Polarizable force fields.

Standard force fields used in biomolecular computing describe electrostatic interactions in terms of fixed, usually atom-centered, charges. Real physical systems, however, polarize substantially when placed in a high-dielectric medium such as water--or even when a strongly charged system approaches a neutral body in the gas phase. Such polarization strongly affects the geometry and energetics of molecular recognition. First introduced more than 20 years ago, polarizable force fields seek to account for appropriate variations in charge distribution with dielectric environment. Over the past five years, an accelerated pace of development of such force fields has taken place on systems ranging from liquid water to metalloenzymes. Noteworthy progress has been made in better understanding the capabilities and limitations of polarizable models for water and in the formulation and utilization of complete specifically parameterized polarizable force fields for peptides and proteins.

Potential energy functions.

When energy is a critical quantity, accurate biomolecular simulations rest in substantial part on accurate potential energy functions (force fields). Improvements in methodology for determining parameters--particularly, in the systematic use of computational data obtained from quantum chemical calculations--and enhancements in functional form are leading to better potential energy functions. New calculations have been developed for water (including calculations that incorporate electronic polarizability to take account of the degree to which a molecule can be polarized), proteins, nucleic acids, carbohydrates, lipids, and general organic molecules. Most notably, two new biomolecular force fields have recently been derived and significant redeterminations of the parameters of two existing biomolecular force fields have been carried out. Some progress has also been made in incorporating polarizability into potential energy functions for molecules in general and in improving the treatment of metal-ligand interactions in systems of biomolecular interest.

A priori prediction of activity for HIV-1 protease inhibitors employing energy minimization in the active site.

We have observed a high correlation between the intermolecular interaction energy (Einter) calculated for HIV-1 protease inhibitor complexes and the observed in vitro enzyme inhibition. A training set of 33 inhibitors containing modifications in the P1' and P2' positions was used to develop a regression equation which relates Einter and pIC50. This correlation was subsequently employed to successfully predict the activity of proposed HIV-1 protease inhibitors in advance of synthesis in a structure-based design program. This included a precursor, 47, to the current phase II clinical candidate, L-735,524 (51). The development of the correlation, its applications, and its limitations are discussed, and the force field (MM2X) and host molecular mechanics program (OPTIMOL) used in this work are described.

Highly potent, orally active diester macrocyclic human renin inhibitors.

Replacing one amide bond in macrocyclic renin inhibitors of the general structure 1 and 2 with an ester linkage gave glutamate-derived inhibitors 3 and serine-derived inhibitors 4. While this oxygen-for-nitrogen exchange had little effect on potency in the glutamate series, potency was dramatically increased in the serine series. In this series, the 14-membered ring compounds proved to be more potent than the corresponding 13-membered ring derivatives. Substitution of the ring at the position corresponding to P2' generally increased potency. The absolute configuration at this center was shown to be R for the 4-morpholinomethyl derivative (4o), both by asymmetric synthesis and X-ray crystallography. Replacing the "Boc-Phe" moiety of inhibitor 4o with a variety of substituents led to subnanomolar inhibitors, one of which (the "3(S)-quinuclidinyl-Phe" derivative 33) lowered blood pressure 20 mmHg and completely inhibited plasma renin activity for 6 h in sodium-depleted rhesus monkeys. This compound proved to have limited bioavailability (1% in rats) due to cleavage of the serine ester bond and rapid hepatic extraction.

Synthesis and use of 3-amino-4-phenyl-2-piperidones and 4-amino-2-benzazepin-3-ones as conformationally restricted phenylalanine isosteres in renin inhibitors.

