Therapeutic Path to Triple Knockout: Investigating the Pan-inhibitory Mechanisms of AKT, CDK9, and TNKS2 by a novel 2-Phenylquinazolinone derivative in Cancer Therapy- An In-Silico Investigation.

BACKGROUND: Blocking the oncogenic Wnt//ß-catenin pathway has of late been investigated as a viable therapeutic approach in the treatment of cancer. This involves the multi-targeting of certain members of the tankyrase-kinase family; tankyrase 2 (TNKS2), protein kinase B (AKT), and cyclin-dependent kinase 9 (CDK9), which propagate the oncogenic Wnt/ß-catenin signalling pathway. METHODS: During a recent investigation, the pharmacological activity of 2-(4-aminophenyl)-7-chloro-3H-quinazolin-4-one was repurposed to serve as a 'triple-target' inhibitor of TNKS2, AKT and CDK9. Yet, the molecular mechanism that surrounds its multi-targeting activity remains unanswered. As such, this study aims to explore the pan-inhibitory mechanism of 2-(4-aminophenyl)-7-chloro-3H-quinazolin-4-one towards AKT, CDK9, and TNKS2, using in silico techniques. RESULTS: Results revealed favourable binding affinities of -34.17 kcal/mol, -28.74 kcal/mol, and -27.30 kcal/mol for 2-(4-aminophenyl)-7-chloro-3H-quinazolin-4-one towards TNKS2, CDK9, and AKT, respectively. Pan-inhibitory binding of 2-(4-aminophenyl)-7-chloro-3H-quinazolin-4-one is illustrated by close interaction with specific residues on tankyrase-kinase. Structurally, 2-(4-aminophenyl)-7-chloro-3H-quinazolin-4-one had an impact on the flexibility, solvent-accessible surface area, and stability of all three proteins, which was illustrated by numerous modifications observed in the unbound as well as the bound states of the structures, which evidenced the disruption of their biological function. Prediction of the pharmacokinetics and physicochemical properties of 2-(4-aminophenyl)-7-chloro-3H-quinazolin-4-one further established its inhibitory potential, evidenced by the favourable absorption, metabolism, excretion, and minimal toxicity properties. CONCLUSION: The following structural insights provide a starting point for understanding the pan-inhibitory activity of 2-(4-aminophenyl)-7-chloro-3H-quinazolin-4-one. Determining the criticality of the interactions that exist between the pyrimidine ring and catalytic residues could offer insight into the structure-based design of innovative tankyrase-kinase inhibitors with enhanced therapeutic effects.

Multi-dimensional structural footprint identification for the design of potential scaffolds targeting METTL3 in cancer treatment from natural compounds.

CONTEXT: [Formula: see text]-adenosine-methyltransferase (METTL3) is the catalytic domain of the 'writer' proteins which is involved in the post modifications of [Formula: see text]-methyladinosine ([Formula: see text]). Though its activities are essential in many biological processes, it has been implicated in several types of cancer. Thus, drug developers and researchers are relentlessly in search of small molecule inhibitors that can ameliorate the oncogenic activities of METTL3. Currently, STM2457 is a potent, highly selective inhibitor of METTL3 but is yet to be approved. METHODS: In this study, we employed structure-based virtual screening through consensus docking by using AutoDock Vina in PyRx interface and Glide virtual screening workflow of Schrodinger Glide. Thermodynamics via MM-PBSA calculations was further used to rank the compounds based on their total free binding energies. All atom molecular dynamics simulations were performed using AMBER 18 package. FF14SB force fields and Antechamber were used to parameterize the protein and compounds respectively. Post analysis of generated trajectories was analyzed with CPPTRAJ and PTRAJ modules incorporated in the AMBER package while Discovery studio and UCSF Chimera were used for visualization, and origin data tool used to plot all graphs. RESULTS: Three compounds with total free binding energies higher than STM2457 were selected for extended molecular dynamics simulations. The compounds, SANCDB0370, SANCDB0867, and SANCDB1033, exhibited stability and deeper penetration into the hydrophobic core of the protein. They engaged in relatively stronger intermolecular interactions involving hydrogen bonds with resultant increase in stability, reduced flexibility, and decrease in the surface area of the protein available for solvent interactions suggesting an induced folding of the catalytic domain. Furthermore, in silico pharmacokinetics and physicochemical analysis of the compounds revealed good properties suggesting these compounds could serve as promising MEETL3 entry inhibitors upon modifications and optimizations as presented by natural compounds. Further biochemical testing and experimentations would aid in the discovery of effective inhibitors against the berserk activities of METTL3.

