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D Suárez

Publications and source records attributed to D Suárez.

At least 19 recordsLinked to original sources
PubMed2001

Molecular dynamics simulations of the mononuclear zinc-beta-lactamase from Bacillus cereus complexed with benzylpenicillin and a quantum chemical study of the reaction mechanism.

Herein, we present results from MD simulations of the Michaelis complex formed between the B. cereus zinc-beta-lactamase enzyme and benzylpenicillin. The structural and dynamical effects induced by substrate-binding, the specific role of the conserved residues, and the near attack conformers of the Michaelis complex are discussed. Quantum chemical methods (HF/6-31G* and B3LYP/6-31G*) are also applied to study the hydrolysis reaction of N-methylazetidinone catalyzed by a monozinc system consisting of the side chains of the histidine residues (His86, His88, and His149) complexed with Zn-OH and the side chains of Asp90 and His210. From this model system, we built molecular-mechanics representations of the prereactive complex and transition state configurations docked into the active site. Linear-scaling semiempirical calculations coupled with a continuum solvent model were then performed on these static models. We propose that the experimental rate data for the B. cereus enzyme is compatible with a one-step mechanism for the hydrolysis of beta-lactam substrates in which His210 acts as a proton donor.

Bacillus cereus↗
PubMed2001

A theoretical study of the aminolysis reaction of lysine 199 of human serum albumin with benzylpenicillin: consequences for immunochemistry of penicillins.

Herein, we present results of a computational study on benzylpenicillin attachment to Lys199 of human serum albumin via an aminolysis reaction. The internal geometry of the reactive part of the system was taken from previous work at the B3LYP/6-31+G* level on the water-assisted aminolysis reaction of a penicillin model compound (Díaz, N.; Suárez, D.; Sordo, T. L. J. Am. Chem. Soc. 2000, 122, 6710--6719). The protein environment around Lys199, the 6-acylamino side chain, and the 2-methyl groups of benzylpenicillin were relaxed by carrying out geometry optimizations with a hybrid QM/MM method (PM3/AMBER). Two different mechanistic routes were explored: a one-step water-assisted process and a carboxylate and water-assisted route in which the beta-lactam carboxylate and the ancillary water molecule mediate the proton transfer from the epsilon-amino group of Lys199 to the beta-lactam leaving N atom. The corresponding energy profiles in the protein combine the B3LYP/6-31+G* and PM3 energies of the reactive subsystem (benzylpenicillin + Lys199 side chain + the ancillary water molecule) and semiempirical PM3 energies of the entire system evaluated with a "divide and conquer" linear-scaling method. It is observed that penicillin haptenation to HSA can proceed through the water-assisted concerted mechanism which is calculated to have a high energy barrier of approximately 38 kcal/mol, in agreement with the experimentally observed slow reaction kinetics.

Humans↗
PubMed2001

Quantum chemical study of ester aminolysis catalyzed by a single adenine: a reference reaction for the ribosomal peptide synthesis.

Herein we report the results of a HF/6-31+G** and B3LYP/6-31+G** computational investigation of the title reaction for the peptide bond synthesis catalyzed by a single adenine. This system constitutes a reference reaction to study the basic chemical events that have been proposed to occur at the peptidyl transferase active site of ribosomes on the basis of structural determinations (Science 2000, 239, 920--931). Thus, the analysis of the geometry, charge distribution, and energetics of the critical structures involved in this title reaction yields insight into the catalytic mode of action of RNA molecules. Our computational results give further support to the hypotheses that the activated nucleotide A2451 in the ribosome acts as a base catalyst and that this role is similar to that of the His residue in the catalytic triad of serine proteases.

Acetates↗
PubMed2001

Evaluation of the catalytic mechanism of AICAR transformylase by pH-dependent kinetics, mutagenesis, and quantum chemical calculations.

