In-silico guided design, screening, and molecular dynamic simulation studies for the identification of potential SARS-CoV-2 main protease inhibitors for the targeted treatment of COVID-19.

COVID-19, the disease responsible for the recent pandemic, is caused by a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The main protease (Mpro) of SARS-CoV-2 is an essential proteolytic enzyme that plays a number of important roles in the replication of the virus in human host cells. Blocking the function of SARS-CoV-2 Mpro offers a promising and targeted, therapeutic option for the treatment of the COVID-19 infection. Such an inhibitory strategy is currently successful in treating COVID-19 under FDA's emergency use authorization, although with limited benefit to the immunocompromised along with an unfortunate number of side effects and drug-drug interactions. Current COVID vaccines protect against severe disease and death but are mostly ineffective toward long COVID which has been seen in 5-36% of patients. SARS-CoV-2 is a rapidly mutating virus and is here to stay endemically. Hence, alternate therapeutics to treat SARS-CoV-2 infections are still needed. Moreover, because of the high degree of conservation of Mpro among different coronaviruses, any newly developed antiviral agents should better prepare us for potential future epidemics or pandemics. In this paper, we first describe the design and computational docking of a library of novel 188 first-generation peptidomimetic protease inhibitors using various electrophilic warheads with aza-peptide epoxides, α-ketoesters, and ß-diketones identified as the most effective. Second-generation designs, 192 compounds in total, focused on aza-peptide epoxides with drug-like properties, incorporating dipeptidyl backbones and heterocyclic ring motifs such as proline, indole, and pyrrole groups, yielding 8 hit candidates. These novel and specific inhibitors for SARS-CoV-2 Mpro can ultimately serve as valuable alternate and broad-spectrum antivirals against COVID-19.Communicated by Ramaswamy H. Sarma.

Evaluation of Oxidative Status, Cytokines, Acute Phase Proteins and Cardiac Damage Markers in Sheep Naturally Infected with Babesia ovis.

PURPOSE: Babesiosis is a tick-borne disease caused by protozoon species in the Babesia genus of the Babesiadae family. The systemic inflammatory response induced by infection is considered to be an important feature of the pathophysiology of ovine babesiosis. In this study, it was aimed to determine serum oxidative status, levels of some cytokines, acute phase proteins and heart damage markers in babesiosis infection. MATERIALS AND METHODS: A sample of 40 sheep was used for this purpose, of which 20 were healthy and 20 were infected with Babesia ovis. Babesia infection was diagnosed from Giemsa-stained peripheral blood smears. Infection was also confirmed by the polymerase chain reaction (PCR). Sera from blood samples was tested for oxidative stress parameters (malondialdehyde [MDA], total antioxidant status [TAS], superoxide dismutase [SOD], catalase [CAT] and glutathione peroxidase [GPx]), cytokines (interleukins IL-6, IL-1ß, IL-10, tumour necrosis factor α (TNF-α) and interferon-ϒ [IFN-ϒ]), acute-phase proteins (C-reactive protein [CRP], serum amyloid A [SAA] and haptoglobin [Hp]) and specific (troponin I [cTnI], creatine kinase-MB [CK-MB]) and nonspecific (lactate dehydrogenase [LDH], aspartate transaminase [AST]) cardiac damage markers. RESULTS: MDA, SOD, CAT, Hp, TAS, IL-6, IL-10, TNF-α, IL-1ß, INF-γ, AST, LDH, CK-MB mass and troponin I values were higher in the patient group than in the healthy group (P < 0.05). However, there was not found to be a statistical difference between the healthy and patient groups in terms of GPx, SAA and CRP values (P > 0.05). CONCLUSIONS: It can be stated that serum levels of oxidative stress, some acute phase proteins and cardiac damage markers may increase in naturally infected sheep with babesiosis.

Ectoparasites of feral horses [Equus ferus caballus (Linnaeus., 1758)] on Karadag Mountain, Karaman, Turkey.