Probing into the Flap-dimer Dynamics of the Mycobacterium tuberculosis Kasa Enzyme Binding Landscape Provides the Underlying Inhibitory Mechanisms of JSF-3285 and 5G.

BACKGROUND: ß-ketoacyl-ACP synthase I (KasA I) enzyme is crucial in mycolic acid synthesis via catalytic condensation reactions, hence implicated in M. tuberculosis's virulence and drug resistance. Presently, there is no known potent KasA inhibitor; thiolactomycin lacks potency. Recently reported indazole compounds JSF-3285/tr1DG167 and 5G/tr2DG167 inhibit the KasA through binding to the substrate cavity. However, the molecular mechanism is still unclear, and the unknown resistance mechanisms raise concerns about JSF-3285's novelty. METHODS: This study is the first to report the flap dimer opening and closing of the KasA pocket using combined metrics to define the symmetry impact of the flap-dimer motions and investigate the underlying inhibitory mechanism of tr1DG167 andtr2DG167 using all-atom MD simulation. RESULTS: The distance/d1 between the flap (PRO147) and dimer (LEU205) residues; TriC-α angle (θ1: PRO147-VAL83-LEU205 & θ2: PRO147-GLU199-LEU205); and the dihedral angle (Φ) were applied to investigate the flap "twisting" and dimer shift closing due to concerted motion by adjacent glycine-rich and glutamic acid-rich loops around the active site during the binding pocket's opening. The full flap-dimer of the unbound opens at 230 ns (d1 = 21.51 Å), corresponding to the largest TriC-α angle θ1 44.5° as θ2 is unreliable to describe the flap-dimer motion. The overall averages θ1 and θ2 for the bounds were ~23.13° and ~23.31°, respectively. Thus, the degree of KasA flap dimer opening is best investigated by distance and θ1. BFE (Kcal/mol) of -44.05 (tr1DG167) showed a higher affinity for the pocket than tr2DG167-KasA (-32.16). Both tr1DG167 and tr2DG167 formed hydrophobic interactions with LEU116, GLY117, ALA119, and tr1DG167 formed strong H-bonds with GLU199. The average RMSD of 2.80 Å (Apo) and RoG of 20.97 Å showed that KasA is less stable and less tightly packed without the inhibitors. CONCLUSION: These findings provide a background for a new structure-based design of novel KasA inhibitors.

Analysis of definitive chemo-radiation outcomes in anal cancer: insights from a tertiary cancer center in the MENA Region.

Background: Outcomes of chemo-radiation (CRT) for anal cancer in Middle East and North Africa (MENA) are scarce. We aim to report treatment outcomes for anal cancer treated at tertiary cancer center, with a particular focus on patients managed with non-oncological surgery prior definitive CRT. Methods: We conducted a retrospective review of patients diagnosed with locally advanced anal carcinoma, who underwent definitive CRT King Hussein Cancer Center, from January 2007 till January 2020. Patient demographics and disease characteristics were extracted, and a univariate chi-squared test was employed to assess the impact of chemotherapy type, HPV status, and pre-treatment non-oncological surgery on outcomes, including complete remission (CR), disease-free survival (DFS), and overall survival (OS). Kaplan-Meier tests were employed to analyze the obtained survival data. Results: Among the 34 initially identified patients, 30 were eligible, 24 (80%) achieved CR. Notably, 20 out of 21 HPV positive patients achieved CR, versus 1 out 4 HPV-negative achieved CR, p=0.006The 5-years OS for HPV-positive patients was 89% compared with 25% for HPV-negative, p=0001. There was no statistical significant difference in patients outcomes as regard type of chemotherapy, radiation technique and non-oncologic resection prior to CRT. Conclusion: Herein, we reported the first series of anal cancer from our region. CRT had yielded an oncologic outcome comparable with series in the literature. HPV-positive patients demonstrated better results. Moreover, we found non-oncologic resection prior to CRT did not seem to impact the outcomes. Further studies are warranted to overcome the limitations of our study.