The catalytic mechanism of 5-aminoimidazole-4-carboxamide ribonucleotide transformylase (AICAR Tfase) is evaluated with pH dependent kinetics, site-directed mutagenesis, and quantum chemical calculations. The chemistry step, represented by the burst rates, was not pH-dependent, which is consistent with our proposed mechanism that the 4-carboxamide of AICAR assists proton shuttling. Quantum chemical calculations on a model system of 5-amino-4-carboxamide imidazole (AICA) and formamide using the B3LYP/6-31G level of theory confirmed that the 4-carboxamide participated in the proton-shuttling mechanism. The result also indicated that the amide-assisted mechanism is concerted such that the proton transfers from the 5-amino group to the formamide are simultaneous with nucleophilic attack by the 5-amino group. Because the process does not lead to a kinetically stable intermediate, the intramolecular proton transfer from the 5-amino group through the 4-carboxamide to the formamide proceeds in the same transition state. Interestingly, the calculations predicted that protonation of the N3 of the imidazole of AICA would reduce the energy barrier significantly. However, the pK(a) of the imidazole of AICAR was determined to be 3.23 +/- 0.01 by NMR titration, and AICAR is likely to bind to the enzyme with its imidazole in the free base form. An alternative pathway was suggested by modeling Lys266 to have a hydrogen-bonding interaction with the N3 of the imidazole of AICAR. Lys266 has been implicated in catalysis based on mutagenesis studies and the recent X-ray structure of AICAR Tfase. The quantum chemical calculations on a model system that contains AICA complexed with CH3NH3+ as a mimic of the Lys residue confirmed that such an interaction lowered the activation energy of the reaction and likewise implicated the 4-carboxamide. To experimentally verify this hypothesis, we prepared the K266R mutant and found that its kcat is reduced by 150-fold from that of the wild type without changes in substrate and cofactor Km values. The kcat-pH profile indicated virtually no pH-dependence in the pH range 6-10.5. The results suggest that the ammonium moiety of Lys or Arg is important in catalysis, most likely acting as a general acid catalyst with a pK(a) value greater than 10.5. The H267A mutant was also prepared since His267 has been found in the active site and implicated in catalysis. The mutant enzyme showed no detectable activity while retaining its binding affinity for substrate, indicating that it plays a critical role in catalysis. We propose that His267 interacts with Lys266 to aid in the precise positioning of the general acid catalyst to the N3 of the imidazole of AICAR.

Binding Sites↗
PubMed2001

Molecular dynamics simulations of the mononuclear zinc-beta-lactamase from Bacillus cereus.

Herein, we report molecular dynamics simulations of the mononuclear form of the Bacillus cereuszinc-beta-lactamase. We studied two different configurations which differ in the presence of a zinc-bound hydroxide or a zinc-bound water and in the protonation state of the essential His210 residue. Contacts of the catalytically important residues (Asp90, His210, Cys168, etc.) with the zinc center are characterized by the MD analyses. The nature of the Zn-OH(2) --> His210 proton transfer pathway connecting the two configurations was studied by means of QM calculations on cluster models while the relative stability of the two configurations was estimated from QM/MM calculations in the enzyme. From these results, a theoretical model for the kinetically active form of the B. cereus metalloenzyme is proposed. Some mechanistic implications and the influence of mutating the Cys168 residue are also discussed.

Bacillus cereus↗
PubMed2001

Molecular dynamics study of the IIA binding site in human serum albumin: influence of the protonation state of Lys195 and Lys199.

The IIA binding site of human serum albumin (HSA) preferentially binds hydrophobic organic anions of medium size (e.g., aspirin, benzylpenicillin, warfarin, etc.) and bilirubin. This binding ability is particularly important for the distribution, metabolism, and efficacy of drugs. In addition, HSA can also covalently link to different IIA substrates owing to the presence of a highly reactive residue, Lys199, which is strategically located in the IIA site. Herein, we present results of three restrained molecular dynamics (MD) simulations of the IIA binding site on the HSA protein. From these simulations, we have determined the influence that the ionization state of the key residue, Lys199, and the nearby Lys195 has on the structure and dynamics of the IIA binding site. When Lys199 is neutral the computed average distances for the most significant interresidue contacts are in good agreement with those estimated from the X-ray coordinates. The analysis of the solvent structure and dynamics indicates that the basic form of Lys199 is likely connected to the acid form of Lys195 through a network of H-bonding water molecules with a donor --> acceptor character. The presence of these water bridges can be important for stabilizing the configuration of the IIA binding site and/or promoting a potential Lys195 --> Lys199 proton-transfer process. These results suggest that both lysine residues located in the IIA binding site of HSA, Lys195 and Lys199, could play a combined and comparable chemical role. Our simulations also give insight into the binding of bilirubin to HSA.

