Computer-Aided Molecular Design Teeming with Change

• Molecular modeling, computational chemistry bid to become mainstream activities as field evolves to meet customer needs

James H. Krieger, C&EN Washington

Computer-aided molecular de­sign (CAMD) is moving into the chemical mainstream. And as it

advances, the rapidly evolving interac­tions of vendors, users, concepts, and technologies that make up the world of CAMD are beginning to redefine the doing of chemistry.

The gee-whiz aspect of molecular modeling and computational chemis­try—to the extent it still ex­ists—is fast receding, being replaced by hard-nosed busi­ness questions: How will it aid productivity? How will it help in generating patents? What will it do for innova­tion? How much does it cost?

At the same time, chemical, biotechnology, and pharma­ceutical companies are in­creasingly making use of mul-tidisciplinary teams on re­search projects. And new research technologies are be­ing employed—particularly in the dynamic area of drug dis­covery—and are generating burgeoning amounts of data and information that must be dealt with efficiently.

All of these thrusts are having an impact on CAMD technology and the support­ing software and hardware. But there is more. Develop­ments on the vendor busi­ness scene are resulting in a realignment in that sector of the modeling community,

which, in different ways affects the ar­ray of software and hardware products being offered.

The national meetings and expositions of the American Chemical Society have in recent years developed into a canvas that periodically captures scenes from the constantly unfolding world of CAMD. The meeting and exposition last month in San Diego were no exception. From the evidence of exposition offerings, inter­views with participants, a panel discus­sion, and an ACS-sponsored molecular modeling short course for undergradu­ates, the current milieu is one marked by accelerated change.

"Computer-aided chemical develop­ment is starting to enter what I would call its third phase or third era," says Lyle E. Ochs, vice president and direc­tor of marketing at CAChe Scientific,

Silicon Graphics Indy, with video camera on top, facilitates interaction among members in work group conferencing.

Beaverton, Ore. The first phase, from a commercial standpoint, began in the early 1980s with the emergence of the first business enterprises formed specif­ically to develop and market computa­tional chemistry products. Those firms were selling to a specialist market.

The second phase, Ochs says, was ini­tiated "when commercial enterprises started addressing seriously the experi­mental chemist, the practicing chemist, the person who was not familiar with maybe even some of the statistical me­chanics techniques associated with dy­namics or dynamic simulations. And cer­tainly not quantum chemistry." But even in this case, he says, the firms were sell­ing to a somewhat special segment of experimental chemists.

The firms are now moving into the third era, where they are selling to main­

stream customers. Main­stream customers, Ochs says, in the sense that they're still experimental chemists, but they're very pragmatic. They are as interested in whether the products fit within their overall computing strategy as they are in whether the products have some of the latest capabilities. "It's a dif­ferent value set," Ochs says, "and it's a different set of buying decisions that go on."

In parallel with these de­velopments, Ochs adds, there has been a very significant advance in the amount of computational power, "so that you can really do serious chemistry, not only with clas­sical mechanics techniques, not only with semiempirical techniques—which are quan­tum chemistry techniques that rely on a fair amount of empirical data to simplify the calculation—-but with ab ini­tio techniques."

APRIL 11,1994 C&EN 31

SCIENCE/TECHNOLOGY

SCIENCE/TECHNOLOGY

Molecular modeling: an aid to chemistry education As the main American Chemical Soci­ety meeting got under way on a Sun­day early last month at the primary venues in downtown San Diego, an­other meeting-related activity was tak­ing place farther inland. In a crowded computer lab at San Diego State Uni­versity, students from around the country were intensely engaged in an ACS-sponsored short course for un­dergraduates in molecular modeling.

The short course—actually two short courses, one in the morning, another in the afternoon—was taught by San Diego State University chemistry pro­fessor Thomas E. Cole. It was arranged by CAChe Scientific's product market­ing manager, Evelyn M. Brosnan, and made use of CAChe molecular model­ing software.

CAChe Scientific began to take a se­rious interest in education about a year ago when it instituted a higher educa­tion grant program. The program, coor­dinated by Brosnan, offers chemistry departments aid in setting up multiple-seat teaching labs where students learn chemistry with CAChe modeling tools in a hands-on environment By May or June, the company expects that some 15 labs that have received its grants will be in place.

