a synthetic setting. MOFs represent a novel category of porous materials possessing distinct superlative features that make MOFs an optimal host matrix for developing enzyme-MOF composites. In this study, we employed molecular modeling approaches, for instance, molecular docking and MD simulation, to explore the interactions between CRL and a specific MOF, ZIF-8. The present study involved conducting secondary structural analysis and homology modeling of CRL, followed by docking ZIF-8 with CRL. The results of the molecular docking analysis indicate that ZIF-8 was situated within the active site pocket of CRL, where it formed hydrogen bonds with Val-81, Phe-87, Ser-91, Asp-231, Thr-132, Lue-297, Phe-296, Phe-344, Thr-347, and Ser-450. The MD simulation analysis revealed that the CRL and ZIF-8 docked complex exhibited stability over the entire simulation period, and all interactions presented in the initial docked complex were maintained throughout the simulation. The findings derived from this investigation could promote comprehension of the molecular mechanisms underlying the interaction between CRL and ZIF-8 as well as the development of immobilized CRL for diverse industrial purposes.

Repurposing Anti-Dengue Compounds against Monkeypox Virus Targeting Core Cysteine Protease

The monkeypox virus (MPXV) is an enveloped, double-stranded DNA virus belonging to the genus Orthopox viruses. In recent years, the virus has spread to countries where it was previously unknown, turning it into a worldwide emergency for public health. This study employs a structural-based drug design approach to identify potential inhibitors for the core cysteine proteinase of MPXV. During the simulations, the study identified two potential inhibitors, compound CHEMBL32926 and compound CHEMBL4861364, demonstrating strong binding affinities and drug-like properties. Their docking scores with the target protein were -10.7 and -10.9 kcal/mol, respectively. This study used ensemble-based protein-ligand docking to account for the binding site conformation variability. By examining how the identified inhibitors interact with the protein, this research sheds light on the workings of the inhibitors' mechanisms of action. Molecular dynamic simulations of protein-ligand complexes showed fluctuations from the initial docked pose, but they confirmed their binding throughout the simulation. The MMGBSA binding free energy calculations for CHEMBL32926 showed a binding free energy range of (-9.25 to -9.65) kcal/mol, while CHEMBL4861364 exhibited a range of (-41.66 to -31.47) kcal/mol. Later, analogues were searched for these compounds with 70% similarity criteria, and their IC50 was predicted using pre-trained machine learning models. This resulted in identifying two similar compounds for each hit with comparable binding affinity for cysteine proteinase. This study's structure-based drug design approach provides a promising strategy for identifying new drugs for treating MPXV infections.

Pharmacological treatment and vaccines in monkeypox virus: a narrative review and bibliometric analysis

Mpox (earlier known as monkeypox) virus infection is a recognized public health emergency. There has been little research on the treatment options. This article reviews the specific drugs used to treat mpox virus infection and the vaccines used here. Instead of focusing on the mechanistic basis, this review narrates the practical, real-life experiences of individual patients of mpox virus disease being administered these medicines. We conducted a bibliometric analysis on the treatment of the mpox virus using data from several databases like PubMed, Scopus, and Embase. The research on this topic has grown tremendously recently but it is highly concentrated in a few countries. Cidofovir is the most studied drug. This is because it is indicated and also used off-label for several conditions. The drugs used for mpox virus infection include tecovirimat, cidofovir, brincidofovir, vaccinia immune globulin, and trifluridine. Tecovirimat is used most frequently. It is a promising option in progressive mpox disease in terms of both efficacy and safety. Brincidofovir has been associated with treatment discontinuation due to elevated hepatic enzymes. Cidofovir is also not the preferred drug, often used because of the unavailability of tecovirimat. Trifluridine is used topically as an add-on agent along with tecovirimat for ocular manifestations of mpox virus disease. No study reports individual patient data for vaccinia immune globulin. Though no vaccine is currently approved for mpox virus infection, ACAM 2000 and JYNNEOS are the vaccines being mainly considered. ACAM 2000 is capable of replicating and may cause severe adverse reactions. It is used when JYNNEOS is contraindicated. Several drugs and vaccines are under development and have been discussed alongside pragmatic aspects of mpox virus treatment and prevention. Further studies can provide more insight into the safety and efficacy of Tecovirimat in actively progressing mpox virus disease.