Nigelladine A among Selected Compounds from Nigella sativa Exhibits Propitious Interaction with Omicron Variant of SARS-CoV-2: An In Silico Study.

COVID-19 has been a threat to the entire world for more than two years since its outbreak in December 2019 in Wuhan city of China. SARS-CoV-2, the causative agent, had been reported to mutate over time exposing new variants. To date, no impeccable cure for the disease has been unveiled. This study outlines an extensive in silico approach to scrutinize certain phytochemical compounds of Nigella sativa (mainly the black cumin seeds) targeting the spike protein and the main protease (Mpro) enzyme of the Omicron variant of SARS-CoV-2. The objective of this study is to investigate the extracted compounds with a view to developing a potential inhibitor against the concerned SARS-CoV-2 variant. The investigation contemplates drug-likeness analysis, molecular docking study, ADME and toxicity prediction, and molecular dynamics simulation which have been executed to elucidate different phytochemical and pharmacological properties of the tested compounds. Based on drug-likeness parameters, a total of 96 phytochemical compounds from N. sativa have been screened in the study. Interestingly, Nigelladine A among the compounds exhibited the highest docking score with both the targets with the same binding affinity which is -7.8 kcal/mol. However, dithymoquinone, kaempferol, Nigelladine B, Nigellidine, and Nigellidine sulphate showed mentionable docking scores. Molecular dynamics up to 100 nanoseconds were simulated under GROMOS96 43a1 force field for the protein-ligand complexes exhibiting the top-docking score. The root mean square deviations (RMSD), root mean square fluctuations (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), and the number of hydrogen bonds have been evaluated during the simulation. From the findings, the present study suggests that Nigelladine A showed the most promising results among the selected molecules. This framework, however, interprets only a group of computational analyses on selected phytochemicals. Further investigations are required to validate the compound as a promising drug against the selected variant of SARS-CoV-2.

Estimating Catastrophic Costs due to Pulmonary Tuberculosis in Bangladesh.

To eliminate TB from the country by the year 2030, the Bangladesh National Tuberculosis (TB) Program is providing free treatment to the TB patients since 1993. However, the patients are still to make Out-of-their Pocket (OOP) payment, particularly before their enrollment Directly Observed Treatment Short-course (DOTS). This places a significant economic burden on poor-households. We, therefore, aimed to estimate the Catastrophic Health Expenditure (CHE) due to TB as well as understand associated difficulties faced by the families when a productive family member age (15-55) suffers from TB. The majority of the OOP expenditures occur before enrolling in. We conducted a cross-sectional study using multistage sampling in the areas of Bangladesh where Building Resources Across Communities (BRAC) provided TB treatment during June 2016. In total, 900 new TB patients, aged 15-55 years, were randomly selected from a list collected from BRAC program. CHE was defined as the OOP payments that exceeded 10% of total consumption expenditure of the family and 40% of total non-food expenditure/capacity-to-pay. Regular and Bayesian simulation techniques with 10,000 replications of re-sampling with replacement were used to examine robustness of the study findings. We also used linear regression and logit model to identify the drivers of OOP payments and CHE, respectively. The average total cost-of-illness per patient was 124 US$, of which 68% was indirect cost. The average CHE was 4.3% of the total consumption and 3.1% of non-food expenditure among the surveyed households. The poorest quintile of the households experienced higher CHE than their richest counterpart, 5% vs. 1%. Multiple regression model showed that the risk of CHE increased among male patients with smear-negative TB and delayed enrolling in the DOTS. Findings suggested that specific groups are more vulnerable to CHE who needs to be brought under innovative safety-net schemes.

What Constitutes Health Care Seeking Pathway of TB Patients: A Qualitative Study in Rural Bangladesh.

Given the targeted 4-5% annual reduction of tuberculosis (TB) cure cases to reach the "End TB Strategy" by 2020 milestone globally set by WHO, exploration of TB health seeking behavior is warranted for insightful understanding. This qualitative study aims to provide an account of the social, cultural, and socioeconomic breadth of TB cases in Bangladesh. We carried out a total of 32 In-depth Interviews (IDIs) and 16 Key Informant Interviews (KIIs) in both rural and urban areas of Bangladesh. We covered both BRAC [a multinational Non-governmental Organization (NGO)] and non-BRAC (other NGOs) TB program coverage areas to get an insight. We used purposive sampling strategy and initially followed "snowball sampling technique" to identify TB patients. Neuman's three-phase coding system was adopted to analyze the qualitative data. Underestimation of TB knowledge and lack of awareness among the TB patients along with the opinions from their family members played key roles on their TB health seeking behavior. Quick decision on the treatment issue was observed once the diagnosis was confirmed; however, difficulties were in accepting the diseases. Nevertheless, individual beliefs, intrinsic ideologies, financial abilities, and cultural and social beliefs on TB were closely inter-connected with the "social perception" of TB that eventually influenced the care seeking pathways of TB patients in various ways. Individual and community level public health interventions could increase early diagnosis; therefore, reduce recurrent TB.

