INTRODUCTION - BOOK II

BOOK II

Collaborating Project Reports and Supporting Appendixes

The following sections detail the reports and plans for SUMEX-AIM
collaborating projects and also contain additional information in the form of
appendixes relating to the core resource progress and operation. The heading and
page numbering of these sections does not continue sequentially from that of the
Book I progress report. The discontinuity reflects the initial organization of
this material as part of our renewal grant application.

J. Lederberg
COLLABORATIVE PROJECTS

6 COLLABORATIVE PROJECT PROGRESS AND OBJECTIVES

The following subsections report on the collaborative use of the SUMEX
facility including the formally authorized projects within the Stanford and AIM
aliquots and the various "pilot" efforts currently under way. These project
descriptions and comments are the result of a solicitation for contributions sent
to each of the project Principal Investigators requesting the following
information:

I) Summary of research program
A) Technical goals
B) Medical relevance and collaboration
C) Progress summary
D) Up-to-date list of publications

II) Interactions with the SUMEX-AIM resource
A) Examples of collaborations and medical use of programs via
SUMEX
B) Examples of sharing, contacts and cross-fertilization with other
SUMEX-AIM projects (via workshops, system facilities, personal
contact, etc.)

We believe that the reports of the individual projects speak for themselves as
rationales for participation; in any case the reports are recorded as submitted
and are the responsibility of the indicated project leaders.

6.1 STANFORD PROJECTS

The following group of projects is formally approved for access to the
Stanford aliquot of the SUMEX-AIM resource. Their access is based on review by
the Stanford Advisory Group and approval by Professor Lederberg as Principal
Investigator. As noted previously, the DENDRAL project was the historical core
application of SUMEX. Although this is described as a "Stanford project," a
Significant part of the development effort and of the computer usage is dedicated
to national collaborator-users of the DENDRAL programs.

44 J. Lederberg
Section 6.1.1 DENDRAL PROJECT

6.1.1 DENDRAL PROJECT

DENDRAL ~ Resource Related Research ~- Computers & Chemistry
Carl Djerassi, Principal Investigator
Professor of Chemistry
Stanford University
I. OVERVIEW OF RESEARCH ACTIVITIES

Technical Goals

Our research, development and future plans focus on both the question of
Structure elucidation in general and the problem of providing computer assistance
to scientists engaged in specific aspects of this important activity.

A simplified representation of major milestones in solving unknown
biomolecular structures by manual methods is presented in Figure 1.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

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Figure 1. Important steps in manual solution of structures of unknown chemical
compounds.

These steps, indicated as separate boxes, may be performed explicitly or
implicitly. There are considerably more complex relationships among the boxes of
Fig. 1 than are indicated when structures are actually solved. Nevertheless, the
Figure provides a good introduction to both our recent work and our future
directions. We describe briefly each of the milestones in the following

paragraphs. More detailed discussions of each topic follow in subsequent
sections.

J. Lederberg 42 Privileged Communication
DENDRAL PROJECT Section 6.1.1

The first step in identification of an unknown structure is to separate it
from other components in a potentially complex mixture and to isolate it in
reasonably pure form. These steps are performed by scientists, frequently with
the assistance of various instruments. Although our research is not directed
toward any part of this separation and isolation procedure (except insofar as
these procedures also yield data which are subject to computer-assisted
interpretation), information about the chemical and physical characteristics of
tne compound may be crucial to further efforts to determine its structure.

Depending on the quantity of sample available and its characteristics,
various spectroscopic and additional chemical data are then collected on the
unknown. A mass spectrum is frequently obtained, e.g., from a combined gas
chromatograph/mass spectrometer (GC/MS) system. An important part of our recent
proposal to the NIH is directed toward automation of combined GC/MS systems
operated at high mass spectrometer resolving powers. Data on elemental
compositions and relative ion abundances are then available in computer-readable
form for further analysis (see MSRANK). The chemist possess an armamentarium of
spectroscopic techniques which can be brought to bear on a structure. One
advantage of our work is that any data so obtained can be used to help solve the
structure as long as it can be expressed, manually or by computer, in
Substructural statements about the unknown.

