Protein structure-based in-silico approaches to drug discovery: Guide to COVID-19 therapeutics

With more than 5 million fatalities and close to 300 million reported cases, COVID-19 is the first documented pandemic due to a coronavirus that continues to be a major health challenge. Despite being rapid, uncontrollable, and highly infectious in its spread, it also created incentives for technology development and redefined public health needs and research agendas to fast-track innovations to be translated. Breakthroughs in computational biology peaked during the pandemic with renewed attention to making all cutting-edge technology deliver agents to combat the disease. The demand to develop effective treatments yielded surprising collaborations from previously segregated fields of science and technology. The long-standing pharmaceutical industry's aversion to repurposing existing drugs due to a lack of exponential financial gain was overrun by the health crisis and pressures created by front-line researchers and providers. Effective vaccine development even at an unprecedented pace took more than a year to develop and commence trials. Now the emergence of variants and waning protections during the booster shots is resulting in breakthrough infections that continue to strain health care systems. As of now, every protein of SARS-CoV-2 has been structurally characterized and related host pathways have been extensively mapped out. The research community has addressed the druggability of a multitude of possible targets. This has been made possible due to existing technology for virtual computer-assisted drug development as well as new tools and technologies such as artificial intelligence to deliver new leads. Here in this article, we are discussing advances in the drug discovery field related to target-based drug discovery and exploring the implications of known target-specific agents on COVID-19 therapeutic management. The current scenario calls for more personalized medicine efforts and stratifying patient populations early on for their need for different combinations of prognosis-specific therapeutics. We intend to highlight target hotspots and their potential agents, with the ultimate goal of using rational design of new therapeutics to not only end this pandemic but also uncover a generalizable platform for use in future pandemics.

Iron Status in Sickle Cell Anemia: Deficiency or Overload?

Background Sickle cell anemia (SCA) is a hereditary disease with defective hemoglobin (Hb) synthesis causing severe hemolytic anemia, pain crisis, and target organ damage. In SCA, several factors independently or in combination lead to derangement in iron stores. Some centers incorrectly prescribe iron therapy on the presumption that SCA would be associated with iron deficiency, but it is not always the case. This study attempts to evaluate the iron status in SCA patients and records the target organ damage present. Methodology A single-center cross-sectional study of 180 patients with sickle cell disease was carried out at a tertiary-care center in Western India. Patients >12 years of age were included in the study after confirming SCA using high-performance liquid chromatography (HPLC). The iron status of each patient was identified and patients were labeled as iron sufficient based on the following values: Hb (8.1-12 gm%), serum iron (S. iron) level (50-150 μg/dl), serum ferritin (S. ferritin) (50-200 ng/ml), and total iron binding capacity (TIBC) (251-450 µg/dl). The iron status of patients with different target organ damage was also analyzed. Results Demographic data revealed that 21-30 years was the most common age group affected by SCA along with a male preponderance. The most common presenting complaint was joint pain (68.9%), the most common sign was pallor (64.4%), most patients had a history of pain crisis (95.6%), and half of the patients had organomegaly (51.1%). Most of the patients had no complications, however, for those who did, hepatopathy (28.9%) was the most common. Conclusion While the majority of patients were iron sufficient, a considerable number had either iron deficiency or iron overload states, which emphasizes the necessity of investigating the iron status before deciding the course of treatment in SCA patients. Although the majority were unaffected, screening for end-organ damage should be carried out in all SCA patients.

A new insight into the diverse facets of microRNA-31 in oral squamous cell carcinoma

Background

Micro-RNAs (miRNAs) have been reported as an emerging biomarker in many cancer types. They are used as diagnostic and prognostic biomarkers and could be considered therapeutic targets in treating the same.

Main body

Studies have proven that miRNAs play an essential role in molecular cancer pathophysiology, including oral squamous cell carcinoma. Distinct expression profiles of different miRNAs have been demonstrated in oral squamous cell carcinoma. Among the miRNAs, the miR-31 has strong potential as a unique biomarker in head and neck squamous cell carcinoma, and the increased expression was correlated to a poor clinical outcome with a likely contribution to oral carcinogenesis.

Short conclusion

The recent research on different aspects of miR-31 as a biomarker and also its potential application in the development of therapy for oral squamous cell carcinoma has been focused in this review.

