Exploring the efficacy of ethnomedicinal plants of Himalayan region against the malaria parasite

ETHNOPHARMACOLOGICAL RELEVANCE

Plasmodium falciparum multi-drug resistant (MDR) strains are a great challenge to global health care. This predicament implies the urgent need to discover novel antimalarial drugs candidate from alternative natural sources. The Himalaya constitute a rich repository of medicinal plants which have been used traditionally in the folklore medicine since ages and having no scientific evidence for their activity. Crambe kotschyana Boiss. and Eremurus himalaicus Baker are used for their antipyretic and hepatoprotective properties in Kinnaur district of Himachal Pradesh, India.

AIM OF THE STUDY

This study would investigate the antiplasmodial efficacy of C. kotschyana and E. himalaicus extracts, their fractions and active components using in vitro, in vivo and in silico approaches to provide a scientific insight into their activity.

METHODS

The methanol extracts of C. kotschyana (CKME) and E. himalaicus (EHME) were prepared by maceration followed by fractionation using ethyl acetate. The isolation of flavonoid glycosides isorhamnetin-3, 7-di-O-glucoside from C. kotschyana and luteolin-6-C-glucoside (isoorientin) from E. himalaicus was carried out by antiplasmodial activity-guided isolation. In vitro antimalarial activity was assessed by WHO method while in vitro cytotoxicity was ascertained employing the MTT assay. Molecular docking and molecular dynamics simulation were performed using the Glide module of Schrödinger Software and Gromacs-2022 software package respectively. In vivo curative activity was assessed by Ryley and Peters method.

RESULTS

The methanol extracts of both the plants illustrated the best antiplasmodial activity followed by the ethyl acetate fractions. Iso-orientin (IC50 6.49 μg/ml) and Isorhamnetin-3,7-di-O-glucoside (IC50 9.22 μg/ml) illustrated considerable in vitro activity even against P. falciparum resistant strain. Extracts/fractions as well as the isolated compounds were found to be non-toxic with CC50 > 640 μg/ml. Molecular docking studies were performed with these 2 O-glucosides against four malaria targets to understand the binding pose of these molecules and the results suggested that these molecules have selectivity for lactate dehydrogenase enzyme. CKME and EHME exhibited curative activity in vivo along with increase in Mean Survival Time of mice.

CONCLUSION

The research delineated the scientific evidence that both the therapeutic herbs possessed antimalarial activity and notably, bioactive compounds responsible to exhibit the antimalarial activity have been isolated, identified and characterized. Further studies are underway to assess the antiplasmodial efficacy of isolated compounds alone and in combination with standard antimalarials.

Water network chemistry to exploit the nature of catalytic water molecules in Mtb DNA gyrase: a computational study to understand the binding mechanism of fluoroquinolones

The dynamics of DNA gyrase and mutants of DNA gyrA such as G88A, A90V, S91P, D94A, D94G, D94N, D94Y; and double-point mutant (S91P-D94G), are meticulously investigated using computational approaches. Molecular dynamics (MD) and hydration thermodynamics have shed light on the fundamental, mechanistic basis of mutations on the conformational stability of Quinolone Binding Pocket (QBP) of DNA gyrase. Analysis of MD results revealed the displacement of a single crystal water molecule (HOH201) from the catalytic site of wild-type (WT) and mutants of DNA gyrA. This prompted our research group to probe the five crystal water molecules present in the QBP of the enzyme using water thermodynamics. Hydration thermodynamics analysis revealed the displacement of HOH201 due to unstable thermodynamic signatures. Further, the analysis highlighted significant changes in thermodynamic signatures and locations of five crystal water hydration sites upon mutation. Integrated MD simulations and water thermodynamics provided promising insights into the conformational changes and inaccessibility of the catalytic water molecule that can influence the design of DNA gyrase inhibitors.Communicated by Ramaswamy H. Sarma.

An in silico study of protein-protein interactions and design of novel peptides for TrkA in ameloblastoma

Ameloblastoma is a benign odontogenic jawbone tumor. The binding of Nerve growth factor (NGF) to receptor tyrosine kinase A (TrkA) promotes cell survival, proliferation, and differentiation via PI3K/AKT and Ras/MAPK signaling. Although the exact cause of ameloblastoma remains unknown, elevated levels of NGF and TrkA expression in ameloblastoma are associated with aggressive tumor behavior and poor patient outcomes. It is previously demonstrated that His 4, Arg 9, and Glu 11 residues of NGF made crucial interactions with the TrkA subunit. The main aim of our present study to develop potential therapeutic strategies by identifying promising peptide candidates. The objectives include starting with a detailed in silico analysis to identify a crucial peptide sequence of NGF that is bound by TrkA, creating a library of novel peptides from the identified peptide sequence through a single-point mutation on interacting residues (His 4, Arg 9, and Glu 11), and selecting the top peptides based on docking score, interactions analysis, and desirable pose analysis. The study ultimately designed a hybrid peptide candidate through the simultaneous and continuous mutation of the top residues, resulting in a peptide that exhibited a more specific interaction with TrkA, blocking the binding site and preventing the interaction between NGF and TrkA.Communicated by Ramaswamy H. Sarma.

