COVID-19Base v3: Update of the knowledgebase for drugs and biomedical entities linked to COVID-19.

COVID-19 has taken a huge toll on our lives over the last 3 years. Global initiatives put forward by all stakeholders are still in place to combat this pandemic and help us learn lessons for future ones. While the vaccine rollout was not able to curb the spread of the disease for all strains, the research community is still trying to develop effective therapeutics for COVID-19. Although Paxlovid and remdesivir have been approved by the FDA against COVID-19, they are not free of side effects. Therefore, the search for a therapeutic solution with high efficacy continues in the research community. To support this effort, in this latest version (v3) of COVID-19Base, we have summarized the biomedical entities linked to COVID-19 that have been highlighted in the scientific literature after the vaccine rollout. Eight different topic-specific dictionaries, i.e., gene, miRNA, lncRNA, PDB entries, disease, alternative medicines registered under clinical trials, drugs, and the side effects of drugs, were used to build this knowledgebase. We have introduced a BLSTM-based deep-learning model to predict the drug-disease associations that outperforms the existing model for the same purpose proposed in the earlier version of COVID-19Base. For the very first time, we have incorporated disease-gene, disease-miRNA, disease-lncRNA, and drug-PDB associations covering the largest number of biomedical entities related to COVID-19. We have provided examples of and insights into different biomedical entities covered in COVID-19Base to support the research community by incorporating all of these entities under a single platform to provide evidence-based support from the literature. COVID-19Base v3 can be accessed from: https://covidbase-v3.vercel.app/. The GitHub repository for the source code and data dictionaries is available to the community from: https://github.com/91Abdullah/covidbasev3.0.

Machine learning based personalized drug response prediction for lung cancer patients.

Lung cancers with a mutated epidermal growth factor receptor (EGFR) are a major contributor to cancer fatalities globally. Targeted tyrosine kinase inhibitors (TKIs) have been developed against EGFR and show encouraging results for survival rate and quality of life. However, drug resistance may affect treatment plans and treatment efficacy may be lost after about a year. Predicting the response to EGFR-TKIs for EGFR-mutated lung cancer patients is a key research area. In this study, we propose a personalized drug response prediction model (PDRP), based on molecular dynamics simulations and machine learning, to predict the response of first generation FDA-approved small molecule EGFR-TKIs, Gefitinib/Erlotinib, in lung cancer patients. The patient's mutation status is taken into consideration in molecular dynamics (MD) simulation. Each patient's unique mutation status was modeled considering MD simulation to extract molecular-level geometric features. Moreover, additional clinical features were incorporated into machine learning model for drug response prediction. The complete feature set includes demographic and clinical information (DCI), geometrical properties of the drug-target binding site, and the binding free energy of the drug-target complex from the MD simulation. PDRP incorporates an XGBoost classifier, which achieves state-of-the-art performance with 97.5% accuracy, 93% recall, 96.5% precision, and 94% F1-score, for a 4-class drug response prediction task. We found that modeling the geometry of the binding pocket combined with binding free energy is a good predictor for drug response. However, we observed that clinical information had a little impact on the performance of the model. The proposed model could be tested on other types of cancers. We believe PDRP will support the planning of effective treatment regimes based on clinical-genomic information. The source code and related files are available on GitHub at:   https://github.com/rizwanqureshi123/PDRP/ .

Hepatitis C Vaccination: Where We Are and Where We Need to Be.

The hepatitis C virus (HCV) is a common cause of chronic liver disease and liver cancer worldwide. Despite advances in curative therapies for HCV, the incidence of new infections is not decreasing at the expected rate to hit the World Health Organization (WHO) target for the elimination of HCV by 2030. In fact, there are still more new cases of infection in the United States and worldwide than are being cured. The reasons for the rise in new cases include poor access to care and the opioid epidemic. The clinical burden of HCV requires a multimodal approach to eradicating the infection. Vaccination would be an excellent tool to prevent incidence of new infections; however, the genetic diversity of HCV and its ability to generate quasispecies within an infected host make creating a broadly reactive vaccine difficult. Multiple vaccine candidates have been identified, but to date, there has not been a target that has led to a broadly reactive vaccine, though several of the candidates are promising. Additionally, the virus is very difficult to culture and testing candidates in humans or chimpanzees is ethically challenging. Despite the multiple barriers to creating a vaccine, vaccination still represents an important tool in the fight against HCV.

Drugs in Development for Hepatitis B.