Bridging the Gap in Malaria Parasite Resistance, Current Interventions, and the Way Forward from in Silico Perspective: A Review.

The past decade has seen most antimalarial drugs lose their clinical potency stemming from parasite resistance. Despite immense efforts by researchers to mitigate this global scourge, a breakthrough is yet to be achieved, as most current malaria chemotherapies suffer the same fate. Though the etiology of parasite resistance is not well understood, the parasite's complex life has been implicated. A drug-combination therapy with artemisinin as the central drug, artemisinin-based combination therapy (ACT), is currently the preferred malaria chemotherapy in most endemic zones. The emerging concern of parasite resistance to artemisinin, however, has compromised this treatment paradigm. Membrane-bound Ca2+-transporting ATPase and endocytosis pathway protein, Kelch13, among others, are identified as drivers in plasmodium parasite resistance to artemisinin. To mitigate parasite resistance to current chemotherapy, computer-aided drug design (CADD) techniques have been employed in the discovery of novel drug targets and the development of small molecule inhibitors to provide an intriguing alternative for malaria treatment. The evolution of plasmepsins, a class of aspartyl acid proteases, has gained tremendous attention in drug discovery, especially the non-food vacuole. They are expressed at multi-stage of the parasite's life cycle and involve in hepatocytes' egress, invasion, and dissemination of the parasite within the human host, further highlighting their essentiality. In silico exploration of non-food vacuole plasmepsin, PMIX and PMX unearthed the dual enzymatic inhibitory mechanism of the WM382 and 49c, novel plasmepsin inhibitors presently spearheading the search for potent antimalarial. These inhibitors impose structural compactness on the protease, distorting the characteristic twist motion. Pharmacophore modeling and structure activity of these compounds led to the generation of hits with better affinity and inhibitory prowess towards PMIX and PMX. Despite these headways, the major obstacle in targeting PM is the structural homogeneity among its members and to human Cathepsin D. The incorporation of CADD techniques described in the study at early stages of drug discovery could help in selective inhibition to augment malaria chemotherapy.

Battling BTK mutants with noncovalent inhibitors that overcome Cys481 and Thr474 mutations in Waldenström macroglobulinemia therapy: structural mechanistic insights on the role of fenebrutinib.

Recently, the non-covalent Bruton tyrosine kinase (BTK) inhibitor fenebrutinib was presented as a therapeutic option with strong inhibitory efficacy against a single (C481S) and double (T474S/C481S) BTK variant in the treatment of Waldenström macroglobulinemia (WM). However, the molecular events surrounding its inhibition mechanism towards this variant remain unresolved. Herein, we employed in silico methods such as molecular dynamic simulation coupled with binding free energy estimations to explore the mechanistic activity of the fenebrutinib on (C481S) and (T474S/C481S) BTK variant, at a molecular level. Our investigations reveal that amino acid arginine contributed immensely to the total binding energy, this establishing the cruciality of amino acid residues, Arg132 and Arg156 in (C481S) and Arg99, Arg137, and Arg132 in (T474S/C481S) in the binding of fenebrutinib towards both BTK variants. The structural orientations of fenebrutinib within the respective hydrophobic pockets allowed favorable interactions with binding site residues, accounting for its superior binding affinity by 24.5% and relative high hydrogen bond formation towards (T474S/C481S) when compared with (C481S) BTK variants. Structurally, fenebrutinib impacted the stability, flexibility, and solvent accessible surface area of both BTK variants, characterized by various alterations observed in the bound and unbound structures, which proved enough to disrupt their biological function. Findings from this study, therefore, provide insights into the inhibitory mechanism of fenebrutinib at the atomistic level and reveal its high selectivity towards BTK variants. These insights could be key in designing and developing BTK mutants' inhibitors to treat Waldenström macroglobulinemia (WM).