Breaking the 'don't eat me' signal: in silico design of CD47-directed peptides for cancer immunotherapy

The leading cause of death worldwide is cancer. Although there are various therapies available to treat cancer, finding a successful one can be like searching for a needle in a haystack. Immunotherapy appears to be one of those needles in the haystack of cancer treatment. Immunotherapeutic agents enhance the immune response of the patient's body to tumor cells. One of the immunotherapeutic targets, Cluster of Differentiation 47 (CD47), releases the "don't eat me" signal when it binds to its receptor, Signal Regulatory Protein (SIRPα). Tumor cells use this signal to circumvent the immune system, rendering it ineffective. To stop tumor cells from releasing the "don't eat me" signal, the CD47-SIRPα interaction is specifically targeted in this study. To do so, in silico peptides were designed based on the structural analysis of the interaction between two proteins using point mutations on the interacting residues with the other amino acids. The peptide library was designed and docked on SIRPα using computational tools. Later on, after analyzing the docked complex, the best of them was selected for MD simulation studies of 100 ns. Further analysis after MD studies was carried out to determine the possible potential anti-SIRPα peptides.

Identification of prospective covalent inhibitors for SARS-CoV-2 main protease using structure-based approach

The rapid global spread of SARS-CoV-2 has recently caused havoc and forced the world into a state of the pandemic causing respiratory, gastrointestinal, hepatic, and neurologic diseases. It persistently, through mutation, develops into new variants of the virus that have appeared over time. As main protease (Mpro) is involved in proteolysis of two overlapping polyproteins pp1a and pp1ab to produce 16 non-structural proteins having a paramount factor in the virus replication that have a cysteine-histidine catalytic dyad. A computational approach, guiding a covalent docking as it offers higher potency, long duration of action and decreased drug resistance advantages over the conventional docking of the ligands on a catalytic dyad, is applied for SARS-CoV-2 main protease (Mpro) in this manuscript to divulge better molecules. Mpro active site contains Cys145 residue which act as a nucleophile and can donate its electron to an electrophilic molecule by interacting covalently. Furthermore, the ligand-protein complexes are allowed to simulate their dynamic studies to look into their time-based interaction stability and also, a parallel study of ADME properties for the hit molecules is also performed. Important insights from the studies revealed that the interactions are persistent and molecules may be considered for further optimization in clinical investigation.Communicated by Ramaswamy H. Sarma.

Bifunctional robots inducing targeted protein degradation

The gaining importance of Targeted Protein Degradation (TPD) and PROTACs (PROteolysis-TArgeting Chimeras) have drawn the scientific community's attention. PROTACs are considered bifunctional robots owing to their avidity for the protein of interest (POI) and E3-ligase, which induce the ubiquitination of POI. These molecules are based on event-driven pharmacology and are applicable in different conditions such as oncology, antiviral, neurodegenerative disease, acne etc., offering tremendous scope to researchers. In this review, primarily, we attempted to compile the recent works available in the literature on PROTACs for various targeted proteins. We summarized the design and development strategies with a focus on molecular information of protein residues and linker design. Rationalization of the ternary complex formation using Artificial Intelligence including machine & deep learning models and traditionally followed computational tools are also included in this study. Moreover, details describing the optimization of PROTACs chemistry and pharmacokinetic properties are added. Advanced PROTAC designs and targeting complex proteins, is summed up to cover the wide spectrum.

Discovery and evaluation of biphenyl derivatives of 2-iminobenzimidazoles as prototype dual PTP1B inhibitors and AMPK activators with in vivo antidiabetic activity

This work describes the synthesis of series hydrobromides of N-(4-biphenyl)methyl-N'-dialkylaminoethyl-2-iminobenzimidazoles, which, due to the presence of two privileged structural fragments (benzimidazole and biphenyl moieties), can be considered as bi-privileged structures. Compound 7a proved to activate AMP-activated kinase (AMPK) and simultaneously inhibit protein tyrosine phosphatase 1B (PTP1B) with similar potency. This renders it an interesting prototype of potential antidiabetic agents with a dual-target mechanism of action. Using prove of concept in vivo study, we show that dual-targeting compound 7a has a disease-modifying effect in a rat model of type 2 diabetes mellitus via improving insulin sensitivity and lipid metabolism.