The next important phase in structure elucidation is interpretation of the
available data (Fig. 1) in terms of structural features of the molecule. These
interpretations may be in terms of known structural units ("superatoms",
polyatomic aggregates of atoms in known configurations), or in terms of
Structural units, ring sizes, proton or carbon distributions. The latter set of
features represents constraints on the kinds of structures which are possible.
Our efforts in the area of computer-assisted data interpretation are focussed on
mass spectral and carbon-13 nuclear magnetic resonance (13CMR) data. We are
developing general approaches to automated analysis of these data in terms of
structural features of unknowns.

Our recent efforts are summarized in Figure 2, and discussed in detail
subsequently. We have been concerned with use of these data from two points of
view, planning and prediction (Fig. 2). During planning, experimental data are
examined in order to extract specific structural information to be used in
assembling candidate structures. In prediction each candidate structure is
tested to determine how closely its predicted spectrum agrees with the observed
Spectrum. The candidates can be ranked accordingly. The Meta~DENDRAL research
is directed toward determination of rules of spectroscopic data which can be used
either for planning or prediction (see below).

Given possible structural fragments of the complete molecule and
constraints on how these fragments may be assembled into complete molecules, a
process of structural assembly follows (Fig. 1). There has been no proven
algorithm for solving this problem prior to earlier work supported by the current
grant. Traditionally, this process has been left to manual, pencil and paper
work. Our CONGEN program, which was designed to solve this problem, is the
farthest advanced of programs designed to assist in various aspects of structure
elucidation. It performs the structural assembly process, under constraints, and

Privileged Communication 43 J. Lederberg
Section 6.1.1

DATA INTERPRETATION

 

“PLANNING”

EXTRACTION OF STRUCTURAL
INFORMATION DIRECTLY FROM
SPECTROSCOPIC DATA,

1. Mass Spectra - MDGGEN
2, t3CNMR

DENDRAL PROJECT

PREDICTION

USE OF SPECTROSCOPIC
DATA TO RANK
CANDIDATE STRUCTURES,

1. MSPRUNE, MSPRED
2, 3CNMR

OL

META - Meta - DENDRAL

FORMATION OF RULES TO BE

USED FOR BOTH PLANNING
AND PREDICTION,

Figure 2. Relationship between use of rules in either planning or prediction.
Both approaches are used in utilizing data for structure elucidation.

J. Lederberg

Privileged Communication
DENDRAL PROJECT Section 6.1.1

allows the scientist using the program to examine structural candidates and
remove those deemed implausible (Fig. 1). A large portion of our recent and
future work is directed toward improving the CONGEN program and building other
facilities around it (see later sections). We have demonstrated the utility of
CONGEN in structural studies, and subsequent sections discuss our recent
developments and applications of CONGEN as well as our interactions with other
scientists desiring access to our programs.

Given a set of structural candidates, the experimenter examines them to
determine what experiments might be performed to focus on the correct structure
by stepwise rejection of alternative hypotheses. When there are only a small
number of possibilities under consideration, manual methods suffice. But CONGEN
provides the capability for exhaustive enumeration of structural possibilities at
a point in a structural problem when there may be many hundreds of possibilities.
It is very difficult to examine these structures and plan experiments by hand.

We have begun exploring ways to provide computer assistance to this important
aspect of structure elucidation. We refer to this research area as the
Experiment Planner, discussed in more detail below.

