Enzyme inhibitors as chemical tools to study enzyme catalysis: rational design, synthesis, and applications

Carefully designed molecules that are intimately related to the reaction mechanism of enzymes are often highly selective and potent inhibitors that serve as extremely useful chemical probes for understanding the reaction mechanism and structure of enzymes. This article describes the design, synthesis, and applications of specific inhibitors of two mechanistically distinct groups of enzymes, ATP-dependent amide ligases and Ser- and Thr-hydrolases. Our strategy is based on the premise that stable analogues of the transition state (transition-state analogues) are highly potent inhibitors that serve as good mechanistic probes, and that a key structure of a good inhibitor of one enzyme is also utilized for the inhibitors of other enzymes that share the same chemistry in their catalyzed reactions, irrespective of the degree of structural similarity and evolutionary link between the enzymes. According to these principles, we designed and synthesized a series of phosphinate- and sulfoximine-based transition-state analogue inhibitors of glutathione synthetase, gamma-glutamylcysteine synthetase and asparagine synthetase. For the second group of enzymes, we synthesized a gamma-monofluorophosphono glutamate analogue for mechanism-based affinity labeling of gamma-glutamyltranspeptidase and fluorescent phosphonic acid esters for the active-site titration of lipase. These inhibitors were used successfully as ligands for detailed kinetic analyses, X-ray crystallography, and mass analysis of the enzymes to identify the key amino acid residues responsible for catalysis and substrate recognition in the transition state.     

Automatic analysis of multiplex ligation-dependent probe amplification products (exemplified by a commercial kit for prenatal aneuploidy detection)

For use in routine prenatal diagnostics, we developed software and methods for automatic aneuploidy detection based on a commercial multiplex ligation-dependent probe amplification (MLPA) kit. Software and methods ensure a reliable, objective, and fast workflow, and may be applied to other types of MLPA kits. Following CE of MLPA amplification products, the software automatically identified the peak area for each probe, normalized it in relation to the neighboring peak areas of the test sample, computed the ratio relative to a reference created from normal samples, and compensated the ratio for a side effect of the normalization procedure that scaled all chromosomally normal DNA peak areas slightly up or down depending on the kind of aneuploidy present. For the chromosomes 13, 18, 21, X, and Y, probe reliability weighted mean ratio values and corresponding SDs were calculated, and the significance for being outside a reference interval around ratio 1.0 was tested. p < or = 1% suggested aneuploidy and 1 < p < or = 5% suggested potential aneuploidy. Individual peaks, where the normalized area was situated more than 4 SD from the corresponding reference, suggested possible partial deletion or gain. Sample quality was automatically assessed. Control probes were not required. Having used the software and methods for two years, we conclude that a reliable, objective, and fast workflow is obtained.     

Genomic variation and point mutations analysis of Indian COVID-19 patient samples submitted in GISAID database

Corona virus disease 2019 (COVID-19) endemic has havoc on the world; the causative virus of the pandemic is SARS CoV-2. Pharmaceutical companies and academic institutes are in continuous efforts to identify anti-viral therapy or vaccines, but the most significant challenge faced is the highly evolving genome of SARS CoV-2, which is imparting evolutionary selective benefits to the virus. To understand the viral mutations, we have retrieved nine hundred and thirty-four samples from different states of India via the GISAID database and analyzed the frequency of all types of point mutation in all structural, non-structural proteins, and accessory factors of SARS CoV-2. Spike glycol protein, nsp3, nsp6, nsp12, N and NS3 were the most evolving proteins. High frequency point mutations were Q496P (nsp2), A380V (nsp4), A994D (nsp3), L37F (nsp6), P323L & A97V (nsp12), Q57H (ns3), D614G (S), P13L (N), R203K (N), G204R (N) and S194L (N).     