Emerging Therapies and Therapeutic Targets for Composite Liver Disease: NASH

BACKGROUND

Liver diseases continue to destroy the lives of people, one of which is known as Non-alcoholic Steatohepatitis (NASH) that becomes a serious liver disease all around the world over the last few years. Non-alcoholic Steatohepatitis (NASH) is a progressive form of Nonalcoholic Fatty Liver Disease (NAFLD) and is characterized by liver steatosis, inflammation, different degrees of fibrosis, and hepatocellular injury. The inflammatory mediators play a vital role in the transition of Non-alcoholic Fatty Liver (NAFL) to Non-alcoholic Steatohepatitis (NASH), which further leads to Hepatocellular Carcinoma (HCC) and becomes a cause of liver transplantation.

OBJECTIVES

Considering the severity and complexity of the disease, we aim to summarize the works of various research groups that are working in the area of NASH to find a sophisticated treatment.

RESULTS

The present review focused on various factors that are responsible for the development and progression of this prevalent disease, emerging pharmacotherapies as well as therapeutic targets that have been utilized for the treatment of NASH. We also have conducted the structural analysis of available targets, which will be helpful for the enhancement of drug discovery through the implementation of in silico methods.

CONCLUSION

Efforts have been made to provide an update on research in the area of NASH, including the pharmacological agents that are currently undergoing clinical trials for the treatment of NASH. Besides the massive research, still, gaps and challenges are there in the drug development for NASH that also have been discussed.

Protein degradation: a novel computational approach to design protein degrader probes for main protease of SARS-CoV-2

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has afflicted many lives and led to approvals of drugs and vaccines for emergency use. Even though vaccines have emerged, the high mortality of COVID-19 and its insurgent proliferation throughout the masses commands an innovative therapeutic proposition for the treatment. Targeted protein degradation has been applied to various disease domains and we propose that it could be incredibly beneficial to tackle the current pandemic. In this study, we have attempted to furnish insights on the design of suitable PROTACs for the main protease (M^pro) of SARS-CoV-2, a protein that is considered to be an essential target for viral replication. We have employed protein-protein docking to predict the possible complementarity between a cereblon E3 ligase and M^pro of SARS-CoV-2, and estimate possible linker length. Molecular Dynamic simulation and analysis on generated ternary complexes demonstrated stable interactions that suggested that designed PROTAC has a potential to cause degradation. The superior characteristics rendered by PROTACS led us to propose them as possibly the next-generation antiviral drugs for SARS-CoV-2.

Identification of Potential ACE2-Derived Peptide Mimetics in SARS-CoV-2 Omicron Variant Therapeutics using Computational Approaches

The COVID-19 pandemic has become a global health challenge because of the emergence of distinct variants. Omicron, a new variant, is recognized as a variant of concern (VOC) by the World Health Organization (WHO) because of its higher mutations and accelerated human infection. The infection rate is strongly dependent on the binding rate of the receptor binding domain (RBD) against human angiotensin converting enzyme-2 (ACE2human) receptor. Inhibition of protein-protein (RBDs(SARS-CoV-2/omicron)-ACE2human) interaction has been already proven to inhibit viral infection. We have systematically designed ACE2human-derived peptides and peptide mimetics that have high binding affinity toward RBDomicron. Our peptide mutational analysis indicated the influence of canonical amino acids on the peptide binding process. Herein, efforts have been made to explore the atomistic details and events of RBDs(SARS-CoV-2/omicron)-ACE2human interactions by using molecular dynamics simulation. Our studies pave a path for developing therapeutic peptidomimetics against omicron.

The Role of Water Network Chemistry in Proteins: A Structural Bioinformatics Perspective in Drug Discovery and Development

BACKGROUND

Although water is regarded as a simple molecule, its ability to create hydrogen bonds makes it a highly complex molecule that is crucial to molecular biology. Water molecules are extremely small and are made up of two different types of atoms, each of which plays a particular role in biological processes. Despite substantial research, understanding the hydration chemistry of protein-ligand complexes remains difficult. Researchers are working on harnessing water molecules to solve unsolved challenges as a result of the development of computer technologies.

OBJECTIVE

The goal of this review is to highlight the relevance of water molecules in protein environments, as well as to demonstrate how the lack of well-resolved crystal structures of proteins functions as a bottleneck in developing molecules that target critical therapeutic targets. In addition, the purpose of this article is to give a common platform for researchers to consider numerous aspects connected to water molecules.

CONCLUSION

Considering structure-based drug design, this review will make readers aware of the different aspects related to water molecules. It will provide an amalgamation of information related to the protein environment, linking the thermodynamic fingerprints of water with key therapeutic targets. The review has mentioned about a large number of computational tools available to study the water network chemistry with the surrounding protein enviornment. It also emphasises the need for computational methods in addressing gaps left by a poorly resolved crystallized protein structure.