Approximately 250 feral horses [Equus ferus caballus (Linnaeus, 1758)] living on Karadag Mountain near Karaman City were caught by Kazakh horse herdsmen with permission of the Turkish Ministry of Agriculture and Forestry and brought to a farm in Karkin village in Konya Province, 70 km from Karadag, in November, 2017. This study was carried out to determine the presence of ectoparasites infesting a subsample of 36 feral horses. The horses were visually inspected, and then their bodies were checked by hand for ectoparasites. Thirty-five (97.2%) were infested with at least one of five species of ectoparasites: Bovicola equi (Linnaeus, 1758), Hippobosca equina (Linnaeus, 1758), Haemaphysalis parva (Neuman, 1897), Hyalomma excavatum (Koch, 18449), Dermacentor marginatus (Sulzer, 1776). Most of the horses were coinfested with two ectoparasite species. Prevalence of infestation with H. equina was 80.6% and with B. equi 72.2%. In addition, prevalence of Ha. parva was 25.0%, Hy. excavatum 13.9%, and D. marginatus was 5.6%. This is the first systematic examination for external parasites of feral horses in Turkey. Further studies are needed to determine ectoparasites of greater numbers of feral horses in different localities.

Design, synthesis, and in vitro evaluation of aza-peptide aldehydes and ketones as novel and selective protease inhibitors.

Aza-peptide aldehydes and ketones are a new class of reversible protease inhibitors that are specific for the proteasome and clan CD cysteine proteases. We designed and synthesised aza-Leu derivatives that were specific for the chymotrypsin-like active site of the proteasome, aza-Asp derivatives that were effective inhibitors of caspases-3 and -6, and aza-Asn derivatives that inhibited S. mansoni and I. ricinus legumains. The crystal structure of caspase-3 in complex with our caspase-specific aza-peptide methyl ketone inhibitor with an aza-Asp residue at P1 revealed a covalent linkage between the inhibitor carbonyl carbon and the active site cysteinyl sulphur. Aza-peptide aldehydes and ketones showed no cross-reactivity towards cathepsin B or chymotrypsin. The initial in vitro selectivity of these inhibitors makes them suitable candidates for further development into therapeutic agents to potentially treat multiple myeloma, neurodegenerative diseases, and parasitic infections.

Demonstration of In Vitro Resurrection of Aged Acetylcholinesterase after Exposure to Organophosphorus Chemical Nerve Agents.

After the inhibition of acetylcholinesterase (AChE) by organophosphorus (OP) nerve agents, a dealkylation reaction of the phosphylated serine, referred to as aging, can occur. When aged, known reactivators of OP-inhibited AChE are no longer effective. Realkylation of aged AChE may provide a route to reversing aging. We designed and synthesized a library of quinone methide precursors (QMPs) as proposed realkylators of aged AChE. Our lead compound (C8) from an in vitro screen successfully resurrected 32.7 and 20.4% of the activity of methylphosphonate-aged and isopropyl phosphate-aged electric-eel AChE, respectively, after 4 days. C8 displays properties of both resurrection (recovery from the aged to the native state) and reactivation (recovery from the inhibited to the native state). Resurrection of methylphosphonate-aged AChE by C8 was significantly pH-dependent, recovering 21% of activity at 4 mM and pH 9 after only 1 day. C8 is also effective against isopropyl phosphate-aged human AChE.

Study of para-Quinone Methide Precursors toward the Realkylation of Aged Acetylcholinesterase.

Acetylcholinesterase (AChE) is an essential enzyme that can be targeted by organophosphorus (OP) compounds, including nerve agents. Following exposure to OPs, AChE becomes phosphylated (inhibited) and undergoes a subsequent aging process where the OP-AChE adduct is dealkylated. The aged AChE is unable to hydrolyze acetylcholine, resulting in accumulation of the neurotransmitter in the central nervous system (CNS) and elsewhere. Current therapeutics are only capable of reactivating inhibited AChE. There are no known therapeutic agents to reverse the aging process or treat aged AChE. Quinone methides (QMs) have been shown to alkylate phosphates under physiological conditions. In this study, a small library of novel quinone methide precursors (QMPs) has been synthesized and examined as potential alkylating agents against model nucleophiles, including a model phosphonate. Computational studies have been performed to evaluate the affinity of QMPs for the aged AChE active site, and preliminary testing with electric eel AChE has been performed.

Efforts toward treatments against aging of organophosphorus-inhibited acetylcholinesterase.