Semi‐classical formulation of time‐dependent discrete variable representation method

In this article, we apply a novel time‐dependent discrete variable representation (TDDVR) method proposed by Barkakaty and Adhikari to investigate tunneling through an Eckart barrier. This semi‐classical method is theoretically rigorous and straightforward to implement. Among the TDDVR formulations, this report presents the first derivation of a rigorous form of quantum force (QF) for the present perspective. The validity of this semi‐classical approach is demanded based on the excellent agreement of the tunneling probability with the corresponding quantum results. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

Stochastic dominance with nonadditive probabilities

Choquet expected utility which uses capacities (i.e. nonadditive probability measures) in place of-additive probability measures has been introduced to decision making under uncertainty to cope with observed effects of ambiguity aversion like the Ellsberg paradox. In this paper we present necessary and sufficient conditions for stochastic dominance between capacities (i.e. the expected utility with respect to one capacity exceeds that with respect to the other one for a given class of utility functions). One wide class of conditions refers to probability inequalities on certain families of sets. To yield another general class of conditions we present sufficient conditions for the existence of a probability measureP with f dC= f dP for all increasing functionsf whenC is a given capacity. Examples includen-th degree stochastic dominance on the reals and many cases of so-called set dominance. Finally, applications to decision making are given including anticipated utility with unknown distortion function.     

Treatment of anions in SINDO1

The SINDO1 method is modified to include the calculation of molecular anions. Two versions of modifications are presented which are based on charge dependent orbital exponents. Calculated heats of formation and electron affinities are much improved compared to the standard version with fixed orbital exponents.Dedicated to Professor J. Koutecký on the occasion of his 65th birthday     

A comparative study of various computational approaches in calculating the structure of pyridoxal 5'-phosphate (PLP)-dependent beta-lyase protein. The importance of protein environment

Various computational approaches, using molecular mechanics (Amber), semiempirical (AM1), density functional (B3LYP), and various ONIOM methods, have been comparatively investigated for the structure of Escherichia coli NifS CsdB protein. The structure of the entire monomer containing 407 amino acid residues and 579 surrounding water molecules has been optimized. The full geometry optimization in the "active site-only" approach (including only active site atoms) has been found to give the largest root-mean-square (RMS) deviation from the X-ray structure; a much better agreement has been achieved by keeping the atoms leading to the backbones of some amino acids frozen in their positions in the X-ray structure. The best agreement has been attained by including the surrounding protein in the calculations using the two-layer ONIOM (B3LYP:Amber) approach. The results presented in this study conclusively demonstrate the importance of the protein/active-site interaction on the active-site structure of the enzyme. The present theoretical study represents the largest system studied at the ONIOM level to date, containing 7992 atoms, including 84 atoms in the QM region and rest in the MM region.     

Synthesis and characterization of temperature‐ and pH‐sensitive hydrogels based on poly(2‐ethyl‐2‐oxazoline) and poly(D,L‐lactide)

A novel series of temperature‐ and pH‐sensitive hydrogels based on poly(2‐ethyl‐2‐oxazoline) and three‐arm poly(D,L ‐lactide) were synthesized via photocopolymerization. For the creation of polymeric networks, two types of macromers terminated with methacrylate groups were prepared: poly(2‐ethyl‐2‐oxazoline) dimethacrylate and three‐arm poly(D,L ‐lactide) trimethacrylate. The chemical structures were analyzed with ¹H NMR and Fourier transform infrared techniques. The thermal behaviors, morphologies, and swelling properties were measured for the characterization of the polymeric networks. All the poly(2‐ethyl‐2‐oxazoline)/three‐arm poly(D,L ‐lactide)hydrogels provided high water retention capacity and exhibited reversible swelling–shrinking behavior in response to temperature and pH variations. The hydrogels with higher poly(2‐ethyl‐2‐oxazoline) dimethacrylate contents were more effective in raising the swelling ratio and temperature and pH sensitivity. However, higher contents of three‐arm poly(D,L ‐lactide) trimethacrylate produced larger particles and pore sizes in the hydrogels. This study effectively proves that this unique combination of water swellability and biodegradability provides hydrogels with a much wider range of applications in biomedical fields. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 1112–1121, 2002     

Enhancedt −3/2 long-time tail for the stress-stress time correlation function

Nonequilibrium molecular dynamics is used to calculate the spectrum of shear viscosity for a Lennard-Jones fluid. The calculated zero-frequency shear viscosity agrees well with experimental argon results for the two state points considered. The low-frequency behavior of shear viscosity is dominated by an ^1/2 cusp. Analysis of the form of this cusp reveals that the stress-stress time correlation function exhibits at ^–3/2 long-time tail. It is shown that for the state points studied, the amplitude of this long-time tail is between 12 and 150 times larger than what has been predicted theoretically. If the low-frequency results are truly asymptotic, they imply that the cross and potential contributions to the Kubo-Green integrand for shear viscosity exhibit at ^–3/2 long-time tail. This result contradicts the established theory of such processes.