Identification of potential SARS-CoV-2 Mpro inhibitors integrating molecular docking and water thermodynamics

The COVID-19 pandemic is an ongoing global health emergency caused by a newly discovered coronavirus SARS-CoV-2. The entire scientific community across the globe is working diligently to tackle this unprecedented challenge. In silico studies have played a crucial role in the current situation by expediting the process of identification of novel potential chemotypes targeting the viral receptors. In this study, we have made efforts to identify molecules that can potentially inhibit the SARS-CoV-2 main protease (Mpro) using the high-resolution crystal structure of SARS-CoV-2 Mpro. The SARS-CoV-2 Mpro has a large flexible binding pocket that can accommodate various chemically diverse ligands but a complete occupation of the binding cavity is necessary for efficient inhibition and stability. We augmented glide three-tier molecular docking protocol with water thermodynamics to screen molecules obtained from three different compound libraries. The diverse hits obtained through docking studies were scored against generated WaterMap to enrich the quality of results. Five molecules were selected from each compound library on the basis of scores and protein-ligand complementarity. Further MD simulations on the proposed molecules affirm the stability of these molecules in the complex. MM-GBSA results and intermolecular hydrogen bond analysis also confirm the thermodynamic stability of proposed molecules. This study also presumably steers the structure determination of many ligand-main protease complexes using x-ray diffraction methods.Communicated by Ramaswamy H. Sarma.

Molecular dynamic assisted investigation on impact of mutations in deazaflavin dependent nitroreductase against pretomanid: a computational study

In the past decade, TB drugs belonging to the nitroimidazole class, pretomanid and delamanid, have been authorised to treat MDR-TB and XDR-TB. With a novel inhibition mechanism and a reduction in the span of treatment, it is now being administered in various combinations. This approach is not the ultimate remedy since the target protein Deazaflavin dependent nitroreductase (Ddn) has a high mutation frequency, and already pretomanid resistant clinical isolates are reported in various studies. Ddn is essential for M.tuberculosis to emerge from hypoxia, and point mutations in critical residues confer resistance to Nitro-imidazoles. Among the pool of available mutants, we have selected seven mutants viz Ddn^L49P, Ddn^Y65S, Ddn^S78Y, Ddn^K79Q, Ddn^W88R, Ddn^Y133C, and Ddn^Y136S, all of which exhibited resistance to pretomanid. To address this issue, through computational study primarily by MD simulation, we attempted to elucidate these point mutations' impact and investigate the resistance mechanism. Hence, the Ddn^WT and mutant (MT) complexes were subjected to all-atom molecular dynamics (MD) simulations for 100 ns. Interestingly, we observed the escalation of the distance between cofactor and ligand in some mutants, along with a significant change in ligand conformation relative to the Ddn^WT. Moreover, we confirmed that mutations rendered ligand instability and were ejected from the binding pocket as a result. In conclusion, the results obtained provide a new structural insight and vital clues for designing novel inhibitors to combat nitroimidazole resistanceCommunicated by Ramaswamy H. Sarma.

A Multi-Perspective Review on Dengue Research

Dengue fever is a disease which is caused by a family of viruses named Flaviviridae which are transmitted by female Aedes mosquitoes. Today, this is endemic in more than 100 nations in the World Health Organization's African, Americas, Eastern Mediterranean, South-East Asia and Western Pacific locales. The treatment of typical dengue is focused on relieving the symptoms and signs. Carica papaya is a very common plant whose leaf extract is used in the treatment of this disease. Despite extensive research on Dengue, not a single vaccine or anti-viral drug was available until 2016 (a partially effective Chimeric Yellow fever virus treated by DENV-Tetravalent Dengue Vaccine for dengue fever made by Sanofi Pasteur). This review highlights dengue fever's current situation and explains the importance of Natural chemical moieties like methionine-proline anilides, tetrapeptide aldehyde uncovered via Structure Activity Relationship studies. Also, we have reviewed the drug candidates currently in the clinical trials that have the potential to solve these issues. Important patents in the past 20 years have been outlined in this review. An in depth Protein Data Bank analysis of the different possible target proteins that can potentially have a major role in curing Dengue fever has been conducted.

Screening and identification of potential PTP1B allosteric inhibitors using in silico and in vitro approaches

Protein tyrosine phosphatase 1B (PTP1B) is a validated therapeutic target for Type 2 diabetes due to its specific role as a negative regulator of insulin signaling pathways. Discovery of active site directed PTP1B inhibitors is very challenging due to highly conserved nature of the active site and multiple charge requirements of the ligands, which makes them non-selective and non-permeable. Identification of the PTP1B allosteric site has opened up new avenues for discovering potent and selective ligands for therapeutic intervention. Interactions made by potent allosteric inhibitor in the presence of PTP1B were studied using Molecular Dynamics (MD). Computationally optimized models were used to build separate pharmacophore models of PTP1B and TCPTP, respectively. Based on the nature of interactions the target residues offered, a receptor based pharmacophore was developed. The pharmacophore considering conformational flexibility of the residues was used for the development of pharmacophore hypothesis to identify potentially active inhibitors by screening large compound databases. Two pharmacophore were successively used in the virtual screening protocol to identify potential selective and permeable inhibitors of PTP1B. Allosteric inhibition mechanism of these molecules was established using molecular docking and MD methods. The geometrical criteria values confirmed their ability to stabilize PTP1B in an open conformation. 23 molecules that were identified as potential inhibitors were screened for PTP1B inhibitory activity. After screening, 10 molecules which have good permeability values were identified as potential inhibitors of PTP1B. This study confirms that selective and permeable inhibitors can be identified by targeting allosteric site of PTP1B.