Graphical abstract

Purification, biochemical and biophysical characterization of lysosomal β-D-glucuronidase from an edible freshwater mussel, Lamellidens corrianus

A lysosomal glycosidase, β-glucuronidase, has been purified to homogeneity, from the soluble extracts of a freshwater mussel, L. corrianus, by a series of chromatography techniques involving phenyl-Sepharose, ion exchange, affinity and gel filtration chromatography. In native PAGE, β-glucuronidase resolved into a single band and the molecular mass determined by gel filtration chromatography was found to be 250 kDa. Zymogram analysis with 4-methyl umbelliferyl β-glucuronide substrate validated the purified enzyme as β-glucuronidase. In SDS-PAGE, the purified enzyme was resolved into four sub-units with molecular weights around 90, 75, 65, and 50 kDa, respectively, and two of the subunits (90 and 50 kDa) cross-reacted with human β-glucuronidase antiserum. The optimum pH and temperature of the purified glycosidase were 5.0 and 70 °C, respectively. The enzyme kinetics parameters, substrate affinity (K_M) and maximum velocity (V_max) of the purified protein estimated with p-nitrophenyl β-D-glucuronide were 0.457 mM and 0.11867 μmol^-1 min^-1 mL^-1, respectively. The secondary structure of β-glucuronidase was determined in the far-UV range (190 nm to 230 nm) using CD spectroscopy. Heat denaturation plots determined by CD spectroscopy showed that the purified enzyme was stable up to 70 °C.

Developmental trends in CO2 methanation using various catalysts

Co₂ methanation-two edged sword to counter global warming and energy crisis.

Thrombosed varicocele - a rare cause for acute scrotal pain: a case report

BACKGROUND

Acute scrotal pain has various causes. Testicular torsion, torsion of appendages and Epididymo-orchitis are common causes, while varicocele thromboses are a rare cause. Varicocele thromboses can occur post operatively or spontaneously. Five cases of post-operative and five cases of spontaneous thromboses have been described till date. The traditional advice in the management of thrombosed varicocele has been to manage it conservatively in all patients by drugs and scrotal support with little description of the surgical treatment. Herein, we present an unusual sixth case of spontaneous thromboses of varicocele and discuss its presentation and surgical management. We would also like to highlight the differentiating points between spontaneous thrombosis and post operative in vitro clot formation in the varicoceles, as these two entities can often be confused for each other.

CASE PRESENTATION

A 68 year-old man presented with excruciating scrotal pain of one week duration. Doppler study of scrotum revealed left varicocele with no evidence of Epididymo-orchitis. He was treated with intravenous antibiotics, analgesics and scrotal elevation. He had no relief and continued to have severe pain. Clinical examination was normal. Patient underwent exploratory surgery on a semi- emergent basis. Exploration revealed normal testis with thrombosed varicoceles. Patient underwent Varicocelectomy. Postoperatively patient had immediate pain relief. Histopathology revealed prominent thrombosed varicocele. A varicocelectomy specimen (done for primary infertility) was used for comparison. The differentiating points between the two entities were noted.

CONCLUSION

Spontaneous thrombosis of varicocele is a rare cause of acute scrotal pain. Pain out of proportion to clinical features is characteristic. Patients not responding to medical therapy may need varicocelectomy. Varicocelectomy may give immediate relief. Histopathology is useful in this disorder.

Green Synthesized Zinc Oxide (ZnO) Nanoparticles Induce Oxidative Stress and DNA Damage in Lathyrus sativus L. Root Bioassay System

