This paper describes the development of a simple empirical scoring function designed to estimate the free energy of binding for a protein-ligand complex when the 3D structure of the complex is known or can be approximated. The function uses simple contact terms to estimate lipophilic and metal-ligand binding contributions, a simple explicit form for hydrogen bonds and a term which penalises flexibility. The coefficients of each term are obtained using a regression based on 82 ligand-receptor complexes for which the binding affinity is known. The function reproduces the binding affinity of the complexes with a cross-validated error of 8.68 kJ/mol. Tests on internal consistency indicate that the coefficients obtained are stable to changes in the composition of the training set. The function is also tested on two test sets containing a further 20 and 10 complexes, respectively. The deficiencies of this type of function are discussed and it is compared to approaches by other workers.

Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes

http://csmres.co.uk/cs.public.upd/article-downloads/Synthetic-therapeutic-peptides-science-and-market.pdf

Synthetic therapeutic peptides: science and market.

The serpins have evolved to be the predominant family of serine-protease inhibitors in man. Their unique mechanism of inhibition involves a profound change in conformation, although the nature and significance of this change has been controversial. Here we report the crystallographic structure of a typical serpin-protease complex and show the mechanism of inhibition. The conformational change is initiated by reaction of the active serine of the protease with the reactive centre of the serpin. This cleaves the reactive centre, which then moves 71 A to the opposite pole of the serpin, taking the tethered protease with it. The tight linkage of the two molecules and resulting overlap of their structures does not affect the hyperstable serpin, but causes a surprising 37% loss of structure in the protease. This is induced by the plucking of the serine from its active site, together with breakage of interactions formed during zymogen activation. The disruption of the catalytic site prevents the release of the protease from the complex, and the structural disorder allows its proteolytic destruction. It is this ability of the conformational mechanism to crush as well as inhibit proteases that provides the serpins with their selective advantage.

Structure of a serpin–protease complex shows inhibition by deformation

Molecular recognition of protein-ligand complexes : applications to drug design

Deuterium, the stable isotope of hydrogen, is known to medicinal chemists for its utility in mechanistic, spectroscopic, and tracer studies. In fact, well-known applications utilizing deuterium exist within every subdiscipline in pharmaceutical discovery and development. Recent emphasis on incorporation of deuterium into the active pharmaceutical ingredient has come about as a result of inquiries into the potential for substantial benefits of the deuterium kinetic isotope effect on the safety and disposition of the drug substance. This Perspective traces the author's experience in reviving and expanding this potential utility, first suggested many decades prior by the discoverer of this, the simplest of all isotopes.

Using Deuterium in Drug Discovery: Leaving the Label in the Drug

Peptides comprising C-terminal boronic acid derivatives of lysine, ornithine, and arginine, homoarginine and corresponding isothiouronium analogs thereof, are reversible inhibitors of trypsin-like serine proteases such as thrombin, plasma kallikrein and plasmin.

Peptide boronic acid inhibitors of trypsin-like proteases

Peptides comprising C-terminal a-aminoboronic acid residues are potent, reversible inhibitors of proteolytic enzymes.

Alpha-aminoboronic acid peptides

Proton magnetic resonance studies of the active center histidine of chymotrypsin complexed to peptideboronic acids: Solvent accessibility to the N.delta. and N.epsilon. sites can differentiate slow-binding and rapidly reversible inhibitors

A synthetic route has been developed which has allowed us to prepare novel alpha-aminoboronic acids as inhibitors of serine proteases. These compounds were prepared to study the roles of proteases in biological systems. This methodology affords alpha-aminoboronic acids with the general formula R'-NHCH(R)BO(2)-pinanediol, where R = -CH(2)CHF(2), -CH(2)CO(2)tBu, and -(CH(2))(2)CO(2)Me and R' = either H or C(O)R". The latter two compounds are the boronic acid analogues of the natural amino acids aspartic acid and glutamic acid with the side chain carboxylate protected as a tert-butyl or a methyl ester, respectively. Following acylation of the amino group, the side chain tert-butyl ester of boroaspartic acid was removed by treatment with TFA. Boroglutamic acid was obtained as the free boronic acid by hydrolysis with HCl. Prior syntheses of alpha-aminoboronic acids involve the initial addition of an organometallic reagent to a trialkyl borate ester. These conditions do not allow the preparation of compounds with functionalities that are not stable to the strongly basic reaction conditions. The methodology described here allows the preparation of alpha-aminoboronic acids by introducing side chains as electrophiles. This is particularly advantageous for side chains which are prone to elimination or unwanted enolate formation. Specifically, BrCH(2)CHF(2), BrCH(2)COO(t)Bu, and CH(2)=CHCOOMe were allowed to react with the stabilized anion of (phenylthio)methane boronate, PhSCH(2)BO(2)C(6)H(12), to give the substituted boronate. The substituted (phenylthio)methane boronate was converted to the corresponding sulfonium ion by treatment with methyl iodide and subsequently displaced with iodide. The alpha-iodo derivative was converted to the amine by conventional methods.

Synthesis of boronic acid analogues of alpha-amino acids by introducing side chains as electrophiles.

Rational design of boropeptide thrombin inhibitors: β,β-dialkyl-phenethylglycine P2 analogs of DuP 714 with greater selectivity over complement factor I and an improved safety profile

Charles A. Kettner

Papers

Peptide boronic acid inhibitors of trypsin-like proteases

Alpha-aminoboronic acid peptides

Proton magnetic resonance studies of the active center histidine of chymotrypsin complexed to peptideboronic acids: Solvent accessibility to the N.delta. and N.epsilon. sites can differentiate slow-binding and rapidly reversible inhibitors

Synthesis of boronic acid analogues of alpha-amino acids by introducing side chains as electrophiles.

Rational design of boropeptide thrombin inhibitors: β,β-dialkyl-phenethylglycine P2 analogs of DuP 714 with greater selectivity over complement factor I and an improved safety profile