When new experiments have been planned the researcher carries them out and
uses the results as additional constraints on the structural candidates (Fig. 1).
New experiments may include collecting of additional Spectroscopic data or
performing a sequence of chemical reactions on the unknown. The latter
experiments may be chosen to convert the unknown into a related compound which
possesses physical or chemical properties more amenable to analysis. During the
past year we have developed a program to assist scientists in carrying out
representations of chemical reactions in the computer and eliminating undesired
structural candidates based on constraints exercised on the products of the
reaction. This work is described in two subsequent sections. One section
describes use of the program, which we call REACT, to explore structural
possibilities exactly as outlined above. A later section describes recent
progress in increasing the power of REACT.

Medical Relevance

Structure elucidation is a fundamental problem for medical practice and
biomedical research. For example, we are collaborating with physicians in the
Department of Pediatrics who monitor the body fluids of newborn infants in order
to detect abnormal compounds. Much of the research leading to new drugs and new
methods for synthesizing drugs also depends on careful analysis and
identification of molecular structures of compounds. The computer tools that we
are developing will aid in the determination of molecular structures by giving
working scientists help with data collection, data interpretation, hypothesis
testing and, most important, systematic consideration of all molecular structures
that are consistent with the interpretations of the available data.

Privileged Communication 45 J. Lederberg
section 6.1.1 DENDRAL PROJECT

PROGRESS SUMMARY
Experiment Planner

We have begun preliminary considerations of design and implementation of an
experiment planner. This program will assist chemists in designing the most
effective set of experiments to perform to solve the structure. Although the
experiment planner will be a future activity of our group, we are developing and

using other structure manipulation functions which will provide groundwork for
future developments.

One important aspect of experiment planning is the ability to examine in
some way the set of candidate structures. Although many can be drawn for visual
review, drawing is impractical when dozens or hundreds of structures are
involved. To assist persons using CONGEN in reviewing their structures we have
developed a function auxiliary to CONGEN which we call SURVEY.

SURVEY

FUNCTION: ArDS IN PERCEPTION OF ANY OF A
PRE-SPECIFIED SET OF STRUCTURAL
FEATURES IN A GROUP OF
STRUCTURAL CANDIDATES.

E.G, A) FUNCTIONAL GROUPS
B) TERPENOID SKELETONS
C) AMINO ACID SKELETONS

Figure 3. Funetion of the SURVEY Program and examples of recent application
areas,

The function of SURVEY is summarized in Figure 3. SURVEY simply acts as a
reminder to the scientist of the presence or absence of certain structures or
Structural features. During the past year we have used SURVEY extensively. For
example, we have used it to detect implausible functional groups ina set of
candidate structures, using a file of substructures representing a wide variety
of functionalities. In many problems, implausible functional groups are
forgotten and CONGEN is never constrained to remove them. Another example of use
of SURVEY is in conjunction with collaborative work with persons in the

J. Lederberg 46 Privileged Communication
DENDRAL PROJECT Section 6.1.1

Department of Genetics. In analysis of serum or urinary metabolites in patients
of high risk of metabolic disorder, we have had occasion to use CONGEN in
exploration of unknown structures [Report HPP-77-11]. Some of these structures
could formally be conjugates of amino acids with organic acids. If so, such
structures will possess backbones of naturally-occurring amino acids. SURVEY was
used to provide a summary of which structural candidates possessed such amino
acid skeletons.

We have recently used SURVEY in a related application involving the
structure of "polyalthenol", discussed by LeBoeuf, et al. (Figure 4).
Superatoms and constraints supplied to CONGEN to derive structural candidates are
summarized in Fig. 4.