Zinc oxide nanoparticles (ZnONP-GS) were synthesised from the precursor zinc acetate (Zn(CH₃COO)₂) through the green route using the milky latex from milk weed (Calotropis gigantea L. R. Br) by alkaline precipitation. Formation of the ZnONP-GS was monitored by UV-visible spectroscopy followed by characterization and confirmation by energy-dispersive X-ray spectroscopy (EDX), transmission electron microscopy (TEM), and X-ray diffraction (XRD). Both the ZnONP-GS and the commercially available ZnONP-S (Sigma-Aldrich) and cationic Zn²⁺ from Zn(CH₃COO)₂ were tested in a dose range of 0–100 mg·L⁻¹ for their potency (i) to induce oxidative stress as measured by the generation reactive oxygen species (ROS: O₂^•−, H₂O₂ and ^•OH), cell death, and lipid peroxidation; (ii) to modulate the activities of antioxidant enzymes: catalase (CAT), superoxide dismutase (SOD), guaiacol peroxidase (GPX), and ascorbate peroxidase (APX); and (iii) to cause DNA damage as determined by Comet assay in Lathyrus sativus L. root bioassay system. Antioxidants such as Tiron and dimethylthiourea significantly attenuated the ZnONP-induced oxidative and DNA damage, suggesting the involvement of ROS therein. Our study demonstrated that both ZnONP-GS and ZnONP-S induced oxidative stress and DNA damage to a similar extent but were significantly less potent than Zn²⁺ alone.

What can be done when the cored specimen in a Frey procedure for chronic pancreatitis is reported as adenocarcinoma?

The aim of this study is to analyze the outcomes of patients with chronic pancreatitis who underwent the Frey procedure and who had a histologic evidence of adenocarcinoma in the cored out specimen.The type of analysis is retrospective. Out of 523 patients who underwent Frey procedure for chronic pancreatitis, seven (five males and two females; age range 42 to 54 years) had histologically proven adenocarcinoma. In the first four cases, intraoperative frozen section was not done. The diagnosis was made on routine histopathology and only one out of four could undergo attempted curative therapy. In the remaining three cases, intraoperative frozen section confirmation was available, and curative resection performed. Only four out of seven had a clear-cut mass lesion: (a) cancer can occur in chronic pancreatitis in the absence of a mass lesion and (b) intraoperative frozen section of the cored specimen is crucial to exercising curative therapeutic options and must be performed routinely. If frozen section is reported as adenocarcinoma, a head resection with repeat frozen of the margins of resection is appropriate. If the adenocarcinoma is reported on regular histopathology after several days, then a total pancreatectomy may be more appropriate.

Urinary Bladder Xanthoma - Is Immunohistochemistry Necessary?

Urinary Bladder Xanthomas (UBX) are non-neoplastic reactive tumor like process. Isolated UBX is rare with only around 15 cases reported (Yu, Patel, & Bonert, 2015). UBX are reported in older patients who present with non specific symptoms like UTI or hematuria. Patients often have associated lipid anomalies. UBX have been vaguely described as yellowish white plaques or patches. Also, recent reports have stressed on the role of Immunohistochemistry in the diagnosis (Al-Daraji, Varghese, & Husain, 2007; Vimal, Masih, Manipadam, & Chacko, 2012). The objective of this report is to provide a cystoscopic view of the tumor which will enable easier identification and also to debate on the role of IHC in diagnosis.

Paradidymis – Fact/Fiction and its Significance

A 30-year old infertile male was admitted for microsurgical sub inguinal varicocelectomy. Intraoperatively, two tubular structures of the caliber of neighboring veins were noted. They were distinct from the vas, which was carefully preserved. Histopathology revealed varicose veins along with two convoluted tubular structures lined by ciliated pseudo-stratified epithelium. There was an incomplete thin muscle coat. The lumina were irregular and contained no spermatozoa (Fig. 1). These structures were identified as paradidymis based on the location in the cord and microscopic morphology. We have tried to analyze the medico-legal significance of these benign lesions in our every day practice.

A randomized control study comparing the pharyngolaryngeal morbidity of laryngeal mask airway versus endotracheal tube

Introduction:

Endotracheal tube (ETT) has been associated with various pharyngolaryngeal morbidities (PLMs) following general anesthesia (GA). Laryngeal mask airway (LMA), currently the most commonly used supraglottic airway device, has several advantageous over the ETT but has been associated with varying results of PLM. The aim of our study was to compare the PLM between them and to know whether LMA is a better alternative.