With high morbidity and mortality worldwide, there is great interest in effective therapies for chronic hepatitis B (CHB) virus. There are currently several dozen investigational agents being developed for treatment of CHB. They can be broadly divided into two categories: (1) direct-acting antivirals (DAAs) that interfere with a specific step in viral replication; and (2) host-targeting agents that inhibit viral replication by modifying host cell function, with the latter group further divided into the subcategories of immune modulators and agents that target other host functions. Included among the DAAs being developed are RNA interference therapies, covalently closed circular DNA (cccDNA) formation and transcription inhibitors, core/capsid inhibitors, reverse transcriptase inhibitors, hepatitis B surface antigen (HBsAg) release inhibitors, antisense oligonucleotides, and helioxanthin analogues. Included among the host-targeting agents are entry inhibitors, cyclophilin inhibitors, and multiple immunomodulatory agents, including Toll-like receptor agonists, immune checkpoint inhibitors, therapeutic vaccines, engineered T cells, and several cytokine agents, including recombinant human interleukin-7 (CYT107) and SB 9200, a novel therapy that is believed to both have direct antiviral properties and to induce endogenous interferon. In this review we discuss agents that are currently in the clinical stage of development for CHB treatment as well as strategies and agents currently at the evaluation and discovery phase and potential future targets. Effective approaches to CHB may require suppression of viral replication combined with one or more host-targeting agents. Some of the recent research advances have led to the hope that with such a combined approach we may have a functional cure for CHB in the not distant future.

Tenofovir alafenamide for the treatment of chronic hepatitis B virus infection.

INTRODUCTION: In April 2017 tenofovir alafenamide (TAF) was added to the list of first-line therapies recommended for chronic hepatitis B (CHB). TAF has pharmacology similar to tenofovir disoproxil fumarate (TDF) with higher cell delivery to the hepatocytes but less systemic exposure. Areas covered: We review here studies leading to TAF's approval and comparing it to TDF. In two major clinical trials, TAF was non-inferior to TDF in achieving HBV DNA levels below 29 IU/ml. TAF-treated patients had significantly smaller decreases in bone mineral density (BMD) at the hip and spine in both HBeAg-positive and HBeAg-negative patients, and smaller mean increases in serum creatinine, although the difference was only statistically significant in HBeAg-positive patients. Patients treated with TDF for 96 weeks and then switched to TAF had improvements in renal and BMD measures only 24 weeks after switching. Expert commentary: With clear evidence from major studies showing that TAF is safe, tolerable, and non-inferior to TDF, its recommendation as a first-line therapy is appropriate. Longer term follow up will be required to determine if the differences in adverse bone and kidney effects seen with TAF in comparison to TDF will be clinically relevant.

Portal vein thrombosis.

Portal vein thrombosis (PVT) is a rare event in the general medical setting that commonly complicates cirrhosis with portal hypertension, and can also occur with liver tumors. The diagnosis is often incidental when a thrombus is found in the portal vein on imaging tests. However, PVT may also present with clinical symptoms and can progress to life-threatening complications of ischemic hepatitis, liver failure, and/or small intestinal infarction. This article reviews the pathophysiology of this disorder, with a major focus on PVT in patients with cirrhosis, and presents detailed guidelines on optimal diagnostic and therapeutic strategies.

Reconstruction of Unstable Hips with Ilizarov Technique. Role of Pelvic Support and Distal Lengthening Realignment Osteotomy.

BACKGROUND: Hips can suffer severe damage due to untreated developmental dysplasia, septic arthritis, tuberculosis, a neglected fracture of the neck of femur and neglected hip dislocation. The Ilizarov technique offers an effective treatment by providing a stable hip with abolished Trendelenburg lurch and equalizing limb length discrepancy through distal lengthening realignment osteotomy. MATERIAL AND METHODS: 20 patients with hip instabilities due to various etiologies were treated with the Ilizarov technique of pelvic support osteotomy and distal lengthening realignment osteotomy. There were 12 females and 8 males in the study group and the age range was 13 to 30 years. Average limb length discrepancy was 5.95 cms (range 4-8.5 cms).The pre-operative and post-operative range of motion and Harris hip score was collected and data analyzed by Student's paired t test. A p value of < 0.05 was taken to be statistically significant Results. The functional Harris hip score improved in all the patients at final follow-up. The mean Harris hip score was 56.95 (range 33-71) pre-operatively, which improved to 83.25 (range 73-85) at final follow up and was statistically significant (P-value < 0.05). The mean length achieved was 5.53 cms (4-8 cms). The mean external fixation time was 8.6 months and the mean healing index was 1.54 months /cm. CONCLUSIONS: 1. Ilizarov hip reconstruction is an excellent method of salvage in patients with unstable hips diverse etiologies especially in this part of the world, where patients demand unrestricted range of motion at hip, and in the younger age group, where other procedures do not offer a long term solution. 2. It provides an excellent functional outcome in hips of different etiologies. 3. However, for an excellent outcome, surgical expertise, patient compliance and meticulous follow-up are mandatory.