Binding Sites↗
PubMed2001

Multicenter randomized study comparing initial daily induction with high dose lymphoblastoid interferon vs. standard interferon treatment for chronic hepatitis C.

One hundred fifty-five chronic hepatitis C patients were assigned at random to receive natural lymphoblastoid interferon (IFN)alpha-n1, s.c., for 13 months in one of three treatment regimens: initial daily induction with 10 million units (MU) followed (group 1, n = 50) or not (group 2, n = 52) by 1 month of rest and then three times weekly 10 MU (2 months), 5 MU (2 months), and 3 MU (8 months); group 3 (n = 53) received tiw 5 MU (2 months) followed by 3 MU (11 months). By intention-to-treat analysis, ALT normalization at completion of treatment was greater in patients who received continuous IFNalpha-n1 therapy with initial daily induction (group 2: 24/52, 46%) compared with those given intermittent therapy with initial daily induction (group 1: 17/50, 34%) and those who received standard IFNalpha-n1 therapy (group 3, 18/53, 34%; P not significant). The sustained ALT response was 26%, 27% and 21% and the sustained virological response was 20%, 27%, and 19%, in groups 1, 2, and 3, respectively. A trend was observed towards a higher biochemical and virological end-of-treatment response in patients given induction therapy (17%) compared with standard therapy (6%, P = 0.053). Sustained biochemical and virological responses were 20%, 27%, and 17% in groups 1, 2, and 3, respectively. Platelet and leukocyte counts decreased following daily high-dose treatment and remained low until therapy cessation (P < 0.001). The data suggest that daily s.c. induction with 10 MU IFNalpha-n1 followed by intermittent or continuous maintenance therapy for 1 year does not improve the results achieved with the standard 1-year IFNalpha course in the treatment of chronic hepatitis C patients.

Adolescent↗
PubMed2001

New developments in applying quantum mechanics to proteins.

Algorithmic improvements of quantum mechanical methodologies have increased our ability to study the electronic structure of fragments of a biomolecule (e.g. an enzyme active site) or entire biomolecules. Three main strategies have emerged as ways in which quantum mechanics can be applied to biomolecules. The supermolecule approach continues to be utilized, but it is slowly being replaced by the so-called coupled quantum mechanical/molecular mechanical methodologies. An exciting new direction is the continued development and application of linear-scaling quantum mechanical approaches to biomolecular systems.

Algorithms↗
PubMed1999

Myelodysplastic syndrome: a search for minimal diagnostic criteria.

We have evaluated dyshemopoietic features in bone marrow (BM) samples obtained from healthy people aged over 50 without peripheral blood (PB) cytopenia patients and compared them with MDS patients. Control group displayed BM features of dyserythropoiesis and dysgranulopoiesis in up to 15 and 27% of the considered cell elements (P90) respectively, overlapping in part with MDS patients. Interobserver agreement in dyshemopoietic features was highest for BM blast cell and pathological sideroblast counts. An algorithm based on BM blast cell and pathological sideroblast counts that has been verified on 613 patients from different Spanish centers may be of help to improve reproducibility in Myelodysplastic syndrome (MDS) diagnosis.

Cells, Cultured↗
PubMed1999

The mechanical behaviour of human mandibles studied by electronic speckle pattern interferometry.

An understanding of the mechanical behaviour of the human mandible during mastication may be useful in several specific medical fields that examine the maxillofacial area. In this research, the Electronic Speckle Pattern Interferometry Optical Technique was applied to study a dry mandible under external stress. Two images of the mandible, i.e. an image of the relaxed mandible and another of the mandible under stress, were processed using this technique and provided information concerning the most stressed areas of the bone. The advantage of interferometric analysis is that it can be carried out in real time on a mandible to which progressively greater stress has been applied. This research may be of value in maxillofacial surgery, for example, in the diagnosis and treatment of fractured mandibles, and in oral surgery and orthodontics, where it can provide information concerning stress dispersion when an osteointegrated implant or orthodontic appliance is placed in the mouth. One of the most important conclusions to be drawn from the experiments of tension, compression, and in- and out-of-plane deformations is that the capability of the mandible to bend is superior to its capability to stretch. Several quantitative results support this conclusion.