Materials and Methods:

One hundred and seventy American Society of Anesthesiologists Grades 1 and 2 women scheduled for elective mastectomy were included in the study, 85 each in either group, E Group (intubated with ETT) and L Group (using LMA) on a random basis. All patients received GA with controlled ventilation using a muscle relaxant. PLMs such as hoarseness, pain on phonation, sore throat, and difficulty in swallowing were documented by an interview done postoperatively. Peroperative parameters such as intubation attempts, trauma during airway device insertion, and intraoperative incidents were also analyzed. A sample size of 85 patients in each group was calculated in order to achieve a study power of 0.8 and alpha level was taken as 0.05. Data were analyzed using SPSS version 16 using Chi-square test, Mann–Whitney U-test and Fisher's exact test were used as nonparametric tests. A two-tailed P< 0.05 was considered significant.

Results:

Patients in E Group had statistically significant increased incidence of a sore throat and voice complaints whereas L Group showed a statistically significant increase of swallowing problems. There was also a significant correlation between traumatic insertion and sore throat, pain on swallowing in the L Group, which could be due to direct trauma.

Conclusions:

ETT was associated with an increased incidence of voice problems and sore throat whereas LMA had an increased incidence of dysphagia and odynophagia. Use of LMA changes the pharyngolaryngeal profile to a more acceptable one.

Selective hydrogenation of levulinic acid to γ-valerolactone over a Ru/Mg–LaO catalyst

Ruthenium on a base support was developed for the conversion of biomass derived levulinic acid to γ-valerolactone at low temperature and pressure. γ-Valerolactone synthesis which can replace ethanol in petrol and in the production of jet fuels.

Disseminated intravascular coagulation

Disseminated intravascular coagulation (DIC) is a reflection of an underlying systemic disorder which affects the coagulation system, simultaneously resulting in pro-coagulant activation, fibrinolytic activation, and consumption coagulopathy and finally may result in organ dysfunction and death. Though septicaemia is the most common cause of DIC, several other conditions can also lead to it. A diagnosis of DIC should be made only in the presence of a causative factor supported by repeated laboratory tests for coagulation profile and clotting factors. An effective scoring system helps to detect an overt DIC and a high score closely correlates with mortality. Treatment of DIC is aimed at combating the underlying disorder followed by supportive management. Low molecular weight heparin is advocated in special situations whereas anti-thrombin III and activated protein C are of doubtful value. Early diagnosis and prompt treatment backed by laboratory support can reduce the morbidity and mortality associated with it. The methodology of search for this review article involved hand search from text books and internet search using Medline (via PubMed) using key words DIC, thrombosis, fibrin degradation products, anti-thrombin and tissue factor for the last 25 years and also recent evidence-based reviews.

Note: A vortex cross-correlation flowmeter with enhanced turndown ratio

In the present study, a novel dual sensor vortex cross correlation technique is suggested and implemented to extend the lower operating range of the flowmeter. The first sensor located at an optimum streamwise location of 0.85 times the width of the bluff body is employed to compute the vortex shedding frequency under high Reynolds number conditions. Under low Reynolds number conditions, when the strength of the vortex signal is poor, the outputs from the two piezoelectric sensors are correlated to compute the vortex convection velocity. This vortex convection velocity is used to compute the volume flow rate. This novel dual flow rate estimation technique has demonstrated its robustness under low Reynolds number flow conditions with a remarkable turndown ratio of 1:66 as compared to 1:20 for conventional vortex flowmeters.

An efficient iterative algorithm for computation of scattering from dielectric objects

We have developed an efficient iterative algorithm for electromagnetic scattering of arbitrary but relatively smooth dielectric objects. The algorithm iteratively adapts the equivalent surface currents until the electromagnetic fields inside and outside the dielectric objects match the boundary conditions. Theoretical convergence is analyzed for two examples that solve scattering of plane waves incident upon air/dielectric slabs of semi-infinite and finite thicknesses. We applied the iterative algorithm for simulation of sinusoidally-perturbed dielectric slab on one side and the method converged for such unsmooth surfaces. We next simulated the shift in radiation pattern of a 6-inch dielectric lens for different offsets of the feed antenna on the focal plane. The result is compared to that of the Geometrical Optics (GO).

CA 19-9 to differentiate benign and malignant masses in chronic pancreatitis: is there any benefit?

BACKGROUND

The role of the tumor marker CA 19-9 in differentiating benign from malignant masses in chronic pancreatitis has not been extensively studied.

AIM

This study aims at assessing the accuracy of CA 19-9 in differentiating inflammatory head masses in chronic pancreatitis from superimposed carcinomas on chronic pancreatitis.