It doesn't hurt the company's future marketing for students to be familiar with CAChe software. But beyond that, there are good reasons for students to gain experience in molecular modeling,

Brosnan points out. As modeling has become an integral part of industrial R&D, industry is requiring a new set of skills from graduating chemists. Stu­dents need to have access to the tools they will be using in the profession, she adds.

From the teaching standpoint, mod­eling provides powerful educational tools, Brosnan says. It's applicable to all levels of the chemistry curriculum and helps explain sophisticated princi­ples and difficult concepts. And, Bros­nan maintains, it helps to attract and retain top students by bringing back the "discovery" element of chemistry and by generating excitement about the science.

These arguments have indeed been borne out in some experiences to date. For example, John C. Kotz, a chemistry professor at the State University of New York, Oneonta, credits the school's new departmental computer center as a sig­nificant factor in his recently being able to attract four of the top five students in his introductory class to become chem­istry or chemical engineering majors. At the university, computer-aided chemis­try has been incorporated into the cur­riculum in three courses: general chem­istry, inorganic chemistry laboratory, and theories of inorganic chemistry. The CAChe system that is the heart of the center has profoundly affected the way chemistry is taught at the school, Kotz says.

Ochs sees the work done by the com­putational chemist starting to undergo a transition. Some companies are be­ginning to decentralize and distribute that expertise, he explains. Hence, the computational chemists are now work­ing as members of project teams, rather than being in more functionally orga­nized groups and doing all of the com­putational chemistry.

"Increasingly," Ochs says, "the com­putational chemistry will be done by individuals and project teams that in­volve some very specialized expertise of the computational chemist. The com­putational chemist won't be doing all or most of the 'computational chemis­try' anymore in the company."

Steven Goldby, president and chief executive officer of MDL Information Systems, San Leandro, Calif., sees the same effect, from a slightly different per­spective. For various competitive, regu­latory, and other reasons, he points out, companies in the chemical, pharmaceu­tical, and agrochemical industries are re­thinking their businesses and reengi­neering their companies. And one of the areas involved in the reengineering is R&D.

R&D, Goldby explains, has now be­come an integrated part of the business. R&D managements, he says, are under tremendous pressures—for example, to speed development cycles. As a result, the R&D operations are responding by moving from a functional organization to a product-team organization.

Those teams, Goldby says, are look­ing for an information system that al­lows team members to communicate. There are tools for the chemist, tools for the biologist, tools for the analytical chemist, tools for the computational chemist, and tools for other specializa­tions. The need now is for an information system that cuts across these lines. "This," he says, "is a fundamental change in the market."

A panel discussion at a reception sponsored by MDL and computer man­ufacturer Silicon Graphics, Mountain View, Calif., expanded on these points. Moderated by Bruce Gelin, an indepen­dent consultant, the panel focused on how current technological trends in the biotechnology industry impact the drug discovery process.

Denise Gilbert, chief financial officer of Affymax, Palo Alto, Calif., for exam­ple, touched on the new field of combi­natorial chemistry—the collection of

technologies employed to simultaneous­ly create a profusion of compounds that can then be examined to discern which have useful properties (C&EN, Feb. 7, page 20). This approach leads to vast numbers of compounds.

"When I say vast numbers," Gilbert emphasizes, "I'm referring to tens of thousands up to millions, and poten­tially, at some point, trillions of com­pounds. These so-called libraries of compounds are then used as a screen­ing vehicle to search for new drug leads and interactive-specific targets."

Gilbert notes that "one of the inter­esting aspects of this is that it really re­quires integration of a large number of disciplines." It requires chemists, for example, to consider the chemical reac­tions for synthesis, biologists to help in choosing targets, instrumentation engi­neers to design miniaturized tech­niques; and software engineers to han­

dle the vast amounts of data that come out of the process.

John (Scooter) Morris, manager of technology development at Genentech, South San Francisco, Calif., sees a great deal of importance being placed on three-dimensional structures and on structure-function information. And in dealing with larger and larger struc­tures, he points out, there is a need for new computational techniques both for visualizing the structures and manipu­lating them.