Aging is a dealkylation reaction of organophosphorus (OP)-inhibited acetylcholinesterase (AChE). Despite many studies to date, aged AChE cannot be reactivated directly by traditional pyridinium oximes. This review summarizes strategies that are potentially valuable in the treatment against aging in OP poisoning. Among them, retardation of aging seeks to lower the rate of aging through the use of AChE effectors. These drugs should be administered before AChE is completely aged. For postaging treatment, realkylation of aged AChE by appropriate alkylators may pave the way for oxime treatment by neutralizing the oxyanion at the active site of aged AChE. The other two strategies, upregulation of AChE expression and introduction of exogenous AChE, cannot resurrect aged AChE but may compensate for lowered active AChE levels by in situ production or external introduction of active AChE. Upregulation of AChE expression can be triggered by some peptides. Sources of exogenous AChE can be whole blood or purified AChE, either from human or nonhuman species.

Mycosis fungoides mimicking nevoid hyperkeratosis of the nipple and areola in an adolescent.

Mycosis fungoides is one of the great imitators in dermatology; it can mimic many dermatoses. Nevoid hyperkeratosis of the nipple and areola is a rare idiopathic disease with typical clinical features of verrucous thickening and brownish discoloration of the nipple, areola or both. Here, a 16-year-old male patient with mycosis fungoides mimicking nevoid hyperkeratosis of the nipple and areola has been reported. To our knowledge, this is the first atypical MF patient to have presented with a NHNA-like lesion. Although the clinical appearance of nevoid hyperkeratosis of the nipple and areola is highly characteristic for diagnosis, histopathological examination is recommended, especially in cases with atypical features such as unexpected age, male gender and unilateral location.

Determination of immunoreactive proteins of Babesia ovis.

Babesia ovis, an intraerythrocytic protozoan parasite transmitted by ticks, causes severe infections in sheep in tropical and subtropical regions of the world. Parasite-specific immunoreactive proteins have been used as antigen in the serological diagnosis of babesiosis. There is no study about determination of B. ovis-specific proteins in sheep. This study was planned to determine the immunoreactive proteins of B. ovis. In this study, two splenectomized lambs, and twelve seropositive sheep and five seronegative lambs for anti-B. ovis antibodies were used as materials. Infected blood samples at 5% of parasitemia from the two splenectomized lambs experimentally infected with a virulent B. ovis field strain were analyzed for B. ovis-specific proteins by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and Western blotting (WB). B. ovis-specific five major proteins were recognized by anti-B. ovis serum but not by healthy sheep serum. They were of approximate molecular weights 154, 109, 77, 58, and 38 kDa. As the control samples, protein profiles of the blood extracts of two lambs before splenectomy operation were also blotted with the immune sera, but none of the five proteins was detected. These proteins were also immunoblotted with heterologous positive and negative sheep sera. All of twelve positive sera recognized the 109 kDa protein with 100 percent sensitivity. The 77 kDa protein reacted in 11 of 12 sera (91.6%). The sensitivities of the other 3 proteins ranged between 83.3% and 25%. The five protein bands immunoblotted with sera of the 5 negative lambs did not give any positive reaction. The results of this study revealed the presence of proteins recognized by the serum antibodies of experimentally and naturally infected sheep with B. ovis. Additional studies on the purification of these proteins and on subsequently their utilization in a serodiagnostic method are required to improve the serological diagnosis of ovine babesiosis.

Babesia ovis infections: detailed clinical and laboratory observations in the pre- and post-treatment periods of 97 field cases.

Ovine babesiosis, caused by Babesia ovis, is of major economic importance in Turkey. The changes in the blood profile of infected animals are informative about the course of infection. The aim of the present study was to evaluate the hematological and biochemical changes in the pre- and post-treatment periods of the natural B. ovis infections. The presence of the parasites was confirmed by microscopy and polymerase chain reaction (PCR) analysis. On the basis of the clinical and laboratory findings, the infections were categorized into different groups according to the degree of anemia and the level of parasitemia. All infected sheep were treated with imidocarb dipropionate (IMDP). The blood pictures in the pre- and post-treatment periods were compared. Pancytopenia occurred in animals with severe anemia and very high parasitemia, and bicytopenia in the other groups. The platelet count (PLT), plateletcrit (PCT) and mean platelet volume (MPV) returned to the normal ranges after treatment, except those in the group with severe anemia. In the biochemical profile, B. ovis infection caused an increase in blood urea nitrogen and total bilirubin, and these parameters returned to normal levels after treatment. The indirect fluorescein antibody test (IFAT) results showed that 38.1% of the cases raised specific antibodies during the period of infection, with titers ranging from 1/160 to 1/640. All of 45 animals re-examined after treatment were seropositive, with high titers that rose up to 1/5120.

