A genetic algorithm for structure-based de novo design

Genetic algorithms have properties which make them attractive in de novo drug design. Like other de novo design programs, genetic algorithms require a method to reduce the enormous search space of possible compounds. Most often this is done using information from known ligands. We have developed the ADAPT program, a genetic algorithm which uses molecular interactions evaluated with docking calculations as a fitness function to reduce the search space. ADAPT does not require information about known ligands. The program takes an initial set of compounds and iteratively builds new compounds based on the fitness scores of the previous set of compounds. We describe the particulars of the ADAPT algorithm and its application to three well-studied target systems. We also show that the strategies of enhanced local sampling and re-introducing diversity to the compound population during the design cycle provide better results than conventional genetic algorithm protocols.     

Some Comments on the Matter Wave-light Wave Hypothesis

From the de Broglie matter wave hypothesis and Planck’s energy quantization law, and assuming conservation of energy in the absorption of a photon and its consequent conversion to kinetic energy of motion by a material particle initially at rest, one can deduce a simple mathematical relationship between the wavelength λ (or frequency ν), of the photon absorbed by the particle at rest, and the resulting de Broglie matter wave length, λ_D, of the particle with kinetic energy of motion of mv²/2. The relationship so deduced, λ_D∝√λ, suggests that visible wavelengths of light, from about 4000 ?, in the violet, to beyond about 7000 ?, in the red, on absorption by an electron at rest, lead to material electron wavelengths, λ_D, of the order of the size of the electron transfer proteins seen in the photosynthetic reaction centers of photosynthesizing organisms, at about a size of 50–100 ?. In addition to understanding the mechanism of photosynthesis as a material wave mediated phenomenon, further areas of importance of the relations pointed out in this paper are in the design of experiments to gain a deeper understanding of the basic tenets of wave mechanics, and in the use of tunable lasers to probe various properties of material waves, and to precisely control their properties for applications including lithography.     

Covering with blocks in the non-symmetric case

Considering an infinite string of i.i.d. random letters drawn from a finite alphabet we define the cover timeW _n as the number of random letters needed until each pattern of lenghtn appears at least once as a substring. Sharp weak and a.s. limit results onW _n are known in the symmetric case, i.e., when the random letters are uniformly distributed over the alphabet. In this paper we determine the limit distribution ofW _n in the nonsymmetric case asn. Generalizations in terms of point processes are also proved.Dedicated to Endre Csáki on his 60th birthday.     

Modèles entiers des courbes hyperelliptiques sur un corps de valuation discrète

Let be a hyperelliptic curve of genus over a discrete valuation field . In this article we study the models of over the ring of integers of . To each Weierstrass model (that is a projective model arising from a hyperelliptic equation of with integral coefficients), one can associate a (valuation of) discriminant. Then we give a criterion for a Weierstrass model to have minimal discriminant. We show also that in the most cases, the minimal regular model of over dominates every minimal Weierstrass model. Some classical facts concerning Weierstrass models over of elliptic curves are generalized to hyperelliptic curves, and some others are proved in this new setting.

     

The regioselectivity of the formation of 2-pyrazolylthiazoles and their precursors from the reaction of 2-hydrazinothiazoles with 4,4,4-trifluoro-1-hetaryl-1,3-butanediones

Reaction of 2-hydrazinothiazoles 1 with 1-thienyl- and 1-furyl-1,3-butanediones 2a,b in methanol in the presence of hydrochloric acid mainly leads to a mixture of pyrazoles 3 and pyrazolines 4 or pyrazoles 3 and 5 in strong acidic conditions. Isomeric hydrazones 6 and pyrazolines 4 were formed and isolated in these reactions in the absence of hydrochloric acid. It has been shown that the regioselectivity in the reaction of diketones 2 with hydrazine 1 is governed by both the concentration of acid and the nature of substituents in the 1,3-diketones 2. Cyclization of hydrazones 6 is shown to occur under milder conditions than dehydration for pyrazolines 4. The new heterocyclic compounds were prepared and fully characterized by NMR spectra and by X-ray analysis for 3c.     

钴配合物的合成晶体结构及活性研究

The complex [Co₂Cl₂(EGTB)]·(ClO₄)₂·5H₂O was synthesized in methanol-aqueous solution and its crystal structure was determined by X-ray diffraction method. The crystal belongs to monoclinic with space group of P2₁/c. The cell parameters are a=1.42231(2)nm,b=2.53181(3)nm,c=1.43392(2)nm,β=102.0518(5)°, Z=4, F(000)=2360,D_c=1.508g·cm^-3, The final R=0.0788,wR₂=0.232, The catalytic rate constant of the dismutation of superoxide radicals has been obtained by means of photo reduction of nitroblue tetrazolium(NBT),and it is 1.875×10⁶mol^-1·L·s^-1.     

Selective formation of AAB- and ABC-type heterotrimeric alpha-helical coiled coils

The alpha-helical coiled coils have a representative amino acid sequence of (abcdefg)(n) heptad repeats. We previously reported that two peptides named IZ-2A and IZ-2W formed an (IZ-2A)(2)/IZ-2W heterotrimer with an Ala-Ala-Trp interaction in the hydrophobic core. In this paper, we describe the selective formation of AAB- and ABC-type heterotrimers. To increase the selectivity of the AAB-type heterotrimeric formation, Lys residues at the f position were mutated to either an Ala or a Gln residue to form IZ-2A(fA) or IZ-2W(fQ). Separately, both IZ-2A(fA) and IZ-2W(fQ) have a random structure at pH 7 and 20 degrees C. However, together IZ-2A(fA) and IZ-2W(fQ) form a 2:1 complex with a thermal transition midpoint (Tm) of 48 degrees C. This procedure was applied to prepare the ABC-type heterotrimer, in which two sets of Ala-Ala-Trp interactions were designed in the hydrophobic core. Interhelical interaction between the e and g positions and the alpha-helical propensity of the amino acid at the f position were also considered in the design. The resultant three peptides selectively formed the ABC-type heterotrimer with a Tm of 51 degrees C. Other peptide combinations had random coil properties.     

Synthese de derives mono- ou disilicies au niveau d'un carbone fonctionnel

Aliphatic saturated amides treated with Me₃SiCl/Li/THF were found to react in two ways. Either alkoxysilanes, mono- or di-silylated at the functional carbon, or C-silylated amines were obtained dependent of the original amide structure and the experimental conditions. (Me₃Si)₂CHN(SiMe₃)₂ exhibited Physicochemical properties that are particular for hindered rotation about the CN bond. A general mechanism is proposed to explain these results.     

Highly diastereoselective chemoenzymatic synthesis of (2′R)- and (2′S)-2′-deoxy[2′-H]guanosines

In an effort to develop an efficient synthetic method of highly diastereoselective (2′R)- and (2′S)-2′-deoxy[2′-²H]guanosines, chemoenzymatic conversion was investigated. The synthesis of (2′R > 98% de)-2′-deoxy[2′-²H]guanosine was achieved by biological transdeoxyribosylation using (2′R > 98% de)-2′-deoxy[2′-²H]uridine, 2,6-diaminopurine, and Enterobacter aerogenes AJ-11125, followed by treatment with adenosine deaminase. (2′S > 98% de)-2′-Deoxy[2′-²H]guanosine was synthesized from (2′S > 98% de)-2′-deoxy[2′-²H]uridine and 2,6-diaminopurine using thymidine phosphorylase and purine nucleoside phosphorylase instead of E. aerogenes AJ-11125.