Female↗
PubMed1998

[Intestinal obstruction and necrotizing thyroiditis secondary to Pneumocystis carinii infection in a seropositive hemophiliac patient seropositive for human immunodeficiency virus].

We report a case of bowel infection by Pneumocystis carinii (PC) that presented as an acute obstruction accompanied by intestinal hemorrhage (melena) in a HIV seropositive hemophilic patient. Laparotomy followed by resection of two plaque-like jejunal tumors was performed, and intravenous therapy with pentamidine was initiated. No other organ was found to be affected by PC (not even the lung), with the exception of the thyroid gland. To our knowledge, this is the first reported case in which acute intestinal obstruction was the presenting symptom of extrapulmonary pneumocystosis.

AIDS-Related Opportunistic Infections↗
PubMed1997

A pilot study on the efficacy of escalating dosage of alpha-interferon for chronic hepatitis C in HIV-infected patients. The Hepatitis/HIV Spanish Study Group.

Chronic liver disease caused by hepatitis C virus (HCV) seems to present a more accelerated course in HIV-infected patients, leading to cirrhosis and liver failure in a shorter period of time than in HIV-negative individuals. As efforts to increase life expectancy in HIV-infected people progress, substantial morbidity and mortality from HCV infection is likely to arise amongst subjects infected parenterally, such as injecting drug users, haemophiliacs and transfusion recipients. Preliminary results have suggested that alpha-interferon (IFN) treatment allows higher rates of response in HIV-infected patients with higher CD4+ lymphocyte counts, suggesting a primary dependence of IFN on a preserved immune system in order to act appropriately. In an open, multicentre, prospective trial we analysed whether the use of larger doses of IFN, through an escalating schedule, might overcome the limits imposed by immune dysfunction. An interim analysis performed in 29 patients concluded that escalating the dosage did not improve the rate of response to IFN. In fact, only one (8.3%) out of 12 patients without response after 3 months of being on IFN therapy achieved response after the dosage was increased from 5 MU to 8 MU s.c. three times a week. Moreover, he relapsed 3 months after completion of treatment for 1 year.

Adult↗
PubMed1997

Multicenter randomized, controlled study of intramuscular administration of interferon-beta for the treatment of chronic hepatitis C.

The intramuscular administration of interferon-beta (IFN-beta) at a dosage of 6 million units three times per week for 6 months has been evaluated in 90 patients included in a multicenter, randomized, controlled trial for the treatment of chronic hepatitis C. Transaminase levels were significantly reduced in IFN-beta-treated patients (p = 0.015) and were significantly lower with respect to those of the untreated controls (p = 0.040 at 6 months). Four treated (8%) and one untreated (2.5%) patients had normal transaminase values after 6 months. At study end (12 months), three quarters of the IFN-beta-treated patients had sustained transaminase normalization, whereas the untreated case had relapsed. Hepatitis C viremia was cleared in 6 (12%) treated patients but in none of the untreated controls (p = 0.058). Side effects of IFN-beta were infrequent (a mild flu-like syndrome in < 10%, asthenia in 16%, anorexia in 8%, headaches and weight loss in 8%, and hair loss in 4%). Leukocyte and platelet counts decreased during IFN-beta treatment, but no dose modifications were necessary. Such decreases were not statistically significant when compared with the levels in the untreated controls. Intramuscular IFN-beta at the dosage used has little efficacy in the treatment of chronic hepatitis C. Because of IFN-beta tolerance, higher doses and alternate routes of injection might prove beneficial for the treatment of this disease.

Adult↗
PubMed1997

Tolerance and efficacy of subcutaneous interferon-beta administered for treatment of chronic hepatitis C.

