Identifying Potential SOS1 Inhibitors via Virtual Screening of Multiple Small Molecule Libraries against KRAS-SOS1 Interaction.

The RAS-MAPK signaling pathway, crucial for cell proliferation and differentiation, involves key proteins KRAS and SOS1. Mutations in the KRAS and SOS1 genes are implicated in various cancer types, including pancreatic, lung, and juvenile myelomonocytic leukemia. There is considerable interest in identifying inhibitors targeting KRAS and SOS1 to explore potential therapeutic strategies for cancer treatment. In this study, advanced in silico techniques were employed to screen small molecule libraries at this interface, leading to the identification of promising lead compounds as potential SOS1 inhibitors. Comparative analysis of the average binding free energies of these predicted potent compounds with known SOS1 small molecule inhibitors revealed that the identified compounds display similar or even superior predicted binding affinities compared to the known inhibitors. These findings offer valuable insights into the potential of these compounds as candidates for further development as effective anti-cancer agents.

A systematic review of computational methods for designing efficient guides for CRISPR DNA base editor systems.

In only a few years, as a breakthrough technology, clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas) gene-editing systems have ushered in the era of genome engineering with a plethora of applications. One of the most promising CRISPR tools, so-called base editors, opened an exciting avenue for exploring new therapeutic approaches through controlled mutagenesis. However, the efficiency of a base editor guide varies depending on several biological determinants, such as chromatin accessibility, DNA repair proteins, transcriptional activity, factors related to local sequence context and so on. Thus, the success of genetic perturbation directed by CRISPR/Cas base-editing systems relies on an optimal single guide RNA (sgRNA) design, taking those determinants into account. Although there is 11 commonly used software to design guides specifically for base editors, only three of them investigated and implemented those biological determinants into their models. This review presents the key features, capabilities and limitations of all currently available software with a particular focus on predictive model-based algorithms. Here, we summarize existing software for sgRNA design and provide a base for improving the efficiency of existing available software suites for precise target base editing.

Aspergillus flavus originated pure compound as a potential antibacterial.

PROBLEM BACKGROUND: Penicillin was the first and most famous fungal secondary metabolite used as broad spectrum antibiotic that revolutionarised pharmaceutical research and also saved millions of lives. The over optimistic belief in 1967 that sufficient antibiotics had been discovered to defeat infectious diseases was quickly crashed with the appearance of multidrug resistant (MDR) bacteria in 1990s. This has posed a serious threat to mankind. Although scientists are making efforts to synthesize and discover new antibiotics there are not enough new drugs in pharmaceutical pipeline to beat the pace at which MDR bacteria are emerging. In view of this there is an urgent and serious medical need for new bioactive compounds to be discovered to treat infections caused by MDR pathogens. The present study is aimed to investigate the antibacterial potential of Aspergillus flavus originated compounds that may act as drug leads to treat future infections. METHODOLOGY: Among the 6 isolated fungal strains from the rhizosphere of Mentha piperetta, one was processed for isolation of secondary metabolites on the basis of preliminary antibacterial testing. Observation of morphological and microscopic features helped in identification of the fungal strain as Aspergillus flavus. Potato Dextrose Agar (PDA) medium was used for fungal growth while Czapec Yeast Broth (CYB) medium was used for production of fungal metabolites. Column chromatography technique was utilized for purification of compound from crude fungal extract and the mass of the compound was determined using Liquid Chromatography Mass Spectrometry (LCMS) method. Structure elucidation of the pure compound was performed using 500 Varian Nuclear Magnetic Resonance (NMR) machine. Docking was performed using Glide SP algorithm. Agar well diffusion method was used to determine the invitro antibacterial potential of the compound against two MDR bacterial strains i.e. Staphylococcus aureus and Proteus vulgaris. For this a total of 4 dose concentrations i.e. (100, 250, 500, 1000 µg mL- 1) of the compound were prepared and applied to bacterial strains on Mueller Hinton agar using tetracycline as control. RESULTS: The chemical name of the purified compound from A. flavus was determined as (2E)-3-[(3S, 4R)-8-hydroxy-3, 4-dimethyl-1-oxo-3, 4-dihydro-1H-2- benzopyran-7-yl] prop-2-enoic acid with the formula C14H14O5 and exact mass of 262.08. The in-Silico analysis showed that this compound has the potential to inhibit the binding pocket of S. aureus TyrRS (1JII) with docking score of - 8.67 Kcal mole- 1. The results obtained from invitro experiments were encouraging as at 1000 µg mL- 1 the compound showed 58.8% inhibition against S. aureus and 28% inhibition against P. vulgaris. CONCLUSIONS: The pure compound with formula C14H14O5 and exact mass of 262 exhibited antibacterial potential both insilico and invitro against both Gram negative and Gram positive bacteria. The compound was more active against S. aureus in comparison to P. vulgaris. From the obtained results it is concluded that this compound can be used as potent antibacterial candidate but further studies will be needed prior to its use as antibiotic.