METHODS

The data of 84 consecutive patients who had mass lesions in chronic pancreatitis were analyzed to determine the sensitivity, specificity and predictive values at cut-off values of 37, 100, 200 and 300 U/mL. Receiver operating characteristic (ROC) curves were used to assess the sensitivity and specificity.

RESULTS

There were 50 benign masses and 34 malignancies. The overall sensitivity and specificity of CA 19-9 for cancer was 68% and 70%, respectively. There was a higher positivity of CA 19-9 in cancers than in benign masses (23/34; 68% versus 15/50; 30%, P<0.01) with cut-off values of 37 U/mL. Higher positivity rates were obtained in cancers using other cut-off values such as 100, 200 and 300 U/mL. Values over 300 U/mL were 100% specific for malignancy, but occurred in only 5 (of whom had distant metastases) of 34 patients.

CONCLUSION

CA 19-9 level in excess of 300 U/mL in mass lesions in chronic pancreatitis was always indicative of malignancy.

Surgical management of chronic pancreatitis with portal hypertension--a 19-year experience

BACKGROUND

The presence of portal hypertension in chronic pancreatitis imposes great challenges on the clinician. The objective of this retrospective analysis is to identify the demographics, presentation, management and outcomes among patients suffering from chronic pancreatitis with associated portal hypertension.

PATIENTS

The data of fifty-seven patients (36 males, 21 females, age range 23 to 54 years; median 34.5) with chronic pancreatitis and portal hypertension who were operated either for intractable pain or complications over a 19-year period were analyzed. The etiology was alcohol abuse in 28 and idiopathic (tropical) in the remainder. The commonest presentation was abdominal pain in 52 patients (91%). Only 11 patients presented with gastrointestinal bleeding (19%), and they were managed by endoscopic therapy (sclerotherapy, banding, or ethoxysklerol injection). The surgical procedures were: 43 Frey procedures, 11 lateral pancreaticojejunostomies, and 3 Whipple's resections with additional procedures (cyst/biliary drainage or distal pancreatectomy) when appropriate. Direct operations for portal hypertension were required in only 19 patients (splenectomy (n = 15) and gastric devascularization (n = 4)).

RESULTS

Operating times ranged from 210 to 490 minutes (median 320), yet only 11 patients required blood transfusion. There were 24 complications in 18 patients, and hospital stay ranged between 11 and 62 days (median 18.5). One patient died of liver failure on day 17 after operation. Forty-nine out of 53 patients available for follow-up had excellent or good pain relief.

CONCLUSION

Surgery provided good relief of pain and complications in patients with chronic pancreatitis and portal hypertension. Isolated surgery for portal hypertension alone was not required in any of the patients.

Intussusception due to ileal metastases from renal cell carcinoma

Small bowel secondaries from renal cell carcinoma are rare. Patients usually present with features of intestinal obstruction or GI bleeding. Management should be aggressive since metastasectomy can improve the quality of life and survival.

Hydroxyapatite-supported Ag-TiO2 as Escherichia coli disinfection photocatalyst

A series of hydroxyapatite (HAP), 1wt% Ag-TiO(2) (AT1), 1wt% Ag-HAP and 5wt% AT1/HAP composite catalysts were prepared by incipient wetness and mechanical mixing methods. They were characterized by X-ray diffraction (XRD), FT-IR, SEM and ESCA analyses and their photocatalytic bactericidal activities were measured in suspension using Escherichia coli (E. coli), a water pollutant indicator. The surface analysis revealed that the Ag/Ti ratio is found to be ca. 0.0273 and also it indicated that the titania is present in the form of Ti(4+) and Ag is present as metallic silver. Both the XRD and ESCA analyses confirmed the phase of metallic Ag particles, which played a significant role on the bactericidal activity of the Ag doped TiO(2) catalysts. The FT-IR analysis of HAP revealed that the peak intensity is due to the absorbance of surface PO(4)(3-) group centered at wave number 1030cm(-1) and is drastically decreased upon exposure to UV for 1h. The HAP displayed high amount of bacteria adsorption, ca. 80% during the dark experiments compared to other catalytic systems tested. The cumulative photocatalytic properties of AT1/HAP catalytic system resulted in 100% E. coli bacteria reduction within 2min.