Informal allopathic provider knowledge and practice regarding control and prevention of TB in rural Bangladesh.

BACKGROUND: BRAC (formerly Bangladesh Rural Advancement Committee), in collaboration with the National Tuberculosis Control Programme, provides one full-day training on TB to make informal allopathic providers knowledgeable for managing TB in rural Bangladesh. This study explored the knowledge and practices of the providers receiving the above training in the control and prevention of TB. METHODS: The study was conducted in 30 subdistricts, with 30 trained and 30 untrained providers randomly selected from each subdistrict. Approximately 3% (49/1800) did not provide complete information. Pre-tested structured and semi-structured questionnaires were used. RESULTS: TB was commonly perceived as a disease of only males (66.1%, 1157/1751). Only one-quarter knew about the bacterial cause of TB. Very few providers (2.1%, 36) had adequate knowledge regarding prevention of TB. They also lacked knowledge about TB treatment duration (71.6%, 1253), the meaning of DOTS (directly observed treatment, short course) (26.0%, 455) and multidrug resistance (20.6%, 360). Antibiotics (79.7%, 1396) and cough syrup (75.0%, 1313) were commonly prescribed by providers despite symptoms suggestive of TB. However, 70.2% (613) and 74.5% (650) of trained providers' knowledge and practice scores were equal to or more than the mean scores (≥6.97 and ≥6.6, respectively), whereas they were only 49.5% (435) and 64.2% (563), respectively, among untrained providers (p<0.0001). CONCLUSIONS: Misperception, lack of knowledge and irrational use of antibiotics are challenges that need to be addressed for controlling and preventing TB efficiently.

A program impact pathway analysis identifies critical steps in the implementation and utilization of a behavior change communication intervention promoting infant and child feeding practices in Bangladesh.

Mapping pathways of how interventions are implemented and utilized enables contextually grounded interpretation of results, differentiates poor design from poor implementation, and identifies factors that might influence the utilization of interventions. Few studies in nutrition have comprehensively examined the steps of implementation and utilization in behavior change communication (BCC) interventions, thus limiting the interpretation of variable impacts of BCC interventions. A program impact pathway (PIP) analysis was used to study a BCC intervention implemented in Bangladesh to improve infant and young child feeding (IYCF) practices. The PIP was developed through an iterative process with the program implementation team; the PIP then guided the choice of methods and tools. Using mixed methods, we reviewed the content of training materials for implementation staff, measured their IYCF knowledge (n = 100), observed their communication with mothers (n = 37), and examined factors influencing promotion of IYCF practices and their trial and adoption by mothers (n = 64). Implementation staff demonstrated good knowledge and maintained fidelity to the intervention to a large extent. Mothers identified them as their primary sources of information, and a majority of mothers tried recommended IYCF practices. Key facilitators included family support and availability of resources, whereas lack of time, maternal and family perceptions of age-appropriate feeding, and lack of resources were salient barriers to adopting recommended practices. Using a PIP analysis identified critical issues pertaining to implementation (e.g., the role of paid and volunteer staff) and utilization (e.g., resource and time constraints that require complementary interventions) and the need for further research and programmatic attention.

Tribal formulations for treatment of pain: a study of the Bede community traditional medicinal practitioners of Porabari Village in Dhaka District, Bangladesh.