Screening of small molecule libraries using combined text mining, ligand- and target-driven based approaches for identification of novel granzyme H inhibitors.

Granzymes are serine proteases synthesized by CTL and NK cells. Five granzyme genes (GzmA, -B, -H, -K, -M) are present in humans, which are located at three different chromosomal loci. Being serine proteases, the binding pocket constitutes a catalytic triad (i.e., His59, Asp103 and Ser197). Granzymes are released into target (cancerous and virally infected) cells by a specialized process known as granule exocytosis pathway. After internalization, these proteases initiate apoptosis. Granzymes are also involved in other non-apoptotic immune associated roles like ECM remodeling, cytokine modulation, killing of pathogens through generation of phagosomes. Their intracellular activity is regulated by specialized inhibitors knows as SERPINs. However, if these proteases are secreted in excess into the extracellular environment, their regulation becomes important as otherwise they start self-damage to the tissues thereby worsening the disease conditions. Efforts are being made to identify potential inhibitors for regulation of these proteases in an extracellular environment. Physiological and synthetic inhibitors have been reported against some members however there is no known inhibitor against extracellular human GzmH. Thus, in the current study, we investigated small molecule databases for the identification of potential molecules having the ability to inhibit GzmH by combined molecular simulations, which can ultimately be used as a potential therapeutic agent.

Potent novel inhibitors against hepatitis C virus NS3 (HCV NS3 GT-3a) protease domain.

HCV NS3, a non-structural hepatitis C viral protein is used as one of the potential targets for inhibition by direct-acting antivirals. It is known that the success rate for HCV genotype-1 treatment remained very high, however, treatment of genotype-3a (GT-3a), is still quite challenging. In the current study, the HCV GT-3a full-length NS3 gene was amplified and sequenced. The complete nucleotide sequence was translated into the amino acid sequence and homology models of HCV-NS3 GT-3a were generated by HCV-NS3 genotype-1b as a template. The objective of the study was to screen novel therapeutic hits from large databases. For this aim, various small molecule databases including, BindingDB (∼45.000 compounds), NCI (∼265.000 compounds), and Specs-SC (∼212.000 compounds) were used. Firstly, all of the compounds were screened using binary-QSAR models from the MetaCore/MetaDrug server, and compounds were filtered based on therapeutic activity predictions by the anti-viral QSAR model. Filtered molecules were used in 26 different toxicity QSAR models and active non-toxic compounds were identified. These selected molecules were then used in docking and molecular dynamics (MD) simulations studies at the binding cavities of the NS3 protease domain of the GT-3a. Results were compared with known inhibitors and novel molecules are proposed against HCV-NS3 GT-3a. These molecules have high ligand efficiencies as compared to the reference molecules suggesting a better alternate to the existing suite of inhibitors. Thus, this study will be a step ahead in the development of new potential compounds as antiviral drugs for the GT-3a target.

Physics-driven identification of clinically approved and investigation drugs against human neutrophil serine protease 4 (NSP4): A virtual drug repurposing study.

Neutrophils synthesize four immune associated serine proteases: Cathepsin G (CTSG), Elastase (ELANE), Proteinase 3 (PRTN3) and Neutrophil Serine Protease 4 (NSP4). While previously considered to be immune modulators, overexpression of neutrophil serine proteases correlates with various disease conditions. Therefore, identifying novel small molecules that can potentially control or inhibit the proteolytic activity of these proteases is crucial to revert or temper the aggravated disease phenotype. To the best of our knowledge, although there is limited data for inhibitors of other neutrophil protease members, there is no previous clinical study of a synthetic small molecule inhibitor targeting NSP4. In this study, an integrated molecular modeling algorithm was performed within a virtual drug repurposing study to identify novel inhibitors for NSP4, using clinically approved and investigation drugs library (∼8000 compounds). Based on our rigorous filtration, we found that following molecules Becatecarin, Iogulamide, Delprostenate and Iralukast are predicted to block the activity of NSP4 by interacting with core catalytic residues. The selected ligands were energetically more favorable compared to the reference molecule. The result of this study identifies promising molecules as potential lead candidates.