Instability of ovine babesiosis in an endemic area in Turkey.

This study was designed to determine the endemic status of Babesia ovis in sheep in Turkey. A total of 2000 sheep, from different age groups (i.e. 0-3, 4-6, 6-9, 10-12, and >12 months), were selected randomly from 132 sheep flocks. The presence of specific antibodies against B. ovis was diagnosed by indirect fluorescent antibody test (IFAT). A total of 843 (42.15%) serum samples were determined to be positive. The seropositivity rates in the age groups stated above were 31.90, 31.64, 47.69, 40.22, and 52.99%, respectively. The endemic status of the disease was determined by calculating the inoculation rate (h) of each group. The h value for each group was determined to be lower than 0.005, which revealed that the endemic status of B. ovis was instable. This report may indicate the necessity of vaccination.

Alterations of blood parameters after intramuscular administration of imidocarb in healthy lambs.

The aim of this study was to determine the safety of imidocarb dipropionate in sheep. Imidocarb dipropionate (IMDP) was administered (2.4 mg/kg, intramuscular; i.m.) to 10 sheep, and blood samples were obtained 0, 1, 6, and 9 days after treatment. Hemacell counts, serum biochemical values, coagulation values, and serum oxidative status were measured. IMDP caused transient decreases in pH, actual bicarbonate, standard bicarbonate, total carbon dioxide, base excess in vivo, base excess in vitro, oxygen saturation, lactate dehydrogenase, and retinol levels and transient increases in serum creatine kinase-MB, blood urea nitrogen, and creatinine levels. IMDP decreased adenosine deaminase activity, antithrombin III, and superoxide dismutase activity and increased white blood cell counts. In conclusion, IMDP may change serum oxidative status and cause coagulation disorders during treatment in sheep.

Idiopathic bilateral central giant cell reparative granuloma of jaws: a case report and literature review.

OBJECTIVES: The central giant-cell reparative granuloma has been defined as a localized benign but sometimes aggressive osteolytic proliferation consisting of fibrous tissue with hemorrhage and hemosiderin deposits, presence of osteoclast-like giant cells and reactive bone formation. It is a benign lesion usually appears as solitary, multilocular, radiolucencies, located in the mandible and maxilla. Multiple CGCRGs of the jaw bones is very rare and, if it occurs, it is usually associated with hyperparathyroidism in majority of the cases .This report presents an unusual case of a 12-year-old girl who has idiopathic, bilateral giant cell granulomas of the angulus mandible. METHODS: A 12 year-old girl was admitted to our department with complain of swelling on both right and left side of her lower jaw. There was no history of trauma, dental problem or neck infection. Blood chemistry, including calcium, alkaline phosphatase and inorganic phosphorus was normal. Patient had not family history, clinical appearance like cherubism or noonan syndrome and systemic anomalies. MRI showed, in right ramus mandible, 37 x mm x 35 mm x 28 mm size mass and in lenf ramus mandible, an expansile, 30 mm 38 mm x 12 mm size mass. The patient underwent surgical curettage of the lesion through an intraoral approach under general anesthesia. RESULT: The histopathologic examination of the lesion was reported as 'giant cell reparative granuloma. CONCLUSION: Our patient had multiple CGCRG in her jaw. In literature there is several reports about multiple CGCRG but unlike of that report our patient had no syndromes like Cherubism, Noonan syndrome, neurofibromatosis type-1 and systemic disease like hyperparathyroidism ,fibrous dysplasia. So we define this case as Idiopathic bilaterally central giant cell reparative granuloma of jaw.

Profiling the substrate specificity of viral protease VP4 by a FRET-based peptide library approach.