The Bedes form one of the largest tribal or indigenous communities in Bangladesh and are popularly known as the boat people or water gypsies because of their preference for living in boats. They travel almost throughout the whole year by boats on the numerous waterways of Bangladesh and earn their livelihood by selling sundry items, performing jugglery acts, catching snakes, and treating village people by the various riversides with their traditional medicinal formulations. Life is hard for the community, and both men and women toil day long. As a result of their strenuous lifestyle, they suffer from various types of pain, and have developed an assortment of formulations for treatment of pain in different parts of the body. Pain is the most common reason for physician consultation in all parts of the world including Bangladesh. Although a number of drugs are available to treat pain, including non-steroidal, steroidal, and narcotic drugs, such drugs usually have side-effects like causing bleeding in the stomach over prolonged use (as in the case of rheumatic pain), or can be addictive. Moreover, pain arising from causes like rheumatism has no proper treatment in allopathic medicine. It was the objective of the present study to document the formulations used by the Bede traditional practitioners for pain treatment, for they claim to have used these formulations over centuries with success. Surveys were conducted among a large Bede community, who reside in boats on the Bangshi River by Porabari village of Savar area in Dhaka district of Bangladesh. Interviews of 30 traditional practitioners were conducted with the help of a semi-structured questionnaire and the guided field-walk method. It was observed that the Bede practitioners used 53 formulations for treatment of various types of pain, the main ingredient of all formulations being medicinal plants. Out of the 53 formulations, 25 were for treatment of rheumatic pain, either exclusively, or along with other types of body pain. A total of 65 plants belonging to 39 families were used in the formulations. The Fabaceae family provided 7 plants followed by the Solanaceae family with 4 plants. 47 out of the 53 formulations were used topically, 5 formulations were orally administered, and 1 formulation had both topical and oral uses. 8 formulations for treatment of rheumatic pain contained Calotropis gigantea, suggesting that the plant has strong potential for further scientific studies leading to discovery of novel efficacious compounds for rheumatic pain treatment.

Discovery of a novel series of nonacidic benzofuran EP1 receptor antagonists.

We describe the discovery and optimization of a novel series of benzofuran EP(1) antagonists, leading to the identification of 26d, a novel nonacidic EP(1) antagonist which demonstrated efficacy in preclinical models of chronic inflammatory pain.

Discovery of sodium 6-[(5-chloro-2-{[(4-chloro-2-fluorophenyl)methyl]oxy}phenyl)methyl]-2-pyridinecarboxylate (GSK269984A) an EP(1) receptor antagonist for the treatment of inflammatory pain.

We describe the medicinal chemistry programme that led to the identification of the EP(1) receptor antagonist GSK269984A (8h). GSK269984A was designed to overcome development issues encountered with previous EP(1) antagonists such as GW848687X and was found to display excellent activity in preclinical models of inflammatory pain. However, upon cross species pharmacokinetic profiling, GSK269984A was predicted to have suboptimal human pharmacokinetic and was thus progressed to a human microdose study.

Discovery of brain penetrant, soluble, pyrazole amide EP1 receptor antagonists.

We describe the discovery of a series of pyrazole amide EP(1) receptor antagonists with good aqueous solubility and CNS penetration. In order to achieve solubility we investigated the incorporation of a basic group in the region of the molecule previously occupied by a carboxylic acid, which was known to be a key element of the pharmacophore. This study led to the identification of compounds such as 4h, 4j and 10b which demonstrated brain-to-blood ratios of 0.8:1-2.0:1 in addition to good solubility and metabolic stability.

Non-acidic pyrazole EP1 receptor antagonists with in vivo analgesic efficacy.

Replacement of the carboxylic acid group in a series of previously described methylene-linked pyrazole EP(1) receptor antagonists led to the discovery of amide, reversed amide and carbamate derivatives. Two compounds, 10a and 10b, were identified as brain penetrant compounds and both demonstrated efficacy in the CFA model of inflammatory pain.

Discovery of a novel indole series of EP1 receptor antagonists by scaffold hopping.

We describe the medicinal chemistry approach that generated a novel indole series of EP(1) receptor antagonists. The SAR of this new template was evaluated and culminated in the identification of compound 12g which demonstrated in vivo efficacy in a preclinical model of inflammatory pain.

Novel methylene-linked heterocyclic EP1 receptor antagonists.

We describe the SAR, in terms of heterocyclic replacements, for a series of pyrazole EP(1) receptor antagonists. This study led to the identification of several aromatic heterocyclic replacements for the pyrazole in the original compound. Investigation of replacements for the methylene linker uncovered disparate SAR in the thiazole and pyridine series.

Identification and optimization of novel 1,3,4-oxadiazole EP1 receptor antagonists.

