Exploring binding potential of two new indole alkaloids from Nauclea officinalis against third and fourth generation EGFR: druglikeness, in silico ADMET, docking, DFT, molecular dynamics simulation, and MMGBSA study.

This study investigates the anti-cancer potential of recently discovered indole alkaloids from Nauclea Officinalis against third and fourth-generation EGFR mutations using computational tools. Through ADMET profiling, druglikeness prediction, docking, and simulations, we assessed their pharmacokinetics, binding interactions, and stability. Promising druglikeness and binding affinity were observed, particularly for (±)-19-O-butylangustoline, which demonstrated stronger binding against both EGFR mutants. MD simulations confirmed stable interactions, with (±)-19-O-butylangustoline exhibiting the highest stability. These findings highlight these indole alkaloids as potential anti-cancer agents, with (±)-19-O-butylangustoline warranting further optimisation for therapeutic development. This study informs their potential through insights into molecular properties and binding energetics.

Therapeutic Delivery of Tumor Suppressor miRNAs for Breast Cancer Treatment.

The death rate from breast cancer (BC) has dropped due to early detection and sophisticated therapeutic options, yet drug resistance and relapse remain barriers to effective, systematic treatment. Multiple mechanisms underlying miRNAs appear crucial in practically every aspect of cancer progression, including carcinogenesis, metastasis, and drug resistance, as evidenced by the elucidation of drug resistance. Non-coding RNAs called microRNAs (miRNAs) attach to complementary messenger RNAs and degrade them to inhibit the expression and translation to proteins. Evidence suggests that miRNAs play a vital role in developing numerous diseases, including cancer. They affect genes critical for cellular differentiation, proliferation, apoptosis, and metabolism. Recently studies have demonstrated that miRNAs serve as valuable biomarkers for BC. The contrast in the expression of miRNAs in normal tissue cells and tumors suggest that miRNAs are involved in breast cancer. The important aspect behind cancer etiology is the deregulation of miRNAs that can specifically influence cellular physiology. The main objective of this review is to emphasize the role and therapeutic capacity of tumor suppressor miRNAs in BC and the advancement in the delivery system that can deliver miRNAs specifically to cancerous cells. Various approaches are used to deliver these miRNAs to the cancer cells with the help of carrier molecules, like nanoparticles, poly D, L-lactic-co-glycolic acid (PLGA) particles, PEI polymers, modified extracellular vesicles, dendrimers, and liposomes. Additionally, we discuss advanced strategies of TS miRNA delivery techniques such as viral delivery, self-assembled RNA-triple-helix hydrogel drug delivery systems, and hyaluronic acid/protamine sulfate inter-polyelectrolyte complexes. Subsequently, we discuss challenges and prospects on TS miRNA therapeutic delivery in BC management so that miRNAs will become a routine technique in developing individualized patient profiles.

Identification of Quorum Quenching N-Acyl Homoserine Lactonases from Priestia aryabhattai J1D and Bacillus cereus G Isolated from the Rhizosphere.

Several pathogenic bacteria communicate using N-acyl homoserine lactone (AHL) as a quorum sensing (QS) molecule. The process of interfering with the QS system is known as quorum quenching (QQ), it is an effective tool to control QS-dependent virulence in pathogens. In the present study, rhizosphere bacterial isolates were screened for their ability to produce AHL lactonase enzyme as QQ molecules, which hydrolyses AHL signalling molecules and consequently blocks the QS system. Potent N-hexanoyl-l-homoserine lactone (C6HSL) hydrolytic QQ activity was detected in rhizosphere isolates namely Bacillus cereus G and Priestia aryabhattai J1D. The cell-free supernatant of the bacterial isolates indicated a reduction in biofilm formation in the human pathogens Vibrio cholerae, Pseudomonas aeruginosa, and Staphylococcus aureus without inhibiting cells, signifying their biocontrol property. Furthermore, liquid chromatography high resolution mass spectrometry analysis confirmed C6HSL hydrolytic activity by AHL lactonase produced by these rhizosphere isolates. Also, the aiiA homologous gene from the bacterial isolates showed similarity with the aiiA lactonase gene from Bacillus species, which was further confirmed by homology modelling. In silico structure analysis by comparing with the structure of Bacillus revealed the similarity in the active site, indicating the same degradation pattern. Based on available reported data, the present study indicates the first report of the presence of the aiiA lactonase gene in P. aryabhattai.

The ratio versus difference optimization and its implications for optimality theory.

Among the classical models of optimization, some models maximize the ratio of returns to investment and others maximize the difference between returns and investment. However, an understanding of under what conditions the ratio or the difference approaches are appropriate is still fragmentary. Under specific contexts, it has been stated that when the investable amount, but not the opportunity for investment, is perceived to be limiting, a ratio optimum is appropriate, whereas a difference optimum is appropriate when the opportunity for investment, but not the investable amount, is perceived to be limiting. The question is important because the strategies indicated by ratio optimum can be substantially different than the ones suggested by difference optimum. We make a general case here to examine and expand this principle and apply it to many evolutionary ecological problems including parental investment, offspring quality-quantity trade-off, nectar production, pollinator behavior viral burst size, and intracellular protein handling. We show that the ratio-difference distinction in optimization models resolves many long-standing debates and conundrums in evolution and behavior.