Knowing the substrate specificity of a protease is useful in determining its physiological substrates, developing robust assays, and designing specific inhibitors against the enzyme. In this work, we report the development of a combinatorial peptide library method for systematically profiling the substrate specificity of endopeptidases. A fluorescent donor (Edans) and quencher (Dabcyl) pair was added to the C- and N-termini of a support-bound peptide. Protease cleavage of the peptide removed the N-terminal quencher, resulting in fluorescent beads, which were isolated and individually sequenced by partial Edman degradation and mass spectrometry (PED-MS) to reveal the peptide sequence, as well as the site of proteolytic cleavage. The method was validated with bovine trypsin and Escherichia coli leader peptidase and subsequently applied to determine the substrate specificity of a viral protease, VP4, derived from the blotched snakehead virus (BSNV). The results show that VP4 cleaves peptides with a consensus sequence of (Abu/Ala/Pro)-X-Ala downward arrowX, in agreement with the previously observed cleavage sites in its protein substrates. Resynthesis and a solution-phase assay of several representative sequences against VP4 confirmed the library screening results.

[Chewing lice (Phthiraptera: Ischnocera, Amblycera) of starlings (Sturnus vulgaris, L.) in Turkey]. / Türkiye'de sigirciklarda (Sturnus vulgaris, L.) görülen bit (Phthiraptera; Ischnocera Amblycera) türleri.

This study was carried out in order to detect chewing lice species occurring on starlings (Sturnus vulgaris, L). For this purpose, 27 starlings which were shot and sent in nylon bags to our laboratory by hunters were inspected for lice. Nine lice specimens were collected from the starlings and they were preserved in vials separately in 70% alcohol. They were cleared in 10% KOH for one or two days and mounted on slides in Canada balsam. They were examined by light microscope and identified to species. Four (14.81%) of 27 starlings were found to be infested with lice. Four species were identified as Myrsidea cucullaris (Nitzsch, 1818), Brueelia nebulosa (Burmeister, 1838), Sturnidoecus sturni (Schrank, 1766) and Brueelia sp. All of them have been reported for the first time from starlings in Turkey.

Unconventional serine proteases: variations on the catalytic Ser/His/Asp triad configuration.

Serine proteases comprise nearly one-third of all known proteases identified to date and play crucial roles in a wide variety of cellular as well as extracellular functions, including the process of blood clotting, protein digestion, cell signaling, inflammation, and protein processing. Their hallmark is that they contain the so-called "classical" catalytic Ser/His/Asp triad. Although the classical serine proteases are the most widespread in nature, there exist a variety of "nonclassical" serine proteases where variations to the catalytic triad are observed. Such variations include the triads Ser/His/Glu, Ser/His/His, and Ser/Glu/Asp, and include the dyads Ser/Lys and Ser/His. Other variations are seen with certain serine and threonine peptidases of the Ntn hydrolase superfamily that carry out catalysis with a single active site residue. This work discusses the structure and function of these novel serine proteases and threonine proteases and how their catalytic machinery differs from the prototypic serine protease class.

A comparative study on the prevalence of Theileria equi and Babesia caballi infections in horse sub-populations in Turkey.

Blood and serum samples were taken from 481 horses, from a stud farm or a racecourse, and tested by microscopic examination of blood smears and cELISA for Theileria equi (T. equi) and Babesia caballi (B. caballi) infections. At the time of sampling, animals were also examined for tick infestations and clinical disease, which were not observed in any of the sampled horses. During the microscopic examination of thin blood smears, parasites were detected in the three horses from the racecourse. Overall seroprevalence of infection was detected as 18.50% (89 of 481 horses) by cELISA, with T. equi being significantly more prevalent than B. caballi. Of the 481 blood samples, 78 (16.21%) were serologically positive for T. equi and 4 (0.83%) were serologically positive for B. caballi. In addition, 7 (1.46%) samples were positive for both T. equi and B. caballi antibodies. Seropositivity rates in the racecourse horses were higher than those determined in the stud farm horses. The rates for T. equi, B. caballi and both species were 13.39, 0.52 and 0% in the horses from the stud farm and 27, 2 and 7% in the racecourse horses, respectively. These results indicate that equine piroplasmosis is more common in racehorses than studhorses and therefore it might be a serious concern in horses that participate to international races.

Follicular dendritic cell sarcoma: a case report.