The design of P2-P3 conformational restrictions in renin inhibitors by the use of a renin computer graphic model led to the synthesis of inhibitors containing N-Boc, N-acetyl, and N-phthalyl derivatives of 3(S)-amino-4(R,S)-2-piperidones and 4(S)-amino-2-benzazepinones in place of phenylalanine in the control compound N-acetyl-L-phenylalanyl-N-[4(S)-[(butylamino)carbonyl]-1(S)- (cyclohexylmethyl)-2(S)-hydroxy-5-methylhexyl]-L-norleuci namide (32). The piperidone inhibitors were prepared by utilization of the Evans chiral auxilliary to introduce the amino group with enantioselectivity and also to act as a leaving group in an intramolecular cyclization to the piperidone. The most potent inhibitor, 3(S)-(acetylamino)-alpha(S)-butyl-N-[4(S)- [(butylamino)carbonyl]-1(S)-(cyclohexylmethyl)-2(S)-hydroxy-5- methylhexyl]-2-oxo-4(R)-phenyl-1-piperidineacetamide (18, IC50 = 21 nM), was 25-fold less potent than the acyclic control 32. Considerable dependence of potency with the size of the P4 derivative was observed as had been expected based on the presynthetic modeling studies. Attempts to rationalize the observed potencies on the basis of further molecular modeling studies suggested that the loss in inhibitor potency was due to the conformational restrictions distorting the 3S center from the geometry present in the putative extended conformation present when the inhibitor is bound within the renin active site.

Design and synthesis of P2-P1'-linked macrocyclic human renin inhibitors.

Using a computer model of the active site of human renin developed at Merck, we designed a series of novel P2-P1'-linked, macrocyclic renin inhibitors 3-10. These unique inhibitors incorporate a transition-state isostere within a 13- or 14-membered ring. The three most active compounds in this family were 13-membered-ring glutamine-derived inhibitor 3, 14-membered-ring diaminopropionic acid derived inhibitor 6, and 13-membered-ring diol 9 (IC50 0.61, 0.59, 0.65 microM, respectively). Modification of inhibitor 3 at P4 led to 56 nM macrocyclic renin inhibitor 39. This study shows the viability of renin inhibitor designs which incorporate a scissile-bond replacement within a macrocycle.

Localized molecular orbital description of nitrogen lone pairs.

The Boys localization procedure is applied to several molecules possessing nitrogen lone pairs. The Boys structures show a tendency for the N lone pairs to participate in bonding to nearby electron sinks. For example, the Boys structure for planar formamide has two equivalent tau-bond orbitals between the carbonyl carbon and nitrogen atoms. The change in this description with variation of geometry at nitrogen is treated, and analogous Edmiston-Ruedenberg localizations on formamide are included for comparison.

Approximations to self-consistent field molecular wavefunctions.

Unparameterized and parameterized versions are outlined of a new method for approximating self-consistent field wavefunctions from first principles at the minimum basis set level for complex molecules containing hydrogen and first-row atoms. The Hartree-Fock self-consistent field equations for closed-shell molecules are solved, retaining all one-electron integrals, and approximating the two-electron Coulomb integrals, hybrid integrals, and exchange integrals of the form (i(A)j(A)[unk]i(A)j(A)) and (i(A)j(B)[unk]i(A)j(B)) for centers A and B. A symmetrically orthogonalized basis set is used and rotational invariance is achieved by transformation to local axes that are unique for atoms in anisotropic environments. Parameterization based upon first-principle self-consistent field wavefunctions for a large number of molecules yields F-matrix elements to 0.007 atomic units (au), density matrix elements to 0.007 electrons, orbital populations and atomic charges to 0.01-0.02 electrons, orbital energies to 0.01 au, and total energies to 0.02 au (all standard deviations), in computational times only a few times larger than those required for complete neglect of differential overlap calculations.

Evidence for hydrogen abstraction by classical radicals in the norbornenyl-nortricyclyl system.

Studies of product compositions and deuterium-label rearrangements at various concentrations of tri-n-butyltin hydride in the reductions of exo-and endo-5-bromonorbornene and 2-bromonortricyclcne to mixtures of norbornene and nortricyclene lead to three main conclusions: (i) at least two radical intermediates contribute to product formation; (ii) each intermediate yields predominantly (80% or more) one product; and (iii) nortricyclene is predominantly derived from a symmetrical intermediate. This constitutes strong evidence for hydrogen abstraction by classical (i.e., single-product) norbornenyl and nortricyclyl radicals. It is argued that the norbornenyl-nortricyclyl system is exceptionally well suited for the generation of a nonclassical (dual-product) radical; hence, the existence of a nonclassical radical in any other system is rather unlikely.