A novel series of oxadiazole EP1 receptor antagonists was identified by replacing the amide of a known glycine sulfonamide derivative with a 1,3,4-oxadiazole. Optimization of the substitution patterns on the three aromatic rings led to the identification of high affinity EP1 receptor antagonists. The derivative with highest affinity displayed a binding IC50 of 2.5 nM (pIC50 8.6).

Discovery of novel, non-acidic 1,5-biaryl pyrrole EP1 receptor antagonists.

Replacement of the carboxylic acid group in a series of previously described 1,5-biaryl pyrrole EP1 receptor antagonists led to the discovery of various novel non-acidic antagonists. Several analogues displayed high binding affinity and high binding efficiency indices.

Identification of novel glycine sulfonamide antagonists for the EP1 receptor.

A high-throughput screen targeting the EP(1) receptor identified non-acidic glycine sulfonamide derivative 2a with a pK(i) of 6.2. Analogue synthesis allowed a thorough investigation of the structure-activity relationship (SAR) and led to a 100-fold increase in recombinant potency.

1,5-Biaryl pyrrole derivatives as EP1 receptor antagonists: Structure-activity relationships of 4- and 5-substituted benzoic acid derivatives.

This paper details the SAR of 1,5-biaryl pyrrole derivatives with substituents in the 2-, 4-, and 5-positions of the benzoic acid group as EP1 receptor antagonists. Substitution at the 2-position was poorly tolerated, whereas only fluorine was tolerated at the 4-position. In contrast, a range of substituents at the 5-position were discovered which enhanced the in vitro affinity and led to compounds with promising oral exposure. Three derivatives showed efficacy in a preclinical model of inflammatory pain when dosed orally to rats.

The discovery of 6-[2-(5-chloro-2-{[(2,4-difluorophenyl)methyl]oxy}phenyl)-1-cyclopenten-1-yl]-2-pyridinecarboxylic acid, GW848687X, a potent and selective prostaglandin EP1 receptor antagonist for the treatment of inflammatory pain.

The discovery of a series of selective EP1 receptor antagonists based on a 1,2-diarylcyclopentene template is described. After defining the structural requirements for EP1 potency and selectivity, heterocyclic rings were incorporated to reduce logD and improve in vitro pharmacokinetic properties. The 2,6-substituted pyridines and pyridazines gave an appropriate balance of potency, in vivo pharmacokinetic properties and a low potential for inhibiting a range of CYP450 enzymes. From this series, GW848687X was shown to have an excellent profile in models of inflammatory pain and was selected as a development candidate.

1,5-Biaryl pyrrole derivatives as EP1 receptor antagonists. Structure-activity relationships of 6-substituted and 5,6-disubstituted benzoic acid derivatives.

Herein we describe the SAR of 1,5-biaryl pyrrole derivatives, with substituents in the 6-position of the benzoic acid moiety, as EP(1) receptor antagonists. Substitution at this position was well tolerated and led to the identification of several analogues with high affinity for the EP(1) receptor that displayed good efficacy in the established FCA model of inflammatory pain. Furthermore, several analogues were prepared which combined substitution at the 5- and 6-positions as well as derivatives with an aromatic ring fused to the 5- and 6-positions.

Identification of novel pyrazole acid antagonists for the EP1 receptor.

The discovery, synthesis and structure-activity relationship (SAR) of a novel series of EP1 receptor antagonists is described. Pyrazole acid 4, identified from a chemical array, had desirable physicochemical properties, an excellent in vitro microsomal inhibition and cytochrome P450 (CYP450) profile and good exposure levels in blood. This compound had an ED50 of 1.3 mg/kg in a rat pain model. A range of more potent analogues in the in vitro assay was identified using efficient array chemistry. These EP1 antagonists have potential as agents in the treatment of PGE2 mediated pain.

Structure-activity relationships of 1,5-biaryl pyrroles as EP1 receptor antagonists.

The preliminary SAR of a series of novel 1,5-biaryl pyrrole EP1 receptor antagonists derived from compound 1 is described. Replacement of the benzyl group of 1 with isosteric groups was investigated. The most effective replacement was found to be the isobutyl group. The cyclopentylmethyl and cyclohexylmethyl groups were also effective benzyl replacements. The cyclohexylmethyl derivative 19 demonstrated the lowest metabolic clearance within this series. In addition, several high affinity substituted benzyl analogues were also identified. Compound 39 was found to have good bioavailability in rats and demonstrated efficacy in the established FCA preclinical model of inflammatory pain with a calculated ED50 of 9.2mg/kg.