BACKGROUND: Follicular dendritic cell (FDC) sarcoma is a neoplastic proliferation of spindled to ovoid cells showing morphologic and phenotypic features of follicular dendritic cells. It is a rare tumor that can present in nodal and extranodal sites. CASE: A 41-year-old woman presented with a 6-week history of an enlarging lump in her neck. Fine needle aspiration (FNA) was performed. FNA findings led to the diagnosis of malignant tumor. We suggested that it was an FDC sarcoma. The tumor was excised. On microscopic examination, the tumor largely replaced the lymph node. It was composed of oval to spindle cells arranged in sheets and interlacing fascicles with a storiform pattern. The tumor cells showed widespread immunopositivity for CD21. Based on these findings the diagnosis of FDC sarcoma was made. Two years later local recurrence occurred. CONCLUSION: FDC sarcoma has characteristic FNA findings. Once FDC sarcoma is suspected cytologically or histologically, immunohistochemical stains must be performed for reaching the correct diagnosis. Awareness of this rare entity is necessary to avoid its underrecognition.

Therapeutic and prophylactic efficacy of imidocarb dipropionate on experimental Babesia ovis infection of lambs.

The objective of this study was to evaluate the therapeutic and prophylactic efficacy of imidocarb dipropionate (IMDP) against babesiosis and to determine specific antibodies against Babesia ovis in experimentally infected lambs. Thirty-six 6-month-old splenectomized lambs were used. The lambs were randomly divided into six groups with six animals each, and were intravenously inoculated with 50 mL B. ovis-infected erythrocytes as follows: group I (therapy group) was treated with IMDP (1.2 mg/kg body weight) starting on the day of onset of clinical signs of babesiosis after the inoculation; group II (untreated control animals) was not treated with any therapeutic treatment after the inoculation; groups III, IV, V and VI (prophylaxis groups) were administered IMDP (2.4 mg/kg body weight) 1, 2, 3 and 4 weeks before the inoculation, respectively. The animals were housed in a tick-proof room with water and food ad libitum up to the 30th day post-inoculation (PI). The lambs were monitored from the first day PI by recording the manifestation of clinical disease, rectal temperature, and the degree of parasitaemia. All the lambs became infected with B. ovis, except five animals from group III, which were treated 1 week prior to experimental infection. Other animals showed signs of acute clinical babesiosis. The animals treated with IMDP (group I) were able to clear the parasite from the blood circulation after 48 h post-treatment. The recrudescence of B. ovis was observed in two lambs 7 days after treatment, and they were treated with the second similar dose of the drug. Six lambs (1, 1, 2 and 2 lambs in group III, IV, V and VI, respectively) from the prophylaxis groups died within 7-17 days after showing high parasitaemia and clinical symptoms of the disease. Regardless of the clinical symptoms, 83.30% and 66.66% of the lambs which were administered IMDP 1-2 and 3-4 weeks before, were determined to be protected against the virulent field strain of B. ovis.

Altered -3 substrate specificity of Escherichia coli signal peptidase 1 mutants as revealed by screening a combinatorial peptide library.

Signal peptidase functions to cleave signal peptides from preproteins at the cell membrane. It has a substrate specificity for small uncharged residues at -1 (P1) and aliphatic residues at the -3 (P3) position. Previously, we have reported that certain alterations of the Ile-144 and Ile-86 residues in Escherichia coli signal peptidase I (SPase) can change the specificity such that signal peptidase is able to cleave pro-OmpA nuclease A in vitro after phenylalanine or asparagine residues at the -1 position (Karla, A., Lively, M. O., Paetzel, M. and Dalbey, R. (2005) J. Biol. Chem. 280, 6731-6741). In this study, screening of a fluorescence resonance energy transfer-based peptide library revealed that the I144A, I144C, and I144C/I86T SPase mutants have a more relaxed substrate specificity at the -3 position, in comparison to the wild-type SPase. The double mutant tolerated arginine, glutamine, and tyrosine residues at the -3 position of the substrate. The altered specificity of the I144C/I86T mutant was confirmed by in vivo processing of pre-beta-lactamase containing non-canonical arginine and glutamine residues at the -3 position. This work establishes Ile-144 and Ile-86 as key P3 substrate specificity determinants for signal peptidase I and demonstrates the power of the fluorescence resonance energy transfer-based peptide library approach in defining the substrate specificity of proteases.