Cell wall permeability assisted virtual screening to identify potential direct InhA inhibitors of Mycobacterium tuberculosis and their biological evaluation

The arising cases of isoniazid-resistance have motivated research interests toward new class of molecules known as direct InhA inhibitors. Here, a combine approach of shape-based pharmacophore and descriptor-based 2D QSAR was used to identify the potential direct InhA inhibitors. The approach is duly assisted with in vitro testing and molecular dynamics simulations. A combination of empirical parameters was derived to use as a filter for cell wall permeability while 2D QSAR was used as another filter to predict the biological activity. Both filters were applied to prioritize the molecules for biological evaluation against anti-TB activity. It led to 6 potential molecules which showed > 90% inhibition of H37Rv strain of Mycobacterium tuberculosis in BACTEC assay. Further, MMGBSA binding free energy of identified molecules was compared with available highly potent molecule, 5-hexyl-2-(2-methylphenoxy) phenol (IC₅₀ = 5nM) using molecular dynamics simulations. It showed two molecules with comparatively higher affinity toward InhA as compared to potent molecule. It indicated the candidature of identified molecules to be further considered in anti-TB drug development pipeline.

Molecular Dynamics Assisted Mechanistic Study of Isoniazid-Resistance against Mycobacterium tuberculosis InhA

Examination of InhA mutants I16T, I21V, I47T, S94A, and I95P showed that direct and water mediated H-bond interactions between NADH and binding site residues reduced drastically. It allowed conformational flexibility to NADH, particularly at the pyrophosphate region, leading to weakening of its binding at dinucleotide binding site. The highly scattered distribution of pyrophosphate dihedral angles and chi1 side chain dihedral angles of corresponding active site residues therein confirmed weak bonding between InhA and NADH. The average direct and water mediated bridged H-bond interactions between NADH and mutants were observed weaker as compared to wild type. Further, estimated NADH binding free energy in mutants supported the observed weakening of InhA-NADH interactions. Similarly, per residue contribution to NADH binding was also found little less as compared to corresponding residues in wild type. This investigation clearly depicted and supported the effect of mutations on NADH binding and can be accounted for isoniazid resistance as suggested by previous biochemical and mutagenic studies. Further, structural analysis of InhA provided the crucial points to enhance the NADH binding affinity towards InhA mutants in the presence of direct InhA inhibitors to combat isoniazid drug resistance. This combination could be a potential alternative for treatment of drug resistant tuberculosis.

Structural basis of conformational variance in phosphorylated and non-phosphorylated states of PKCβII

PKCβII activation is achieved by primary phosphorylation at three phosphorylation sites, followed by the addition of secondary messengers for full activation. Phosphorylation is essential for enzyme maturation, and the associated conformational changes are known to modulate the enzyme activation. To probe into the structural basis of conformational changes on phosphorylation of PKCβII, a comprehensive study of the changes in its complexes with ATP and ruboxistaurin was performed. ATP is a phosphorylating agent in its phosphorylation reaction, and ruboxistaurin is its specific inhibitor. This study provides insight into the differences in the important structural features in phosphorylated and non-phosphorylated states of PKCβII. Less conformational changes when PKCβII is bound to inhibitor in comparison to when it is bound to its phosphorylating agent in both states were observed. The interactions of ruboxistaurin significant in restricting PKCβII to attain the conformational state competent for full activation are reported.

2,5-Diaryl-1,3,4-oxadiazoles as selective COX-2 inhibitors and anti-inflammatory agents

A new series of compounds comprising of 2,5-diaryl-1,3,4-oxadiazoles was synthesized and evaluated as potential COX-2 inhibitors.

Essential gene identification and drug target prioritization in Leishmania species

Leishmaniasis is one of the neglected tropical diseases (NTDs), mainly affecting impoverished communities and having varied ranges of pathogenicity according to the diverse spectrum of clinical manifestations. It is endemic in many countries and poses major challenges to healthcare systems in developing countries. Despite the fact that most of the current mono and combination therapies are found to be failures, clear perception of gene essentiality for parasite survival are now desideratum to identify potential biochemical targets through selection. Here we used the metabolic network of L. major, to perform a comprehensive set of in silico deletion mutants and have systematically recognized a clearly defined set of essential proteins by combining several essential criteria. In this paper we summarize the efforts to prioritize potential drug targets up to a five-fold enrichment compared with a random selection.