Factors influencing the use of adaptive radiation therapy in vulvar carcinoma.

AIM: We aim to evaluate the variables affecting the frequency of adaptive radiotherapy (ART) in vulvar cancer. BACKGROUND: ART may be needed throughout a definitive RT course for vulvar carcinoma due to changes in patient's anatomy and tumor response. MATERIALS AND METHODS: Charts of patients charts who had been treated with definitive concurrent chemo-radiotherapy for vulvar carcinoma, between January 2015 and December 2019 were inquired. Radiation therapy was delivered using intensity modulated radiotherapy (IMRT) with daily image-guided radiotherapy (IGRT). ART was defined as re-simulation and re-planning based on deformation in the irradiated volume by more than 1 cm. Univariate analysis was conducted to study the impact of patient's demographics as well as tumor characteristics on the frequency of ART. RESULTS: 22 patients were eligible for analysis. Median age at diagnosis was 55 years (range 43-82). Radiotherapy dose was 60-66 Gy over 30-35 fractions (fx). Median primary tumor volume was 30cc (9-140). Median Body Mass Index (BMI) was 32 (range 21-40). Thirteen out of 22 patients (59%) required ART, with median timing at 25 fx (19-31). On univariate analysis, larger primary tumor volume (> = 30cc) was associated significantly with increased frequency of ART (p value = 0.0005). There was no significant impact of ART on the frequency with respect to patient's age, BMI, tumor stage, grade and location. CONCLUSION: Changes in radiation target volume are common among vulvar carcinoma patients who are treated with definitive radiotherapy, especially large primary tumors. This review highlights the importance of ART for patients with vulvar carcinoma treated with definitive radiotherapy.

Bacterial uropathogens isolates and antibiograms in children under 5 years of age.

BACKGROUND: Childhood urinary infections are among the most common febrile illnesses occurring during this period with varying susceptibility to antibiotic. AIM: The aim of this study was to identify uropathogens responsible to for urinarytract infection (UTIs) in children less than 5 years of age, and determine the antibiograms of the isolates to commonly used antibiotics. PATIENTS AND METHODS: Hundred and four children (2 months - 5 years old) seen at the Gadarif Teaching Hospital from January 2012 and December 2013 were evaluated. A urine specimen was obtained by a plastic bag with an adhesive backing around an opening or by direct voiding into sterile container. Urine was examined microscopically and those with significant pyuria and bacteruria were further cultured and microorganisms were identified and tested for antimicrobial susceptibility. RESULTS: Out of 304 children suffering from UTIs; 145(47.7%) had significant pyuria of them; 54(17.8 %) had positive bacterial growth. The frequency of sex and residency were almost the same. E. coli (42.6%) was the most common uropathogen, sensitive to ciprofloxacin (91.3%), followed by Pseudomonas aeruginosa (29.6%) sensitive to Ciprofloxacin (75%)and Norofloxacin (68.8%), Klebsiellapneumoniae (18.5%) sensitive to Ciprofloxacin and Norofloxacin and Nalidixic acid (90%) and Proteus mirabilis sensitive to Ciprofloxacin and Norofloxacin (90%), Amoxicillin / clavulanic acid (Augmentin(80%). CONCLUSION: The most common uropathogens were E. coli, Pseudomonas aeruginosa,Klebsiellapneumoniae, and Proteus mirabilis. Ciprofloxacin is the recommended initial empirical therapy while awaiting the culture and sensitivity results.

Computer and Internet Utilization among the Medical Students in Qassim University, Saudi Arabia.