We summarize in Figure 5 the structural possibilities which resulted.
There are five structures possessing a bicyclo[2.1.1] system, and six which
possess a bicyclo[4.3.1] system (Fig. 5, top). These structures are energeticaly
less favorable. For example, several possess a double bond at a bridgehead atom,
which violates Bredt’s Rule. There remain, however, 11 structures which are not
formally excluded by data presented by LeBoeuf, et al. Because these workers
based their structural assignment on biogenetic grounds, we used SURVEY and REACT
to test their hypothesis. We have, in computer-accessible libraries, known
terpenoid ring systems which can be used within SURVEY to test sets of structures
for known skeletons. None of the 22 structural candidates possesses a previously
known skeleton. Because the authors postulated a relationship to a known
Skeleton via a single methyl shift, we used REACT to exercise a single methyl
shift in all possible ways on each of the 22 candidates. SURVEY was then used to
test the results for the presence of known terpenoid systems, and the drimane
skeleton, the postulated precursor of polyathenol, was the only known skeleton
which resulted. This does not prove the hypothesis of LeBoeuf, et al., but
certainly helps strengthen it.

SURVEY is, however, only the barest beginning of an experiment planner,
even though it has proven useful. We plan to build from this beginning toward a
much more powerful system.

Privileged Communication 47 J. Lederberg
Section 6.1.1 DENDRAL PROJECT

M. LeBoeuf, M. Hamonniere, A. Cave, H. Gottleib, N. Kunesch, and E. Wenkert,
Tet. Lett., 3559 (1976).

"POLYALTHENOL” ——-CogHzNO

SUPERATOMS ArBITRARY NAME NuMBER _
FV
N
bee EV
F CH-FV
/
CHz-C-CH-CHo-CH=C BI 1
| \
| OH Za
CH3 CHz FV
CHz-FV ME ]
FV-CHo-FV CH 3
IV
FV-CH-FV CH l
CONSTRAINTS
1) ALL FREE VALENCES BONDED TO NON-HYDROGEN ATOMS
2) GOODLIST IN-CH2-B1 1 To ANY
(EVENTUALLY IN-CHo-CHy 5.9)
ME-(BI CH) 1 To ANY
(EVENTUALLY CHz-CH, EXACTLY 1)
4) GOODRINGS 2 EXACTLY 5
4) BADRINGS 3

Figure 4. Superatoms and constraints supplied to CONGEN in investigations of

plausible structural alternatives to the proposed structure of
Polyalthenol.

J. Lederberg 48 Privileged Communication
DENDRAL PROJECT Section 6.1.1

OH

 

 

 

 

 

 

 

 

 

 

 

 

HCHyCH  INCH5
ech | OH
He CH
(5) IN (G)
on \ OH \ OH \ OH
| 2 CH CHa
IN IN IN
CHIN HIN CH5IN
OH OH OH
CH5IN {CHSIN CHsIN
HO LO HO
Figure 5.
HO CHsIN HO CHa!N  Sbivaltheno! based on data

given in Figure 4.

 

 

 

 

 

 

 

 

Privileged Communication 49 J. Lederberg
Section 6.1.1 DENDRAL PROJECT

Figure 6.

J. Lederberg 50

REACTION CHEMISTRY DEVELOPMENTS

SEPARATION FROM CONGEN - COMMUNICATION VIA FILES OF
STRUCTURES,

ADDING CONSTRAINTS - SITE - AND TRANSFORM - SPECIFIC,

CONTROL STRUCTURE - RAMIFICATION

A, ESTABLISH RELATIONSHIPS AMONG PRODUCTS AND REACTANTS
B. DEAL PROPERLY WITH RANGES OF NUMBERS OF PRODUCTS

INTERACTION ~ DEVELOP MANIPULATION COMMANDS WHICH
PARALLEL LABORATORY OPERATIONS, E.G.,
SEPARATE INTO FLASKS, TEST CONTENTS OF
VARIOUS FLASKS, INCOMPLETE SEPARATIONS,
ETC,

REPRESENTATION OF REACTIONS
PROSPECTIVE DETECTION OF DUPLICATE PRODUCTS BASED ON

SYMMETRY PROPERTIES OF: A) STARTING MATERIAL; AND
B) TRANSFORMATION,

Current and future direction for improvement and extension of REACT, a

program for exploration of applications of reaction chemistry to
structure elucidation problems.

Privileged Communication