Synthesis, biological evaluation and docking analysis of 3-methyl-1-phenylchromeno[4,3-c]pyrazol-4(1H)-ones as potential cyclooxygenase-2 (COX-2) inhibitors

As a part of our continued efforts to discover new COX inhibitors, a series of 3-methyl-1-phenylchromeno[4,3-c]pyrazol-4(1H)-ones were synthesized and evaluated for in vitro COX inhibitory potential. Within this series, seven compounds (3a-d, 3h, 3k and 3q) were identified as potential and selective COX-2 inhibitors (COX-2 IC50's in 1.79-4.35μM range; COX-2 selectivity index (SI)=6.8-16.7 range). Compound 3b emerged as most potent (COX-2 IC50=1.79μM; COX-1 IC50 >30μM) and selective COX-2 inhibitor (SI >16.7). Further, compound 3b displayed superior anti-inflammatory activity (59.86% inhibition of edema at 5h) in comparison to celecoxib (51.44% inhibition of edema at 5h) in carrageenan-induced rat paw edema assay. Structure-activity relationship studies suggested that N-phenyl ring substituted with p-CF3 substituent (3b, 3k and 3q) leads to more selective inhibition of COX-2. To corroborate obtained experimental biological data, molecular docking study was carried out which revealed that compound 3b showed stronger binding interaction with COX-2 as compared to COX-1.

Leishmania donovani eukaryotic initiation factor 5A: molecular characterization, localization and homology modelling studies

Eukaryotic translation initiation factor 5A (eIF5A) is a small acidic protein highly conserved from archaea to mammals. eIF5A is the only protein which undergoes a unique lysine residue modification to hypusine. Hypusinylation is important for the function of eIF5A which is reported to be essential for cell viability. eIF5A promotes formation of the first peptide bond at the onset of protein synthesis. However, its function in Leishmania donovani is unclear. The present study focuses on the characterization and localization of L. donovani eIF5A protein. The eIF5A gene contains an ORF of 501×bp encoding 166 amino acid residues with a predicted molecular mass and isoelectric point of 17.8 kDa and 4.83 respectively. A phylogenetic tree analysis revealed its close proximity to trypanosomes however it is distantly located from Trichomonas vaginalis and Plasmodium falciparum. The L. donovani eIF5A was expressed as a 6× His tagged protein whose identity was confirmed by western blot and MALDI. Biophysical investigation by CD revealed the predominant presence of 49% β sheet structure which correlated well with secondary structure prediction. To gain insight into the role of eIF5A in L. donovani, we investigated the subcellular distribution of eIF5A. A GFP-fusion of L. donovani eIF5A was found to be localized in cytoplasm as confirmed by subcellular fractionation. Our studies indicated that eIF5A is primarily localized to cytoplasm and is undetectable in nuclear fraction. The homology model of eIF5A of L. donovani was built and the resulting model showed acceptable Ramachandran statistics. The model is reliable and can be used to study eIF5A binding with its effector molecules.

Protein kinase C inhibitors: a patent review (2008 - 2009)

INTRODUCTION

The protein kinase C (PKC) is a family of multifunctional isoenzymes involved in apoptosis, migration, adhesion, tumorgenesis, cardiac hypertrophy, angiogenesis, platelet function and inflammation. It also plays a vital role in the regulation of signal transduction, cell proliferation and differentiation through positive and negative regulation of the cell cycle. In this work, we reviewed the existing PKC inhibitors and several patents linked to PKC inhibitors.

AREAS COVERED

Thorough survey on the PKC inhibitors having clinical importance and patents filed for these inhibitors from 2008 - 2009 is reported.

EXPERT OPINION

PKCs are highly potential therapeutic targets for treating diabetic complications, oncological, inflammatory, immunological and dermatological disorders. The clinical trial candidates of PKCs mainly target the catalytic domain, which is highly conserved throughout the PKC family making it difficult to target a particular isoform selectively. Relatively less chemical space and fewer bisubstrate inhibitors targeting both ATP and regulatory domain are explored for PKCs, more research in these areas will be helpful in overcoming existing problems.

Structure-based design and analysis of MAO-B inhibitors for Parkinson's disease: using in silico approaches

Parkinson's disease (PD) is a degenerative disorder of the CNS, characterized by cerebral depletion of dopamine (DA), hence one of the approaches to delay the depletion of DA is to inhibit its oxidative deamination. Monoamine oxidases (MAO) carry out the oxidative deamination of monoamines like DA. These are intracellular enzymes, located on the outer mitochondrial membrane. MAO-A and MAO-B are the two subtypes of which MAO-B is the most predominant enzyme and is commonly found in the brain. Inhibition of the MAO-B enzyme boosts the effect of both endogenous and exogenous DA. In this study, we have carried out crystal structure analysis and structure-based design of MAO-B inhibitors. We also performed molecular dynamics, flexible docking, induced-fit docking and ADME prediction of the newly designed compounds.