BACKGROUND: Computer-based training (CBT) and internet-based training (IBT) have become a vital part of the Medical Education. A cross-sectional study was carried out in Qassim University-Kingdom of Saudi Arabia (KSA), with the objective of assessing the pattern of the computer and Internet utilization among both male and female medical students. METHODS: A total of 500 medical students from 4 different medical colleges of Qassim University participated in this study. A semi-structured, pre-tested questionnaire was used to collect the data and the data analysis was done by using SPSS, Version 17. RESULTS: Forty two percent female and twenty four percent male students used computers to get general information, 80% of the students reported using computers for academic activities and 52% females and 22% males used computers for entertainment. Most of the females preferred using computers at home (84%), while 54% males used computers at cyber cafés. For the information retrieval, 84% males used the internet, followed by journals/library (36%) and textbooks (35%), while the females preferred textbooks (75%) and the internet (14%). Google was found to be most commonly used search engine. CONCLUSION: The internet creates an educational delivery system; it is highly needed to increase the credit hours for the university requirement courses in computer application and the internet use for both among the male and female students.

Puerperal sepsis in a rural hospital in Sudan.

BACKGROUND: Increasingly, women in rural areas in Sudan reported to hospital with puerperal infections. AIMS: This study was design to identify the common pathogens causing puerperal infections and their susceptibility to current antibiotics. SUBJECTS AND METHODS: We prospectively studied 170 women from January, 2011 through January 2012 attended Hussein Mustafa Hospital for Obstetrics and Gynecology at Gadarif State, Sudan. We included patients if they met the criteria proposed by the WHO for definition of maternal sepsis. Blood was collected on existing infection guidelines for clean practice and equipments. RESULTS: Out of the 170 samples, 124 (72.9%) were pathogen-positive samples. Out the 124 positive cases, aerobes were the predominant isolates 77 (62.1 %%) which included Staph.aureus 49 (39.5%), Staph. epidemics 7 (5.6%) and Listeria monocytogenes 21 (16.9%). The anaerobes isolates were Clostridium perfringens 34 (27.4 %) and Entrobactor cloacae 13 (10.5%). Standard biochemical test were for bacterial isolation. Higher rate of infections followed vaginal delivery compared to Cesarean section 121 (97.6%), 3 (2.5%) respectively. All strains of Staph were sensitive to Vancomycin, Gentamicin and Ceftriaxone. C. perfringens were sensitive to Ceftriaxone, Penicillins, Vancomycin and Metronidazole, while E. cloacae were sensitive to Gentamicin and Ceftriaxone. CONCLUSION: Despite the limited resources in the developing countries, treatment based on cultures remains the only solution to reduce maternal morbidity and mortality rates following puerperal infections.

Prevalence of nosocomial wound infection among postoperative patients and antibiotics patterns at teaching hospital in Sudan.

BACKGROUND: Postoperative nosocomial infections remain a major problem in health care facilities, resulting in extended length of stay, substantial morbidity and mortality, high excess of cost, and less frequent cause of death in the surgical patient. AIMS: To determine the prevalence of aerobic nosocomial pathogens among patients with postoperative wound infections at Gadarif state which located in Eastern part of Sudan. MATERIALS AND METHODS: 109 wound swabs were collected from patients who had developed postoperative wound infection. Conventional technique for isolation of bacteria was applied with analytical profile index (API system) for identification to confirm primary and secondary isolates. Antibiotics susceptibility was applied for all isolated bacteria. RESULTS: Aerobic bacterial isolates were S. aureus (n=55, 55.0%), P. mirabilis (n=35, 35.0%), E. coli (n=5, 5.0%), Ps. aeruginosa (n=3, 3.0%), and Pr. vulgaris (n=2, 2.0%). The prevalence rate of hospital acquired infection were 25.23% CONCLUSION: The highest prevalence rate of nosocomial postoperative wound infection, in Sudan was due to poor antibiotic selection, for prophylaxis during and after surgery and increased level of contamination in most part of the hospital.