"So one of the things that I see that is happening more and more," Morris says, "is tike internetworking of more and more companies, the sharing of in­formation over large-scale networks, the broad availability of different kinds of information on the so-called WANs or wide-area networks, and the importance of increased computational technology and capabilities." All this, he says, is op-

32 APRIL 11,1994 C&EN

The CAChe Scientific grant program is designed to help chemistry depart­ments equip a teaching laboratory with the company's products. Various criteria are used to determine success­ful applications, and sizes of awards depend on the nature of the products requested, with applicants expected to provide a portion of the funding for the CAChe products, up to a maximum of one half for certain of them. (More information is available from CAChe Scientific Inc., Higher Education Pro­gram, P.O. Box 500, MS 13-400, Beaver-ton, Ore. 97077; phone 800-544-6634.)

The molecular modeling short course in San Diego (pictured above) provided an example of what a teaching lab might accomplish. Students began by learning to build molecules—butane, ethylene glycol, and glycerol. They then learned, using butane, to optimize the geometry of a molecule. Searching for different conformers of butane fol­lowed. A medicinal chemistry example investigated the prediction of drug ac­tivity. And the course wound up with an investigation of chemical reactivity in aromatic electrophilic substitution reactions.

erating to allow companies to take ad­vantage of things like combinatorial chemistry and other kinds of computa­tionally intensive tasks.

William Ripka, vice president for pharmaceutical research at Corvas Inter­national, San Diego, represents a small therapeutically based company. "We ask not what we can do for technology/' he says, "but what technology can do for us. And in that regard, we are aggres­sively pursuing a number of technolo­gies, including, specifically, things such as homology model building of potential clinical targets."

Hence, Ripka says, one of the trends that has been particularly important to Corvas, as a small company, has been the availability of low-cost, high-perfor­mance workstations that have enabled companies such as Corvas to adopt mo­lecular modeling, specifically 3-D molec­ular modeling. Underlying the need for

such systems, he explains, has been the explosion in the amount of information coming from the new drug discovery technologies, as people seek to integrate that information into the whole drug discovery process.

Part of that drug discovery process is structure elucidation, and Mark Berger, chemistry market manager at Silicon Graphics, notes developments in model­ing and simulation technology that are helping the structure elucidation process become more refined and faster. Today, he says, some of the major modeling workers are creating computer pro­grams that simulate instruments, like x-ray diffractometers and nuclear mag­netic resonance spectrometers. "What they're doing," he explains, "is simulat­ing the theoretical structure of what the output of that instrument might be, go­ing into the lab, making the compound, putting it through real live instruments,

and then looking at the theoretical out­put versus the real output."

Carol J. Frischmann, manager of phar­maceutical marketing at MDL, adds em­phasis to the multidistiplinary aspect of drug discovery R&D today. "If I could pick one thing that I hear a lot about," she says, "it's that engineers and molec­ular biologists and organic chemists and structural chemists are all working to­gether in very highly integrated mul-tidisciplinary teams."

Evolving market forces, such as those touched on by the panel, have joined with other influences on the CAMD vendor community to create a dynamic and changing mix of participants and products. Among the influences are those of a business nature—ownership changes, for example. So, too, are cus­tomer demands for ease of use, for prod­ucts that work together regardless of computer platform. As MDL's Goldby notes, "Customers need to know they can use the software readily—plug and play." And partnerships of varying sorts are being formed by firms to combine their different strengths directly or indi­rectly in their product offerings.

All these influences are at work, for example, on MDL, a supplier of soft­ware products for chemical information management. Last July, what was then Molecular Design Ltd., a part of Max­well Communication Corp., became MDL Information Systems Inc., an inde­pendent publicly held company.

Last month, the firm announced an agreement with Sigma-Aldrich Corp., which will deliver the most recent list­ings of chemical products available from Sigma, Fluka, Supelco, and Aid-rich—including an expanded Sigma-Aldrich Rare Chemical Library—to cus­tomers of MDL's Available Chemical Di­rectory (ACD). That agreement will add a current Sigma-Aldrich listing of more than 90,000 chemical products to the ACD listing of more than 300,000 chem­ical products.