Structure prediction and molecular dynamics simulations of a G-protein coupled receptor: human CCR2 receptor

CC chemokine receptor type-2 (CCR2) is a member of G-protein coupled receptors superfamily, expressed on the cell surface of monocytes and macrophages. It binds to the monocyte chemoattractant protein-1, a CC chemokine, produced at the sites of inflammation and infection. A homology model of human CCR2 receptor based on the recently available C-X-C chemokine recepor-4 crystal structure has been reported. Ligand information was used as an essential element in the homology modeling process. Six known CCR2 antagonists were docked into the model using simple and induced fit docking procedure. Docked complexes were then subjected to visual inspection to check their suitability to explain the experimental data obtained from site directed mutagenesis and structure-activity relationship studies. The homology model was refined, validated, and assessed for its performance in docking-based virtual screening on a set of CCR2 antagonists and decoys. The docked complexes of CCR2 with the known antagonists, TAK779, a dual CCR2/CCR5 antagonist, and Teijin-comp1, a CCR2 specific antagonist were subjected to molecular dynamics (MD) simulations, which further validated the binding modes of these antagonists. B-factor analysis of 20 ns MD simulations demonstrated that Cys190 is helpful in providing structural rigidity to the extracellular loop (EL2). Residues important for CCR2 antagonism were recognized using free energy decomposition studies. The acidic residue Glu291 from TM7, a conserved residue in chemokine receptors, is favorable for the binding of Teijin-comp1 with CCR2 by ΔG of -11.4 kcal/mol. Its contribution arises more from the side chains than the backbone atoms. In addition, Tyr193 from EL2 contributes -0.9 kcal/mol towards the binding of the CCR2 specific antagonist with the receptor. Here, the homology modeling and subsequent molecular modeling studies proved successful in probing the structure of human CCR2 chemokine receptor for the structure-based virtual screening and predicting the binding modes of CCR2 antagonists.

Protein kinase C βII in diabetic complications: survey of structural, biological and computational studies

INTRODUCTION

PKC-βII is a conventional isoform of PKC. It is overexpressed in hyperglycemic conditions and is known to trigger various diabetic complications, mainly cardiovascular complications and to a certain extent nephropathy, neuropathy, retinopathy etc. Selective inhibition of this enzyme will be one of the favorable approaches to treat diabetes-mellitus-related complications. Due to high sequence similarities among PKC isoforms, selective inhibition of PKC-βII is difficult and yet to be achieved successfully.

AREAS COVERED

This review discusses the studies carried out in various aspects of PKC-βII. The biological aspects, crystal structure data, structure–activity relationship study (SAR) and in silico studies related to PKC-βII such as homology modeling, molecular docking, molecular dynamics, quantitative structure–activity relationship (QSAR) studies and pharmacophore modeling etc. are summarized.

EXPERT OPINION

PKC-βII is a potential target for treating diabetes-related complications. Selective inhibitors of this enzyme are under clinical trials but to date, success has not been achieved. Thus, extensive research is essential in this direction; the contribution of in silico tools in designing and optimizing selective inhibitors of PKC-βII is valuable.

Simplified receptor based pharmacophore approach to retrieve potent PTP-LAR inhibitors using apoenzyme

The design of biological active compounds from the apoenzyme is still a challenging task. Herein a simple yet efficient technique is reported to generate a receptor based pharmacophore solely using a ligand-free protein crystal structure. Human leukocyte antigen-related phosphatase (PTP-LAR) is an apoenzyme and a receptor like transmembrane phosphatase that has emerged as a drug target for diabetes, obesity and cancer. The prior knowledge of the active residues responsible for the mechanism of action of the protein was used to generate the LUDI interaction map. Then, the complement negative image of the binding site was used to generate the pharmacophore features. A unique strategy was followed to design a pharmacophore query maintaining crucial interactions with all the active residues, essential for the enzyme inhibition. The same query was used to screen several databases consisting of the Specs, IBS, MiniMaybridge, NCI and an in-house PTP inhibitor databases. In order to overcome the common bioavailability problem associated with phosphatases, the hits obtained were filtered by Lipinski's Rule of Five, SADMET properties and validated by docking studies in Glide and GOLD. These docking studies not only suggest the essential ligand binding interactions but also the binding patterns necessary for the LAR inhibition. The ligand pharmacophore mapping studies further validated the screened protocol and supported that the final screened molecules, presumably, showed potent inhibitory activity. Subsequently, these molecules were subjected to Derek toxicity predictions and nine new molecules with different scaffold were obtained as non-toxic PTP-LAR inhibitors. The present prospective strategy is a powerful technique to identify potent inhibitors using the protein 3D structure alone and is a valid alternative to other structure-based and random docking approaches.