Evaluating alternative hypotheses to explain the downward trend in the indices of the COVID-19 pandemic death rate.

BACKGROUND: In the ongoing Covid-19 pandemic, in the global data on the case fatality ratio (CFR) and other indices reflecting death rate, there is a consistent downward trend from mid-April to mid-November. The downward trend can be an illusion caused by biases and limitations of data or it could faithfully reflect a declining death rate. A variety of explanations for this trend are possible, but a systematic analysis of the testable predictions of the alternative hypotheses has not yet been attempted. METHODOLOGY: We state six testable alternative hypotheses, analyze their testable predictions using public domain data and evaluate their relative contributions to the downward trend. RESULTS: We show that a decline in the death rate is real; changing age structure of the infected population and evolution of the virus towards reduced virulence are the most supported hypotheses and together contribute to major part of the trend. The testable predictions from other explanations including altered testing efficiency, time lag, improved treatment protocols and herd immunity are not consistently supported, or do not appear to make a major contribution to this trend although they may influence some other patterns of the epidemic. CONCLUSION: The fatality of the infection showed a robust declining time trend between mid April to mid November. Changing age class of the infected and decreasing virulence of the pathogen were found to be the strongest contributors to the trend.

Molecular dynamics simulations and statistical coupling analysis of GPI12 in L. major: functional co-evolution and conservedness reveals potential drug-target sites.

GPI12 represents an important enzyme in the GPI biosynthetic pathway of several parasites like 'Leishmania'. GPI activity is generally regulated through either the hindrance in GPI complex assembly formation or the modulation of the lipophosphoglycan (LPG) flux to either reduce or enhance the pathogenicity in an organism. Of the various GPI molecules known, GPI12 is an important enzyme in the GPI biosynthetic pathway which can be exploited as a target due to the substrate specificity difference in parasites and humans. In the present study, the functional importance of the co-evolving residues of the GPI12 protein of Leishmania has been highlighted using the GPI proteins belonging to the GlcNAC-deacetylase family. Exploring the active site of the GPI12 protein and designing inhibitors against the functional residues provide ways and means to change the efficiency of deacetylation activity of the enzyme. The activity of de-N-acetylase is low in the absence of metal ions like zinc. Hence we designed eight small molecules in order to modulate the activity of GPI12. Compound 8 was found to be an appropriate choice to target the agonist (GPI12) active site thereby targeting the residues which were essential in the Zn binding and chelation activity. Inhibition of these sites offered a strong constraint to block the protein activity and in turn GPI biosynthesis.

Regulatory networks, genes and glycerophospholipid biosynthesis pathway in schistosomiasis: a systems biology view for pharmacological intervention.

Understanding network topology through embracing the global dynamical regulation of genes in an active state space rather than traditional one-gene-one trait approach facilitates the rational drug development process. Schistosomiasis, a neglected tropical disease, has glycerophospholipids as abundant molecules present on its surface. Lack of effective clinical solutions to treat pathogens encourages us to carry out systems-level studies that could contribute to the development of an effective therapy. Development of a strategy for identifying drug targets by combined genome-scale metabolic network and essentiality analyses through in silico approaches provides tantalizing opportunity to investigate the role of protein/substrate metabolism. A genome-scale metabolic network model reconstruction represents choline-phosphate cytidyltransferase as the rate limiting enzyme and regulates the rate of phosphatidylcholine (PC) biosynthesis. The uptake of choline was regulated by choline concentration, promoting the regulation of phosphocholine synthesis. In Schistosoma, the change in developmental stage could result from the availability of choline, hampering its developmental cycle. There are no structural reports for this protein. In order to inhibit the activity of choline-phosphate cytidyltransferase (CCT), it was modeled by homology modeling using 1COZ as the template from Bacillus subtilis. The transition-state stabilization and catalytic residues were mapped as 'HXGH' and 'RTEGISTT' motif. CCT catalyzes the formation of CDP-choline from phosphocholine in which nucleotidyltransferase adds CTP to phosphocholine. The presence of phosphocholine permits the parasite to survive in an immunologically hostile environment. This feature endeavors development of an inhibitor specific for cytidyltransferase in Schistosoma. Flavonolignans were used to inhibit this activity in which hydnowightin showed the highest affinity as compared to miltefosine.

Molecular evolution of the enzymes involved in the sphingolipid metabolism of Leishmania: selection pressure in relation to functional divergence and conservation.