Meanwhile, MDL has expanded to 42 participants its Affinity developer group of software companies, which market a wide variety of MDL-compat-ible applications. In addition, MDL has strengthened its relationships with cer­tain companies, such as Digital Equip­ment (to port its Integrated Scientific Information System, ISIS, and other programs to Digital's new Alpha plat­form); Silicon Graphics (to port ISIS to that manufacturer's Challenge server);

APRIL 11,1994 C&EN 33

SCIENCE/TECHNOLOGY

Molecular Simulations (clockwise from above), Biosym, ana CAChe Scientific draw browsers at ACS exposition in San Diego. and modeling software supplier Bio­

sym (to provide new computational tools for mining archival systems).

Silicon Graphics, for its part, is putting a focus on chemical database services based on its Challenge line of network resource servers which are designed for distributed computing. When it is ready, the ISIS porting will add to a range of parallelized databases now running on Challenge servers: BioCAD's Catalyst/ Info, Chemical Design Ltd.'s Chem-X, Daylight Chemical Information Systems' Thor and Merlin, and Tripos Associates' Unity.

Another collaborative agreement, an­nounced in late February, involves St. Louis-based Tripos and Sadtler Divi­sion of Bio-Rad Laboratories, Philadel­phia. Tripos' product family includes its Sybyl molecular modeling software, Triad NMR processing software, and Unity software for chemical informa­tion management. The company notes that all are important tools for scientists who characterize materials by NMR spectroscopy. Under the new agree­ment, the Tripos software family has been interfaced with Sadtler's database and search system for carbon NMR spectroscopy.

Sadtler's Csearch system permits us­ers to search carbon NMR databases from Sadtler and those created by users by searching for matches to peak listings or by searching for structures. It predicts carbon chemical shifts for compounds that aren't in the database. The interface enables users to produce peak lists or structures within Tripos software and to

use the data for searches with Csearch. Csearch estimations can be utilized in modeling and processing experiments. The Tripos and Sadtler software prod­ucts are available to run on Silicon Graphics workstations.

Elsewhere, the industry profile is changing as a result of the demise of Autodesk Inc.'s venture into molecular modeling, launched with fanfare two years ago. Autodesk, which had made a major impact on the computer-aided design market with its AutoCAD sys­tem by mass marketing at relatively low prices, had hoped to do the same with molecular modeling. It had ac­quired an exclusive sales and market­ing license from the Canadian firm Hypercube, in Waterloo, Ontario, for HypeiChem, a molecular modeling sys­tem for PCs with Windows.

In January, Hypercube announced that it had negotiated a mutual release from its agreement with Autodesk that returned the sales and marketing rights for Hyper-Chem to Hypercube. The current Auto­desk version of HypeiChem, Release 3, has been sold worldwide through distri­bution and reseller channels. Hypercube expects to continue selling through the same channels.

Hypercube expects to begin shipping a new HypeiChem Release 4 this month. In San Diego, Tom Slee, director of scientific support at Hypercube, noted that the company will be expanding its range of products and the range of platforms sup­ported. The company recently brought out a companion product to HypeiChem called ChemPlus, a suite of extensions to Hyperchem. On tap for release next month is HyperNMR, a software package for the a priori prediction of one-dimen­sional NMR spectra. It can be used alone or in conjunction with the HypeiChem software.

Meanwhile, some of the people from Autodesk who had been involved with HyperChem have launched a new op­eration in Novato, Calif. Called Mega-Ion, it is a U.S. sister company fully owned by the Swiss firm Megalon S.A. Among Megalon's products is a high-performance design program for chem­ical and structural formulas, schemat­ics, and experimental setups called ChemStructure that runs on PCs with Windows.