SARS-CoV-2 RNA Dependent RNA polymerase (RdRp) - A drug repurposing study.

The outbreak of SARS-CoV-2 in December 2019 in China subsequently lead to a pandemic. Lack of vaccine and specific anti-viral drugs started a global health disaster. For a sustained control and protection, development of potential anti-viral drugs is one of the targeted approach. Although, designing and developing a panel of new drugs molecules are always encouraged. However, in the current emergency, drug repurposing study is one of the most effective and fast track option. The crystal structure of a SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) RNA Dependent RNA Polymerase (RdRp) has recently been deciphered through X-ray crystallography. The single-chain of core RNA Dependent RNA Polymerase relies on virus-encoded cofactors nsp7 and two units of nsp8 for its optimum function. This study explored the FDA approved database of 7922 molecules and screened against the core polymerase along with cofactors. Here we report a panel of FDA approved drugs that show substantial interactions with key amino acid residues of the active site. Interestingly, some of the identified drugs (Ornipressin, Lypressin, Examorelin, Polymyxin B1) bind strongly within the binding pockets of both forms of RdRp. Besides, we found strong candidates for the complex form as well which include Nacortocin, Cistinexine, Cisatracurium (among others). These drugs have the potential to be considered while contriving therapeutic options.

Screening of FDA approved drugs for finding potential inhibitors against Granzyme B as a potent drug-repurposing target.

Granzyme B is one of the best-characterized and extensively studied member of cytotoxic lymphocytes (CL) proteases. Initially, it is thought to be involved in eliminating virally infected or cancerous cells by using a specialized mechanism through which they are internalized into target cells. In the last decade, however this dimension has changed as there are several reports show that not only CL but also other immune cells can also synthesize Granzyme B. This leads to the possibility of the presence of these proteases in extracellular environment. Being active protease, it then raises the possibility of damaging host tissues as evident from the available reported literature. In many instances, Granzyme B is directly involved in pathogenicity, however in others, it contributes to the disease severity as their over expression makes the clinical situation quite worse which ultimately leads to the chronic state of the disease. Serine protease inhibitor-9 is a natural known intracellular inhibitor of Granzyme B, however there is less data available about the potential inhibitors that can regulate its activity in an extracellular environment. Current study is an effort to identify potential novel inhibitors of Granzyme B. For this aim, drug repurposing study was performed. Around 7900 FDA approved drugs were screened using both ligand- and target-driven approaches. Initially, all molecules were docked using induced fit docking (IFD) approach and selected 318 high-docking scored molecules were used in short (1-ns) molecular dynamics (MD) simulations. Based on MM/GBSA binding free energy calculations, 6 compounds were selected and used in long (100-ns) MD simulations. These compounds were then used in binary QSAR analysis. Therapeutic activity potentials of studied compounds were investigated by Clarivate Analytics's MetaCore/MetaDrug platform which uses binary QSAR models. It is developed based on manually curated database of molecular interactions, molecular pathways, gene-disease associations, chemical metabolism and toxicity information. Results of selected compounds were compared with a positive control molecule. Current drug repurposing study is a step ahead in finding potential lead compounds by screening database of FDA approved molecules. We have identified novel inhibitors (Tannic acid, Mupirocin, Phytonadiol sodium diphosphate, Cefpiramide, Xenazoic acid) that have potential to decrease the activity of Granzyme B.

Effects of Cholesterol on GPCR Function: Insights from Computational and Experimental Studies.

The extensive experimental and computational evidences revealed that cholesterol is involved in the drug binding to G protein-coupled receptor (GPCR) targets that is influenced by the membrane environment and external functions. These multifunctional factors make the understanding of the molecular mechanism of action in greater detail an entirely difficult task. Significant efforts have been made for better understanding the role of multi-directional specific, receptor-dependent interactions of cholesterol, and its effects on drug design and development. Additional efforts must be made in this complex system in order to shed more light on cholesterol molecular basis of action. The results of molecular simulations that complemented experimental data may reveal new aspects of GPCR-cholesterol interactions and may provide a comprehensive understanding of receptor function.