We studied tolerance to subcutaneous (s.c.) administration of 6 million units of interferon-beta (IFN-beta), given three times per week for 6 months, and its efficacy in the treatment of 15 patients with chronic hepatitis C. At the end of the treatment, alanine aminotransferase (ALT) levels were significantly reduced (p = 0.024) in all patients, and 4 (27%) had a normal ALT value. However, at the end of the study (12 months), only 1 of these 4 had a sustained response. No patient cleared hepatitis C virus (HCV) RNA completely, but the RNA could be detected only by polymerase chain reaction (PCR) in the sustained responder. Adverse side effects to the s.c. IFN-beta were infrequent. Leukocyte (p = 0.012) and platelet (p = 0.013) counts decreased significantly during treatment but did not necessitate dose modifications. Thus, although s.c. IFN-beta at the dosage used had little efficacy in the treatment of chronic hepatitis C, the excellent tolerance to the treatment suggests that the effects of higher doses should be explored.

Adult↗
PubMed1996

[The treatment of chronic hepatitis C with interferon in patients infected with the human immunodeficiency virus. The Spanish Group for the Study of Viral Hepatitis in HIV+ Patients].

BACKGROUND: Alfa-interferon (aIFN) is widely recommended for the treatment of chronic hepatitis C (CHC). Hepatitis C virus (HCV) infection is very common in injecting drug users (IDUs), which in Spain represent the large number of HIV-infected persons. Interaction between human immunodeficiency virus (HIV) and HCV in coinfected patients might accelerate the clinical course of HCV-associated liver disease. The efficacy and safety of aIFN therapy in HIV-infected patients with CHC is not well known. PATIENTS AND METHODS: In a multicenter, prospective, open, non randomized and partially controlled study, we compared the efficacy and safety of aIFN therapy in 119 patients with CHC, of whom 90 were HIV-positive and 29 HIV-negative. Interferon was started at 5 mega U tiw for 3 months, followed in responders by 3 megaU tiw for additional 9 months. RESULTS: One hundred seven patients completed the study. A normalization of the aminotransferase values at the end of treatment (complete response, CR) was observed in 26/80 (32.5%) HIV-positive and 10/27 (37.0%) HIV-negative individuals (p = 0.666). Relapses at 12 months of stopping aIFN were seen in 30.8% of HIV-positive subjects and 12.5% of HIV-negatives (p = 0.403). Side effects were uncommon and did not have severity; only one patient required to stop the medication. However, 3 HIV-positive subjects treated with aIFN (3.5% of them) showed an irreversible fall of CD4+ T-cells below half the baseline values. CONCLUSION: HIV-infected patients with CHC seems to respond to aIFN with a similar rate than HIV-negatives. Moreover, the drug is similarly well tolerated in both groups of patients, although a fall of CD4+ T-cells is an unusual side effect of particular relevance observed in HIV-infected patients.

AIDS-Related Opportunistic Infections↗
PubMed1996

Interferon alpha for the treatment of chronic hepatitis C in patients infected with human immunodeficiency virus. Hepatitis-HIV Spanish Study Group.

Liver disease secondary to hepatitis C virus (HCV) infection is a rising cause of morbidity and mortality among individuals who have been infected parenterally with human immunodeficiency virus (HIV) such as injection drug users, hemophiliacs, and transfused patients. We analyzed both the efficacy of interferon (IFN) alpha therapy in these patients and the predictors of response to this agent. A total of 119 patients with chronic hepatitis C (90 of whom were infected with HIV and 29 of whom were not) were included in a multicenter, prospective, open, nonrandomized observational study. IFN-alpha was given subcutaneously in a dosage of 5 million units three times a week during a 3-month period; those patients who responded received a dose of 3 million units given subcutaneously three times a week for an additional 9 months. One hundred seven patients completed the study; the level of aminotransferases returned to normal and sera became negative (complete response) for HCV RNA in 26 (32.5%) of 80 HIV-infected patients and 10 (37.0%) of 27 non-HIV-infected patients (P = .666) after completion of the treatment. Two variables were independently associated with a response in HIV-infected patients: a CD4+ T lymphocyte count of > 500 x 10(6)/L and a baseline HCV viremia level of < 10(7) copies/mL. In the 12 months following treatment, relapses occurred in 30.8% of the HIV-infected patients and 12.5% of non-HIV-infected patients (P = .403).

Adult↗