Megalon has made an investment in

34 APRIL 11,1994 C&EN

Re-engineering the drug discovery process demands the evolution of new methodologies that bring the worlds of chemical information and computational chemistry closer together. This seminar showcases the tremendous synergy of these combined technologies, featuring applications which illustrate their potential in drug design. Whether you're a synthetic chemist, molecular modeler

or any other member of a multidisciplinary drug discovery team, developments in these areas will soon change your role in, and approach to, the design and development of novel bioactive compounds. Learn how recent developments in automated pharmacophore identification and 3D QSAR, 3D database searching, de novo design and assessment of synthetic feasibility will improve your effectiveness The methods will be presented on the SGI range of

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a Palo Alto firm, Helix Systems Inc., which expects to begin shipping a new product in July called ResearchStation. Helix describes ResearchStation as a sci­entific information manager that can capture, organize, visualize, and share information and data at the desktop. It can function as an electronic laboratory notebook through automatic record keep­ing and is designed for collaboration and communication among researchers by en­abling them to share information, analyti­cal processes, and tools.

ResearchStation's goal is to provide an integrated environment for using gener­al purpose and scientific tools such as document preparation, molecular mod­eling, sequence analysis tools, and infor­mation control software. Megalon views ResearchStation as a broad system that can run vertical programs developed by Megalon. Stéphane Boudon of Megalon sales in Europe notes that Helix is now focused primarily on large corporate sales. Megalon, in contrast, will sell to more of a mass market, he says, trying

different sales avenues—for example, distribution by Internet.

Two of the more significant new part­nership agreements, announced last month in San Diego, are between CAChe Scientific and IBM and between Molecular Simulations Inc. (MSI), Bur­lington, Mass., and Gaussian Inc., Pitts­burgh. In both instances, the moves join the modeling and user interface capabil­ities of one partner with the quantum chemistry capabilities of the other.

From its start, CAChe Scientific has focused on the experimental chemist. It offers an application called ProjectLead-er that, along with the company's graph­ical user interface and chemistry model­ing packages, runs on Macintosh desk­top platforms backed up by compute servers that include IBM RISC System/ 6000, Silicon Graphics, and Macintosh. ProjectLeader simplifies project plan­ning, experiment setup, program execu­tion, and documentation.

The IBM contribution to the partner­ship will come from IBM's Research

Division in San Jose, Calif., and more specifically its chemical services and applica­tions (CSA) unit. From quan­tum chemistry's beginnings, IBM Research has had an ac­tive program. But its role was that of market support for IBM hardware platforms. Now moving to commercialize its expertise, the company formed the CSA unit to provide ser-

Megalon (left) and MDL Information Systems provide information on new products.

vices and application software for the chemical, petrochemical, pharmaceutical, and biotechnology markets. The partner­ship agreement gives CAChe worldwide exclusive distribution rights for computa­tional chemistry applications developed by the group.

IBM Research has played a strong pi­oneering role in quantum chemistry, says CSA program director Michael Hehenberger. It's no accident, he ex­plains. Quantum chemistry has driven the limits of computing. Whenever hardware developers were looking for a computer application that required more memory and disk space and pushed all the limits of computer tech­nology, he says, they would go to the quantum chemists, who had no prob­lem in pushing the limits. He notes that his group now includes more than 30 software developers, most with a Ph.D. degree in chemistry.

IBM Research doesn't plan to just add existing programs to the CAChe system. "We have ideas now to create a new architecture for the whole field of computational chemistry," Hehen­berger says. "We call it Archem, an ar­chitecture for chemistry."

The idea of Archem is to create an architecture that has open interfaces, sô that anyone accepting the architecture will be able to provide modules to the system. "We don't believe we can pro­vide everything an experimental bench chemist needs, nor everything the ex­pert theoretical chemist needs," Hehen­berger says.

CAChe Scientific's Ochs notes that these open interfaces represent com­munication interfaces between pro­grams, as opposed to user interfaces. So, he says, CAChe will be able not only to integrate codes and programs and capabilities coming directly from IBM Research but, through Archem, to interface to more third-party software at the same time.

The MSI-Gaussian Inc. collaboration builds on a new generation of software for chemical computing introduced in San Diego by MSI. Called Cerius2, it is designed, according to the company, to integrate all the chemical computing needs of an R&D organization so that in the same programming environment chemists can build and visualize mod­els of chemical structures, predict prop­erties with targeted problem-solving modules, and apply well-validated computational methodologies to simu-

38 APRIL 11,1994 C&EN

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SCIENCE/TECHNOLOGY

late materials behavior. It provides dis­tributed computing, the company says, that allows researchers to share data and protocols in the system using a common user interface.