BACKGROUND: Selection pressure governs the relative mutability and the conservedness of a protein across the protein family. Biomolecules (DNA, RNA and proteins) continuously evolve under the effect of evolutionary pressure that arises as a consequence of the host parasite interaction. IPCS (Inositol phosphorylceramide synthase), SPL (Sphingosine-1-P lyase) and SPT (Serine palmitoyl transferase) represent three important enzymes involved in the sphingolipid metabolism of Leishmania. These enzymes are responsible for maintaining the viability and infectivity of the parasite and have been classified as druggable targets in the parasite metabolome. RESULTS: The present work relates to the role of selection pressure deciding functional conservedness and divergence of the drug targets. IPCS and SPL protein families appear to diverge from the SPT family. The three protein families were largely under the influence of purifying selection and were moderately conserved baring two residues in the IPCS protein which were under the influence of positive selection. To further explore the selection pressure at the codon level, codon usage bias indices were calculated to analyze genes for their synonymous codon usage pattern. IPCS gene exhibited slightly lower codon bias as compared to SPL and SPT protein families. CONCLUSION: Evolutionary tracing of the proposed drug targets has been done with a viewpoint that the amino-acids lining the drug binding pocket should have a lower evolvability. Sites under positive selection (HIS20 and CYS30 of IPCS) should be avoided during devising strategies for inhibitor design.

Molecular modeling and molecular dynamics simulations of GPI 14 in Leishmania major: insight into the catalytic site for active site directed drug design.

Leishmania major causes cutaneous form of Leishmaniasis affecting 21 million people in developing countries. Overuse of the chemotherapeutics against leishmaniasis has resulted in the development of drug resistance in the parasite. To surmount this emerging threat we have attempted to target the surface molecules. Glycosylphosphatidylinositol is one such molecule that is present abundantly and thus our work revolves around the enzyme mannosyltransferase (GPI 14), an enzyme essential to add mannose on the glycosylphosphatidyl. It has been targeted for drug discovery on account of growing resistance to miltefosine in L. major. This paper serves as the first attempt to detect GPI 14 gene in L. major supported with modeling and molecular dynamic analysis of complete three dimensional structure of GPI 14. The functional analysis revealed multiple transmembrane regions in GPI 14 and a close phylogenetic relation with Trypanosoma species and Schistosoma mansoni with highest bootstrap values. The protein model obtained was subjected to minimization for 14ns simulation. Eight derivatives of N-4-(-5(trifluromethyl)-1-methyl-1H benzo[d]imidazole-2 yl) phenyl) were docked onto GPI 14. The contact frequency of GPI 14 with the docked compounds suggested the inhibition of mannosylation proposing the druggability for leishmaniasis therapy.

Synthetic circuit of inositol phosphorylceramide synthase in Leishmania : a chemical biology approach.

Building circuits and studying their behavior in cells is a major goal of systems and synthetic biology. Synthetic biology enables the precise control of cellular states for systems studies, the discovery of novel parts, control strategies, and interactions for the design of robust synthetic systems. To the best of our knowledge, there are no literature reports for the synthetic circuit construction for protozoan parasites. This paper describes the construction of genetic circuit for the targeted enzyme inositol phosphorylceramide synthase belonging to the protozoan parasite Leishmania. To explore the dynamic nature of the circuit designed, simulation was done followed by circuit validation by qualitative and quantitative approaches. The genetic circuit designed for inositol phosphorylceramide synthase (Biomodels Database-MODEL1208030000) shows responsiveness, oscillatory and bistable behavior, together with intrinsic robustness.

Biological network modeling identifies IPCS in Leishmania as a therapeutic target.

Systems biology aims to develop mathematical models of biological systems by integrating experimental and theoretical techniques by leveraging on the genome wide data to unravel the complexity of gene regulation. Despite the availability of effective chemotherapy, leishmaniasis continues to be one of the major parasitic infections that affect the human population worldwide. Currently, little is known of the structural biology of the parasites that are responsible for the disease and few attempts have been made to develop second generation drugs, which may become essential if multi-drug resistance arises. These facts make the discovery of novel drug targets a priority. Multiscale modeling and simulation techniques permit us to study the spatial and temporal properties of large systems to be simulated using atomic-detail structures. The estimation of kinetic parameters for the mathematical modeling provides a basis for iterative manipulation of biochemical pathways. In this paper, emphasis is laid on the discrete regulation of gene or protein expression as modeling can be done based on pure qualitative knowledge about interaction between genes or proteins that is widely available from the existing experimental methodologies. IPC synthase is one of them, believed to play a pivotal role in the pathogenesis of Leishmania sp. and resides in an acidic macrophage phagolysosome, defining a new class of eukaryotic sphingolipid synthases. This work will facilitate the rational development of inhibitors against a protozoan enzyme with no mammalian equivalent, leading to the prospect of anti-protozoal compounds with minimal toxic side effects. Henceforth, it can be said that exploiting the interactome for novel human drug targets could provide new therapeutic avenues towards the treatment of infectious diseases, which could ameliorate the growing clinical challenge of drug-resistant infections.