Molecular dynamics directed CoMFA studies on carbocyclic neuraminidase inhibitors

Zanamivir is the known potent anti-influenza agent targeting the key enzyme neuraminidase that cleaves sialic acid from cell receptors allowing release of newly formed virions. Molecular dynamics simulation was carried out to determine the dynamic behavior of Zanamivir upon its binding to flexible loops of neuraminidase and to analyse its interactions in the bioactive state. Neuraminidase exhibits wide range of affinity with structurally similar compounds. CoMFA study was used to determine quantitative structure-activity relationship for 36 carbocyclic Neuraminidase inhibitors (NIs). The CoMFA model was also successfully built using cross-validated r²cv = 0.580 and r²pred = 0.638.

Novel insights into the structural requirements for the design of selective and specific aldose reductase inhibitors

Aldose reductase (ALR2) plays a vital role in the etiology of long-term diabetic microvascular complications (DMCs) such as retinopathy, nephropathy and neuropathy. It initializes the polyol pathway and under hyperglycemic conditions, catalyzes the conversion of glucose into sorbitol in the presence of NADPH. Many ALR2 inhibitors have been withdrawn from clinical trial studies due to their cross reactivity with other analogues enzymes or due to impairment with detoxification role of ALR2. To address these issues we characterized the possible rationalities behind the selectivity problem associated with the enzyme-inhibitor interactions. Novel molecules were designed for the induce fit cavity region of ALR2. Docking studies were carried out using Glide to analyze the binding affinity of the designed molecules for ALR2. The analysis showed that the designed ALR2 inhibitors are selective for ALR2 over its close analogs. These inhibitors are also specific for the induced cavity region of ALR2 and do not interfere with the detoxification role of ALR2.

Targeting PKC-β II and PKB Connection: Design of Dual Inhibitors

Protein kinase C (PKC) has been the center of many cell signaling pathways. PKC isoforms, specifically PKC-β II is linked to both diabetic complications as well as in promotion of angiogenesis and regulation of cancers. PKC-β II activates the PKB/Akt pathway. Enzastaurin, a selective PKC-β II inhibitor has been found to inhibit PKB/Akt by suppressing the regulation of various cancerous pathways. In the present work, we carried out an in depth study on the binding mode of inhibitors of PKC-β II, enzastaurin and ruboxistaurin with the active site residues of PKB and PKC-β II. A ligand based approach has been further used to determine the pharmacophoric features and spatial arrangement of molecules, having common properties necessary for appropriate binding to the active site of both targets. Virtual screening of the respective pharmacophores of both proteins led to identification of hits which may be useful for treatment of diabetic complications and cancer. The study has highlighted important features that may be considered in the future for designing novel inhibitors.

Targeting PKC-β II by Peptides and Peptidomimetics Derived from RACK 1: An In Silico Approach

Diabetes causes contractile myocardial dysfunction through accelerated atherosclerosis and hypertension, termed Diabetic Cardiomyopathy. Experimental results reveals liaison between cardiovascular disease and diabetic complications. Protein kinase C (PKC), a heterogeneous family of phospholipid dependent kinases was found to be specifically involved in diabetic complications, of which PKC-β II isoform played a significant role in induction of this fatal disease. Members of PKC family share high degree of similarity in both structure and functions, which has given rise to specificity related issues. In the present study, we have designed peptides and peptidomimetics based on RACK 1 (Receptor for Activated C Kinases) region, as this protein increases the substrate phosphorylation and stabilizes the activated form of PKC-β II. RACK 1 being specific for PKC-β II could resolve the specificity issue and also peptides and peptidomimetics, being conformationally restrained structures offers potential advantages of being used as drug molecules over organic molecules. This study has provided useful insights that may contribute to the development of molecules which may be useful in the treatment of diabetic complications.

Characterization of solid-state forms of mebendazole

This study deals with the generation and characterization of various solid-state forms of mebendazole (MBZ), a benzimidazole antihelmentic. The drug was subjected to polymorphic screen using different solvents to explore the possibility of existence of different solid forms. Different reported polymorphic forms of MBZ, i.e. form A, B and C were found to be recrystallized from acetic acid:methanol mixture (1:1), ethyl acetate and methanol, respectively. N,N-Dimethyl acetamide (DMA) and N,N-dimethyl formamide (DMF) yielded two new solvates of MBZ. These solid-state forms were characterized by thermoanalytical (DSC, TGA, HSM), crystallographic (XRD), microscopic (optical, polarized), and spectroscopic (FTIR) techniques. Solubility studies were carried out for the solvates to identify the solubility advantage. Molecular modeling studies revealed moderately strong hydrogen bonding between the solvent molecules and MBZ.