The software architecture employed by Cerius2 incorporates MSI's chemis­try backplane, an open, object-oriented software environment that other soft­ware modules plug into easily. Because of the plug-in modularity, Cerius2 can be tailored to specific needs.

Gaussian Inc. develops, sells, and sup­ports the Gaussian series of electronic structure programs. Under the new agreement, MSI and Gaussian Inc. will design a new graphical user interface for

Chemical Design (top) and Tripos demonstrate modeling software.

the Gaussian programs based on the MSI Cerius2 chemistry backplane. Gaus­sian Inc. will also use the MSI chemistry backplane development environment to produce new products.

The companies plan to have the Gaus­sian interface available from MSI later this year. It will enable Gaussian users to set up, initiate, and monitor Gaussian jobs from within Cerius2, including jobs on remote computer systems. Users will be able to use Cerius s structure-build­ing capabilities or input from any other source accessible from Cerius2 to sketch molecular structures for Gaussian jobs. And the interface will be able to graphi­cally display a wide variety of Gaussian results.

"Gaussian adds powerful, high-accur­acy ab initio electronic structure model­ing of chemical structures and properties to the capabilities of the MSI product suite," explains Michael J. Savage, MSI president and chief executive officer. "The Cerius2 interface to Gaussian," he says, "will let users attack chemical problems of interest with the entire range of computational chemistry capa­bilities from within a single, consistent modeling environment."

Still other new products were intro­duced or had their first showing in San Diego. The U.K/s Chemical Design, for example, has over the past few years rewritten all of its Chem-X modeling and computation software, issuing a large number of updates. That process was recently capped when the final portion, the user interface, was rewrit­

ten. The interface is styled very much in line with the Windows motif—with View, Compute, and Search, for example, all being Windows menus.

"The interface has been de­signed the way a Windows user would expect the product to work, rather than the way a pro­grammer thinks the product should work," says Chemical Design technical director Keith Davies. Davies also points out that Chem-X is available across the entire range of platforms— PC Windows, Apple Macintosh, IBM RS/6000, Silicon Graphics, and Digital Equipment Alpha.

Tripos introduced Power-Search, software for performing conformational searching of com­pounds on PCs running Win­dows. Developed in collabora­

tion with CheMicro Research & Develop­ment of Hungary, PoweiSearch provides a way to find low-energy conforma­tions with Systematic or Monte Carlo searches.

BioCAD, Mountain View, Calif., dem­onstrated Catalyst/Info, which it intro­duced at the end of last year. Catalyst/ Info is tightly integrated with the Cata­lyst/Hypo hypothesis generation system in the company's Catalyst drug discovery software. Catalyst/Info is a 1-D/2-D/3-D chemical database system that can com­bine in one query all three types of con­straints—conformation, structure, and property information. It is designed to be queried on general chemical func­tions, such as hydrogen bonding inter­actions, hydrophobic interactions, and charge interactions, rather than sim­ply on specific chemical substructures. Three-dimensional queries can include any combination of location constraints, distance constraints, angles, torsions, and excluded volumes. Queries in 2-D and 3-D include stereochemical con­straints, with the system maintaining stereochemical integrity by considering all possible isomers when stereochemis­try is unknown.

One display at the exposition was perhaps emblematic of the current CAMD scene. With the product team or work group mode of organization picking up steam, a view of the future working environment for many chem­ists was provided by Silicon Graphics: Indy, the company's newest member of its Indigo family of desktop worksta­tions, and InPerson software for desk­top conferencing. The system enables up to six or eight work group members to share high-quality audio and video, text, images, and 3-D models interac­tively, in real time, over standard net­work connections.

The Indy comes standard with Indy-Cam, a color digital video camera that sits on top of the monitor and provides an on-screen view of each work group member. Participants can be added to the conference and materials distribut­ed through drag-and-drop icons. A shared Media Board lets everyone view, mark up, and interact with the conference data, with each participant having a unique cursor and color for all to keep track of comments and edits. And InPerson is application indepen­dent, so that a view from any applica­tion window can be imported for re­view and mark up. Π

40 APRIL 11,1994 C&EN